{"text_format":"3","workbook":"xls","n_sheets":14,"sheets":["1998-2005","3JournalSubset","1998","1999","2000","2001","2002","2003","2004","2005","2006","Nucacid2004","Genetics2004","Bioinformatics2004"],"not_rendered":{"charts":4,"external_links":1,"defined_names":20},"read":"whole","date_system":"1904","formulas":"cached_only"}

{"sheet":"1998-2005","index":0,"n_rows":28,"n_cols":10,"rows_kept":28,"flags":["formulas_cached_only"]}
["Year","count","Live","Dead","Other","%live","% unavailable","Dead Journal","Dead Non-journal"]
[1998,8,3,4,1,{"v":0.375,"d":"0.38"},{"v":0.625,"d":"63%"},0,4,0]
[1999,6,5,1,0,{"v":0.8333333333333334,"d":"0.83"},{"v":0.16666666666666663,"d":"17%"},0,1,0]
[2000,9,4,4,1,{"v":0.4444444444444444,"d":"0.44"},{"v":0.5555555555555556,"d":"56%"},1,3,-1]
[2001,28,20,8,0,{"v":0.7142857142857143,"d":"0.71"},{"v":0.2857142857142857,"d":"29%"},0,8,0]
[2002,78,71,6,0,{"v":0.9102564102564102,"d":"0.91"},{"v":0.08974358974358976,"d":"9%"},0,6,0]
[2003,86,69,17,0,{"v":0.8023255813953488,"d":"0.80"},{"v":0.19767441860465118,"d":"20%"},0,17,0]
[2004,172,158,13,1,{"v":0.9186046511627907,"d":"0.92"},{"v":0.08139534883720934,"d":"8%"},0,13,0]
[2005,240,215,24,1,{"v":0.8958333333333334,"d":"0.90"},{"v":0.10416666666666663,"d":"10%"},4,21,-3]
["2006 (1/31)",28,27,1,0,{"v":0.9642857142857143,"d":"0.96"},{"v":0.0357142857142857,"d":"4%"},null,null,-1]
[]
[]
["Totals",655,572,78,4,{"v":0.7620410202774544,"d":"0.76"},{"v":0.23795897972254565,"d":"24%"},5]
[]
[]
[]
[]
[]
["Year","Journal","Non-Journal"]
[1998,0,4]
[1999,0,1]
[2000,1,3]
[2001,0,8]
[2002,0,6]
[2003,0,17]
[2004,0,13]
[2005,4,21]
["Totals",5,73]

{"sheet":"3JournalSubset","index":1,"n_rows":18,"n_cols":11,"rows_kept":18,"flags":["formulas_cached_only"]}
[null,"Total Unique (9/1/04-12/31/04","Accessible Journal","inaccessible Journal","Accessible Non- Journal","Inaccessible non-journal",null,"Total Inaccessible %","Total Accessible %","Total inaccessible Non- Journal","Total Inaccessible Journal"]
[]
["Bioinformatics",71,3,2,52,13,null,{"v":0.2112676056338028,"d":"21%"},{"v":0.7887323943661972,"d":"79%"},{"v":0.18309859154929578,"d":"18%"},{"v":0.028169014084507043,"d":"3%"}]
["Nucleic Acids Research",61,59,0,0,2,null,{"v":0.03278688524590164,"d":"3%"},{"v":0.9672131147540983,"d":"97%"},{"v":0.03278688524590164,"d":"3%"},{"v":0,"d":"0%"}]
["Genetics",30,14,10,6,0,null,{"v":0.3333333333333333,"d":"33%"},{"v":0.6666666666666667,"d":"67%"},{"v":0,"d":"0%"},{"v":0.3333333333333333,"d":"33%"}]
[]
["Total",162,76,12,58,15]
{"$rows_empty":7}
[null,"% Total","% Accessible  @ Journal","% Inaccesible @ Journal","% Accesible Non-Journal","% Accessible non-journal"]
["Bioinformatics",{"v":0.9859154929577465,"d":"99%"},{"v":0.04225352112676056,"d":"4%"},{"v":0.028169014084507043,"d":"3%"},{"v":0.7323943661971831,"d":"73%"},{"v":0.18309859154929578,"d":"18%"}]
["Nucleic Acids Research",{"v":1,"d":"100%"},{"v":0.9672131147540983,"d":"97%"},{"v":0,"d":"0%"},{"v":0,"d":"0%"},{"v":0.03278688524590164,"d":"3%"}]
["Genetics",{"v":1,"d":"100%"},{"v":0.4666666666666667,"d":"47%"},{"v":0.3333333333333333,"d":"33%"},{"v":0.2,"d":"20%"},{"v":0,"d":"0%"}]

{"sheet":"1998","index":2,"n_rows":9,"n_cols":7,"rows_kept":9,"flags":["formulas_cached_only"]}
[null,"Live?","Journal?","Reference"]
["submitted search results is available using the BCM Search Launcher Batch Client (version 2.6) (ftp://gc.bcm.tmc. edu/pub/software/search-launcher/). SUPPLEMENTARY INFORMATION: Example figures are available at http://dot.bcm.tmc. edu:9331/papers/beautypp.html CONTACT: (kworley,culpep)@bcm.tmc.edu PM","No","no","1: Bioinformatics. 1998;14(10):890-1.","BEAUTY-X: enhanced BLAST searches for DNA queries.","Worley KC, Culpepper P, Wiese BA, Smith RF.","PMID: 9927720 [PubMed - indexed for MEDLINE]"]
["ver architecture of the asthma and allergy gene database. AVAILABILITY: Database and server templates are available on request from the first author. Supplementary Information : The URL of the asthma and allergy gene database is http://cooke.gsf.de PMID: 9918958 [PubMed - indexed for MEDLINE]","Yes","no","2: Bioinformatics. 1998;14(9):827-8.","An Internet linkage and mutation database for the complex phenotype asthma.","Wjst M, Immervoll T.","PMID: 9918958 [PubMed - indexed for MEDLINE]"]
["evaluated (optimally, the result of a MEDLINE search by keyword) and the results are returned in the form of Web pages for keywords, sentences and s. SUPPLEMENTARY INFORMATION: Web pages containing full information on the examples mentioned in the text are available at: http://www.cnb.uam.es/ approx","yes","no","3: Bioinformatics. 1998;14(7):600-7.","Automatic extraction of keywords from scientific text: application to the","knowledge domain of protein families.","PMID: 9730925 [PubMed - indexed for MEDLINE]"]
[" it a good thing? Why will it happen? Where are we now? What developments are fostering and what developments are impeding progress towards this end? SUPPLEMENTARY INFORMATION: A list of WWW resources devoted to database issues in molecular biology is available at http://www.mips.biochem.mpg.de CONT","No","no","4: Bioinformatics. 1998;14(7):551-61.","Comprehensive, comprehensible, distributed and intelligent databases: current","status.","PMID: 9730920 [PubMed - indexed for MEDLINE]"]
["uam.es/EUCLID, with the corresponding dictionaries for the generation of three, eight and 14 functional classes. Contact: E-mail: valencia@cnb.uam.es SUPPLEMENTARY INFORMATION: The results of the EUCLID classification of different genomes are available at http://www.sander.ebi.ac. uk/genequiz/. A de","yes","no","5: Bioinformatics. 1998;14(6):542-3.","EUCLID: automatic classification of proteins in functional classes by their","database annotations.","PMID: 9694995 [PubMed - indexed for MEDLINE]"]
["ctive interface for ease of querying the database and displaying maps. AVAILABILITY: The extensions can be obtained via ftp.sanger.ac.uk/pub/zmapper. Supplementary information: The User's Manual can be viewed from http:/www.sanger.ac.uk/Users/cari/Z.shtml. CONTACT: cari@sanger.ac.uk PMID: 9694993 [P","No","no","6: Bioinformatics. 1998;14(6):538-9.","Z extensions to the RHMAPPER package.","Soderlund C, Lau T, Deloukas P.","PMID: 9694993 [PubMed - indexed for MEDLINE]"]
["ecular modelling and 3D survey. AVAILABILITY: TITO is available by anonymous ftp at: ftp://lmcp.jussieu. fr/pub/tito CONTACT: labesse@lmcp.jussieu.fr Supplementary information: http://www.lmcp.jussieu.fr/ approximately labesse/TITO/TITO.html PMID: 9545453 [PubMed - indexed for MEDLINE]","No","no","7: Bioinformatics. 1998;14(2):206-11.","Incremental threading optimization (TITO) to help alignment and modelling of","remote homologues.","PMID: 9545453 [PubMed - indexed for MEDLINE]"]
[" (when possible) relative atomic or formula masses, and mass/amount and amount/mass concentration conversion factors. This paper gives background and supplementary information which should be borne in mind when providing interpretation or using the Web table. Supplementary tables listing (i) common ","No Link","no","8: Ann Clin Biochem. 1998 Mar;35 ( Pt 2):261-7.","Guidelines for the interpretation of analytical toxicology results and unit of","measurement conversion factors.","PMID: 9547898 [PubMed - indexed for MEDLINE]"]

{"sheet":"1999","index":3,"n_rows":8,"n_cols":7,"rows_kept":8,"flags":["formulas_cached_only"]}
["Reference","Live?","Journal?"]
["rated by an example taken from sugar metabolism. AVAILABILITY: METATOOL is available from ftp://bmsdarwin.brookes.ac. uk/pub/software/ibmpc/metatool. SUPPLEMENTARY INFORMATION: http://www. biologie.hu-berlin.de/biophysics/Theory/tpfeiffer/metatoo l.html PMID: 10222413 [PubMed - indexed for MEDLINE]","No","no","4: Bioinformatics. 1999 Mar;15(3):251-7.","METATOOL: for studying metabolic networks.","Pfeiffer T, Sanchez-Valdenebro I, Nuno JC, Montero F, Schuster S.","PMID: 10222413 [PubMed - indexed for MEDLINE]"]
["WEET is accessible via the Internet at http://www.dkfz-heidelberg.de/spec/. CONTACT: a. bohne@dkfz-heidelberg.de or w.vonderlieth@ dkfz-heidelberg.de SUPPLEMENTARY INFORMATION: The current version of SWEET generates only one conformation out of a manifold. Several authors have analysed possible conf","yes","no","2: Bioinformatics. 1999 Sep;15(9):767-8.","SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides.","Bohne A, Lang E, von der Lieth CW.","PMID: 10498779 [PubMed - indexed for MEDLINE]"]
["ITY: http://www.icgeb.trieste.it/domain. Mirror site is available at http://sbase.abc.hu/domain. A standalone programme will be available on request. SUPPLEMENTARY INFORMATION: A series of help files is available at the above addresses. PMID: 10320404 [PubMed - indexed for MEDLINE]","yes","no","3: Bioinformatics. 1999 Apr;15(4):343-4.","The domain-server: direct prediction of protein domain-homologies from BLAST","search.","PMID: 10320404 [PubMed - indexed for MEDLINE]"]
["uss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://","yes","no","5: Bioinformatics. 1999 Jan;15(1):72-84.","E-CELL: software environment for whole-cell simulation.","Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K,","PMID: 10068694 [PubMed - indexed for MEDLINE]"]
["pairs. This data set complements earlier sets on the basis of cDNA sequences and will be useful for further comparative studies. [This paper contains supplementary data that can be found at http://www.genome.org [corrected]]. PMID: 10508839 [PubMed - indexed for MEDLINE]","yes","yes","1: Genome Res. 1999 Sep;9(9):815-24.","Erratum in:","Genome Res 1999 Nov;9(11):1156.","PMID: 10508839 [PubMed - indexed for MEDLINE]"]
["genome.org","yes","yes","1: Genome Res. 1999 Jul;9(7):662-71. ","A 3-Mb high-resolution BAC/PAC contig of 12q22 encompassing the 830-kb consensus","Murty VV, Montgomery K, Dutta S, Bala S, Renault B, Bosl GJ, Kucherlapati R,"]
[{"$nulls":4},"minimal deletion in male germ cell tumors.","Chaganti RS."]

{"sheet":"2000","index":4,"n_rows":10,"n_cols":7,"rows_kept":10,"flags":["formulas_cached_only"]}
["Reference","Live?","Journal?"]
["VAILABILITY: Secondary structure alignment homepage at http://lutece.rutgers.edu/ssas CONTACT: anders@rutchem.rutgers.edu; ronlevy@lutece.rutgers.edu Supplementary Information: Genome sequence/structure alignment results at http://lutece.rutgers.edu/ss_fold_predictions. PMID: 11159310 [PubMed - inde","No","no","3: Bioinformatics. 2000 Nov;16(11):988-1002.","Iterative sequence/secondary structure search for protein homologs: comparison","with amino acid sequence alignments and application to fold recognition in","PMID: 11159310 [PubMed - indexed for MEDLINE]"]
["red for AZ expression. However, no homolog was detected in the completed genome of the budding yeast Saccharomyces cerevisiae. Procedural details and supplementary information can be found at http://itsa.ucsf.edu/ approximately czhu/AZ. PMID: 10871270 [PubMed - indexed for MEDLINE]","no","no","6: Bioinformatics. 2000 May;16(5):478-81.","A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces","pombe but not detected in budding yeast Saccharomyces cerevisiae.","PMID: 10871270 [PubMed - indexed for MEDLINE]"]
["erimental crosses of plants or animals. AVAILABILITY: The add-on packages are freely available at http://www.mathsource.com/cgi-bin/msitem?0209-30 4. SUPPLEMENTARY INFORMATION: A tutorial notebook file is included with the packages at the mathsource site. PMID: 10869043 [PubMed - indexed for MEDLINE","No","No","7: Bioinformatics. 2000 Apr;16(4):408-10.","Mathematica packages for simulation of experimental genetics.","Manly KF.","PMID: 10869043 [PubMed - indexed for MEDLINE]"]
["tp from snipe.pharmacy. ualberta.ca/pub. The training","No","yes","1 : Bioinformatics. 2000 May;16(5):425-38. ","Prediction of genetic structure in eukaryotic DNA using reference point logistic","Hooper PM, Zhang H, Wishart DS.","PMID: 10871265 [PubMed - indexed for MEDLINE]"]
["ts; for N(2)H(4), assignments have been found for 14 new FIRL transition systems and verified for five others. Lists have been produced (deposited as supplementary data with the JMS archive reached at www.idealibrary.com or available on request from the authors) of CH(3)OH and N(2)H(4) FIRL lines po","no link","no","5: J Mol Spectrosc. 2000 Nov;204(1):48-54.","LaseRitz: Far-Infrared Laser Line Assignment and Prediction by the Ritz","Combination Principle, with Application to Methanol and Hydrazine.","PMID: 11034841 [PubMed - as supplied by publisher]"]
["AVAILABILITY: The model.it server is freely available at http://www.icgeb.trieste.it/dna/ CONTACT: kristian@icgeb.trieste.it; pongor@icgeb.trieste.it SUPPLEMENTARY INFORMATION: a series of help files is available at the above address. PMID: 11269231 [PubMed - indexed for MEDLINE]","yes","no","1: Bioinformatics. 2000 Nov;16(11):1044-5.","Model.it: building three dimensional DNA models from sequence data.","Vlahovicek K, Pongor S.","PMID: 11269231 [PubMed - indexed for MEDLINE]"]
["ures used, and major features of the revised charts. METHODS: Data from five national health examination surveys collected from 1963 to 1994 and five supplementary data sources were combined to establish an analytic growth chart data set. A variety of statistical procedures were used to produce smoo","yes","no","2: Adv Data. 2000 Jun 8;(314):1-27.","CDC growth charts: United States.","Kuczmarski RJ, Ogden CL, Grummer-Strawn LM, Flegal KM, Guo SS, Wei R, Mei Z,","PMID: 11183293 [PubMed - indexed for MEDLINE]"]
["various origin but these data are often inconsistent. A number of specialized databases dealing with BIMs and attempts to classify them are reviewed. SUPPLEMENTARY INFORMATION: The additional bibliography and list of Internet resources on bioinorganic chemistry are available at http://www.ebi.ac.uk/","yes","no","4: Bioinformatics. 2000 Oct;16(10):851-64.","Bioinorganic motifs: towards functional classification of metalloproteins.","Degtyarenko K.","PMID: 11120676 [PubMed - indexed for MEDLINE]"]
["methods may be extended to characterize the evolution of any phylogenetically","yes","no","2: Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3304-8. ","An archaeal genomic signature.","Graham DE, Overbeek R, Olsen GJ, Woese CR.","PMID: 10716711 [PubMed - indexed for MEDLINE]"]

{"sheet":"2001","index":5,"n_rows":29,"n_cols":37,"rows_kept":29,"flags":["formulas_cached_only"]}
["Reference","Live?","Journal?"]
["the command-line and for the www-version are available on request. CONTACT: Georg.Schneider@nt.imp.univie.ac.at; Frank.Eisenhaber@nt.imp.univie.ac.at SUPPLEMENTARY INFORMATION: Documentation for the taxonomy workbench can be accessed at http://mendel.imp.univie.ac.at/taxonomy/help.html. PMID: 117512","no","n","4: Bioinformatics. 2001 Dec;17(12):1179-82.","Taxonomy workbench.","Wildpaner M, Schneider G, Schleiffer A, Eisenhaber F.","PMID: 11751226 [PubMed - indexed for MEDLINE]"]
["vailable at http://www.stat.washington.edu/fraley/mclust. The software for the diagonal model is under development. CONTACT: kayee@cs.washington.edu. SUPPLEMENTARY INFORMATION: http://www.cs.washington.edu/homes/kayee/model. PMID: 11673243 [PubMed - indexed for MEDLINE]","no","n","7: Bioinformatics. 2001 Oct;17(10):977-87.","Model-based clustering and data transformations for gene expression data.","Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL.","PMID: 11673243 [PubMed - indexed for MEDLINE]"]
["h a common threading tool making their comparisons easier. AVAILABILITY: The meta-server is available free at http://www.infobiosud.cnrs.fr/bioserver SUPPLEMENTARY INFORMATION: http://www.infobiosud.cnrs.fr/bioserver/hah1.html Publication Types: Validation Studies PMID: 11524382 [PubMed - indexed fo","No","n","12: Bioinformatics. 2001 Aug;17(8):752-3.","Easier threading through web-based comparisons and cross-validations.","Douguet D, Labesse G.","PMID: 11524382 [PubMed - indexed for MEDLINE]"]
["lts in a format for viewing with the software 'GOLD'. AVAILABILITY: The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. SUPPLEMENTARY INFORMATION: Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. Arlequin is available at:","no","n","14: Bioinformatics. 2001 Aug;17(8):738-9.","Genotype transposer: automated genotype manipulation for linkage disequilibrium","analysis.","PMID: 11524375 [PubMed - indexed for MEDLINE]"]
["equence to structure threading. AVAILABILITY: Example substitution matrices are available from http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices.html. SUPPLEMENTARY INFORMATION: The list of proteins used for data collection and the optimized parameters for the alignment are given as supplementary mat","no","n","16: Bioinformatics. 2001 Aug;17(8):686-99.","Amino acid similarity matrices based on force fields.","Dosztanyi Z, Torda AE.","PMID: 11524370 [PubMed - indexed for MEDLINE]"]
["equence to structure threading. AVAILABILITY: Example substitution matrices are available from http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices.html. SUPPLEMENTARY INFORMATION: The list of proteins used for data collection and the optimized parameters for the alignment are given as supplementary mat","no","n","11: Bioinformatics. 2001 Aug;17(8):686-99.","Amino acid similarity matrices based on force fields.","Dosztanyi Z, Torda AE.","PMID: 11524370 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Substitution*","Chemistry, Physical","Comparative Study","Computational Biology","Mutation","Proteins/chemistry*","Proteins/genetics","Sequence Alignment/statistics & numerical data","Thermodynamics","Substances:","Proteins"]
["can bind to several HLA-DR alleles. AVAILABILITY: The server is available at http://www.imtech.res.in/raghava/propred/ CONTACT: raghava@imtech.res.in SUPPLEMENTARY INFORMATION: http://www.imtech.res.in/raghava/propred/page3.html PMID: 11751237 [PubMed - indexed for MEDLINE]","no","no","2: Bioinformatics. 2001 Dec;17(12):1236-7.","ProPred: prediction of HLA-DR binding sites.","Singh H, Raghava GP.","PMID: 11751237 [PubMed - indexed for MEDLINE]"]
["b-sib.ch and the distribution is available from ftp://ftp.isrec.isb-sib.ch/pub/software/unix/mmsearch-1.0.tar.gz CONTACT: Thomas.Junier@isrec.unil.ch SUPPLEMENTARY INFORMATION: The full documentation about mmsearchis available from http://hits.isb-sib.ch/~tjunier/mmsearch/doc. PMID: 11751236 [PubMed","no","no","3: Bioinformatics. 2001 Dec;17(12):1234-5.","mmsearch: a motif arrangement language and search program.","Junier T, Pagni M, Bucher P.","PMID: 11751236 [PubMed - indexed for MEDLINE]"]
["at http://BioInfo.PL/ToolShop/. The administrator should be contacted to couple the tested server to the evaluation suite. CONTACT: leszek@bioinfo.pl SUPPLEMENTARY INFORMATION: The evaluation procedures are similar to those implemented in the continuous online server evaluation program, LiveBench. A","yes","n","1: Bioinformatics. 2001 Dec;17(12):1240-1.","ToolShop: prerelease inspections for protein structure prediction servers.","Rychlewski L.","PMID: 11751239 [PubMed - indexed for MEDLINE]"]
["www.biosci.ohio-state.edu/~ray/bioinformatics/tricross.html. CONTACT: ray@biosci.ohio-state.edu; daniels.7@osu.edu; munsonr@pediatrics.ohio-state.edu Supplementary information: Additional data from the cross-genomic comparisons examined in the discussion section are linked from http://www.biosci.ohi","yes","n","5: Bioinformatics. 2001 Dec;17(12):1105-12.","Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic","features.","PMID: 11751218 [PubMed - indexed for MEDLINE]"]
[" gene products were 0-6% different in amino acid sequence, but the differences did not alter residues thought to be involved in protein function (see supplementary data at http://mic.sgmjournals.org or http://www.uic.edu/depts/mcmi/individual/gupta/index.htm). For representative IncH plasmid R476b a","yes","n","6: Microbiology. 2001 Dec;147(Pt 12):3393-402.","Diversity of silver resistance genes in IncH incompatibility group plasmids.","Gupta A, Phung LT, Taylor DE, Silver S.","PMID: 11739772 [PubMed - indexed for MEDLINE]"]
["hydrogen. AVAILABILITY: Programs available from http://geometry.molmovdb.org. CONTACT: JerryTsai@TAMU.edu; neil.voss@yale.edu; Mark.Gerstein@yale.edu SUPPLEMENTARY INFORMATION: Available at http://geometry.molmovdb.org. PMID: 11673240 [PubMed - indexed for MEDLINE]","yes","n","8: Bioinformatics. 2001 Oct;17(10):949-56.","Determining the minimum number of types necessary to represent the sizes of","protein atoms.","PMID: 11673240 [PubMed - indexed for MEDLINE]"]
["TACT: e.bolten@science-factory.com; schliep@zpr.uni-koeln.de; s.schneckener@science-factory.com; d.schomburg@uni-koeln.de; schrader@zpr.uni-koeln.de. SUPPLEMENTARY INFORMATION: http://www.zaik.uni-koeln.de/~schliep/ProtClust.html. PMID: 11673238 [PubMed - indexed for MEDLINE]","yes","n","9: Bioinformatics. 2001 Oct;17(10):935-41.","Clustering protein sequences--structure prediction by transitive homology.","Bolten E, Schliep A, Schneckener S, Schomburg D, Schrader R.","PMID: 11673238 [PubMed - indexed for MEDLINE]"]
["e apex may be proportional to stress on the cell wall.  We propose that turgor-pressure wall stress modulates local apical cell wall growth rates.  A supplementary model, relating cell wall curvature and growth rate in the cut-interwhorl, characterizes how the stalk's final dimensions and nearly cyl","yes","n","10: Planta. 2001 Aug;213(4):659-66.","Relationships between growth, morphology and wall stress in the stalk of","Acetabularia acetabulum.","PMID: 11556799 [PubMed - indexed for MEDLINE]"]
["ure, but we suggest that secondary structure profiles may also be useful in the future. The classification forms a framework around which a wealth of supplementary information about the peptidases is organized. This includes images of three-dimensional structures, alignments of matching human and mo","yes","n","11: J Struct Biol. 2001 May-Jun;134(2-3):95-102.","The MEROPS database as a protease information system.","Barrett AJ, Rawlings ND, O'Brien EA.","PMID: 11551172 [PubMed - indexed for MEDLINE]"]
["ent tissues, 13 genes appeared differentially expressed among tissues. AVAILABILITY: The expression data of the ribosomal protein genes together with supplementary material (complete transcriptional profiles of the considered human tissues) are freely available at the site GETProfiles (http://teleth","yes","n","6: Bioinformatics. 2001 Dec;17(12):1152-7.","Differential expression of genes coding for ribosomal proteins in different","human tissues.","PMID: 11751223 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Data Interpretation, Statistical","Databases, Nucleic Acid","Expressed Sequence Tags","Gene Expression Profiling","Gene Expression Regulation*","Humans","Research Support, Non-U.S. Gov't","Ribosomal Proteins/genetics*","Substances:","Ribosomal Proteins"]
["from our model is an estimation of the fold composition of the initial genome, which potentially relates to the common ancestor for modern organisms. Supplementary material pertaining to this work is available from www.partslist.org/powerlaw. Copyright 2001 Academic Press. MeSH Terms: Animals Comput","yes","n","8: J Mol Biol. 2001 Nov 2;313(4):673-81.","Protein family and fold occurrence in genomes: power-law behaviour and","evolutionary model.","PMID: 11697896 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Computational Biology","Computer Simulation","Evolution, Molecular*","Genes, Duplicate/genetics","Genome*","Humans","Models, Genetic","Multigene Family*/genetics","Protein Folding*","Proteins/chemistry*","Proteins/classification","Proteins/genetics*","Proteins/metabolism","Proteome","Research Support, Non-U.S. Gov't","Substances:","Proteins","Proteome"]
["y available at http://BioInfo.PL/meta/, some remote servers have however restrictions for non-academic users, which are respected by the meta server. SUPPLEMENTARY INFORMATION: Results of several sessions of the CAFASP and LiveBench programs for assessment of performance of fold-recognition servers ","yes","no","13: Bioinformatics. 2001 Aug;17(8):750-1.","Structure prediction meta server.","Bujnicki JM, Elofsson A, Fischer D, Rychlewski L.","PMID: 11524381 [PubMed - indexed for MEDLINE]"]
["s based on sorting signals. AVAILABILITY: A web server implementing the prediction method is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/. PMID: 11524373 [PubMed - indexed for MED","yes","no","15: Bioinformatics. 2001 Aug;17(8):721-8.","Support vector machine approach for protein subcellular localization prediction.","Hua S, Sun Z.","PMID: 11524373 [PubMed - indexed for MEDLINE]"]
["s based on sorting signals. AVAILABILITY: A web server implementing the prediction method is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.bioinfo.tsinghua.edu.cn/SubLoc/. MeSH Terms: Amino Acid Sequence Amino Ac","yes","no","10: Bioinformatics. 2001 Aug;17(8):721-8.","Support vector machine approach for protein subcellular localization prediction.","Hua S, Sun Z.","PMID: 11524373 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Amino Acids/analysis","Comparative Study","Computational Biology","Computer Simulation*","Databases, Protein","Internet","Models, Biological*","Proteins/chemistry","Proteins/metabolism*","Research Support, Non-U.S. Gov't","Software","Subcellular Fractions/metabolism*","Substances:","Amino Acids","Proteins"]
["[VO(naph-tris)](2)] [where naph-tris is the Schiff base formed between o-hydroxynaphthaldehyde and tris(hydroxymethyl)amine] are reported. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0311-5. MeSH Te","yes","y","1: J Biol Inorg Chem. 2002 Apr;7(4-5):384-96. Epub 2001 Dec 19.","Erratum in:","J Biol Inorg Chem 2002 Jun;7(6):675.","PMID: 11941496 [PubMed - indexed for MEDLINE]","MeSH Terms:","3T3 Cells","Animals","Cells, Cultured","Fibroblasts","Glucose/pharmacokinetics","Humans","Insulin/pharmacology*","Mice","Molecular Mimicry","Reproducibility of Results","Research Support, Non-U.S. Gov't","Toxicity Tests","Vanadium Compounds/chemical synthesis","Vanadium Compounds/chemistry*","Vanadium Compounds/pharmacology*","Substances:","Vanadium Compounds","Insulin","Glucose"]
["tative performance with semi-quantitative results in the concentration predictions of both the standard mixture and the real-world sample. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00216-001-1125-6. PMID: 1","yes","y","2: Anal Bioanal Chem. 2002 Jan;372(1):205-15. Epub 2001 Dec 12.","A laser-induced fluorescence dual-fiber optic array detector applied to the","rapid HPLC separation of polycyclic aromatic hydrocarbons.","PMID: 11939196 [PubMed]"]
["meotic genes has been completely overlooked until recently and awaits further evaluation of its developmental and evolutionary importance. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00438-001-0615-8. MeSH Te","yes","y","3: Mol Genet Genomics. 2002 Feb;266(6):942-50. Epub 2001 Dec 15.","A novel MADS-box gene subfamily with a sister-group relationship to class B","floral homeotic genes.","PMID: 11862488 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Angiosperms/classification","Angiosperms/genetics*","Arabidopsis/genetics","Cloning, Molecular","DNA, Complementary/chemistry","DNA, Complementary/genetics","Gene Expression Regulation, Plant","Genes, Plant/genetics*","In Situ Hybridization","MADS Domain Proteins/genetics*","Molecular Sequence Data","Phylogeny","Research Support, Non-U.S. Gov't","Sequence Alignment","Sequence Analysis, DNA","Sequence Homology, Amino Acid","Zea mays/genetics","Substances:","DNA, Complementary","MADS Domain Proteins","Secondary Source ID:","GENBANK/AJ271208","GENBANK/AJ307056","GENBANK/AJ318098"]
["tion to these data, we present a few examples of the many possible applications of this transgenic line for developmental studies in vivo. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00427-001-0196-x MeSH Ter","yes","y","4: Dev Genes Evol. 2001 Dec;211(12):603-10. Epub 2001 Dec 15.","A zebrafish histone variant H2A.F/Z and a transgenic H2A.F/Z:GFP fusion protein","for in vivo studies of embryonic development.","PMID: 11819118 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Animals, Genetically Modified/embryology","Animals, Genetically Modified/genetics*","Animals, Genetically Modified/physiology","Genes, Reporter","Green Fluorescent Proteins","Histones/genetics*","Histones/physiology","Luminescent Proteins","Molecular Sequence Data","Recombinant Fusion Proteins/genetics","Research Support, Non-U.S. Gov't","Zebrafish/embryology*","Zebrafish/genetics*","Substances:","Histones","Luminescent Proteins","Recombinant Fusion Proteins","Green Fluorescent Proteins","Secondary Source ID:","GENBANK/AF414110"]
["tween amoC and amoA is variable in length and may be used to profile the community of ammonia-oxidizing bacteria in environmental samples. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-001-0369-z. MeSH Te","yes","y","5: Arch Microbiol. 2002 Feb;177(2):139-49. Epub 2001 Dec 6.","Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing","bacteria.","PMID: 11807563 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Ammonia/metabolism*","Betaproteobacteria/classification","Betaproteobacteria/enzymology","Betaproteobacteria/genetics*","Chromatiaceae/classification","Chromatiaceae/enzymology","Chromatiaceae/genetics","Comparative Study","Environmental Microbiology","Gammaproteobacteria/classification","Gammaproteobacteria/enzymology","Gammaproteobacteria/genetics*","Gene Dosage","Molecular Sequence Data","Nitrosomonas/classification","Nitrosomonas/enzymology","Nitrosomonas/genetics","Operon","Oxidoreductases/genetics*","Protein Structure, Secondary","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Sequence Homology, Amino Acid","Variation (Genetics)","Substances:","Ammonia","Oxidoreductases","ammonia monooxygenase"]
["e would provide a rationale why during exercising or physical stress radicals are formed without necessarily being deleterious. This article contains supplementary material that may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/23/v23_11.1064.html. ","yes","y","7: Bioessays. 2001 Nov;23(11):1064-9.","Plectin repeats and modules: strategic cysteines and their presumed impact on","cytolinker functions.","PMID: 11746222 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Animals","Ankyrins/chemistry*","Ankyrins/physiology","Cysteine/chemistry*","Cysteine/physiology","Humans","Intermediate Filament Proteins/chemistry*","Intermediate Filament Proteins/physiology","Models, Molecular","Molecular Sequence Data","Oxidants/physiology","Plectin","Protein Structure, Tertiary","Repetitive Sequences, Amino Acid/physiology*","Research Support, Non-U.S. Gov't","Substances:","Ankyrins","Intermediate Filament Proteins","Oxidants","PLEC1 protein, human","Plectin","Cysteine"]
["fect on cell cycle progression and apoptosis, whereas in signal transduction they may act as stimulatory or inhibitory factors. This article contains supplementary material which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/Suppmat/23/v23_10.936. Copyr","yes","y","9: Bioessays. 2001 Oct;23(10):936-46.","14-3-3 proteins: key regulators of cell division, signalling and apoptosis.","van Hemert MJ, Steensma HY, van Heusden GP.","PMID: 11598960 [PubMed - indexed for MEDLINE]","MeSH Terms:","14-3-3 Proteins","Animals","Apoptosis*","Cell Cycle","Cell Division","Humans","Signal Transduction/physiology*","Tyrosine 3-Monooxygenase/metabolism","Tyrosine 3-Monooxygenase/physiology*","Substances:","14-3-3 Proteins","Tyrosine 3-Monooxygenase"]
["hat CtBP proteins might regulate gene expression directly by means of their enzymatic activities, in addition to serving as simple bridging proteins. Supplementary material for this article can be found on the BioEssays homepage at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/v23_8.684","yes","y","12: Bioessays. 2001 Aug;23(8):683-90.","The CtBP family: enigmatic and enzymatic transcriptional co-repressors.","Turner J, Crossley M.","PMID: 11494316 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Motifs","Amino Acid Sequence","Animals","Binding Sites","DNA-Binding Proteins/chemistry","DNA-Binding Proteins/genetics","DNA-Binding Proteins/metabolism*","Histone Deacetylases/metabolism","Phosphoproteins/metabolism*","Repressor Proteins/metabolism*","Substances:","C-terminal binding protein","DNA-Binding Proteins","Phosphoproteins","Repressor Proteins","Histone Deacetylases"]

{"sheet":"2002","index":6,"n_rows":79,"n_cols":53,"rows_kept":79,"flags":["formulas_cached_only"]}
["Reference","Live?","Journal?"]
["esults clearly show that DTSCORE is more accurate than all the other methods we studied. Finally, we report the results of DTSCORE on a real dataset. Supplementary information: http://www.lirmm.fr/w3ifa/MAAS/ Publication Types: Evaluation Studies PMID: 12385990 [PubMed - indexed for MEDLINE]","No","n","3: Bioinformatics. 2002;18 Suppl 2:S92-9.","An efficient and accurate distance based algorithm to reconstruct tandem","duplication trees.","PMID: 12385990 [PubMed - indexed for MEDLINE]"]
["n functional genomics. AVAILABILITY: Java class files are freely available at http://mendel.mc.duke.edu/bioinformatics/ CONTACT: mccon012@mc.duke.edu SUPPLEMENTARY INFORMATION: For more information on TreeMapClusterView (see http://mendel.mc.duke.edu/bioinformatics/software/boxclusterview/), and htt","no","n","5: Bioinformatics. 2002 Sep;18(9):1278-9.","Applications of Tree-Maps to hierarchical biological data.","McConnell P, Johnson K, Lin S.","PMID: 12217926 [PubMed - indexed for MEDLINE]"]
["ools/mpicode. The 'message passing interface' package (MPICH) is available from http:/www.unix.mcs.anl.gov/mpi/mpich. CONTACT: jhering@nimr.mrc.ac.uk SUPPLEMENTARY INFORMATION: Praline is accessible at http://mathbio.nimr.mrc.ac.uk/praline. PMID: 12217922 [PubMed - indexed for MEDLINE]","no","n","7: Bioinformatics. 2002 Sep;18(9):1270-1.","Parallelized multiple alignment.","Kleinjung J, Douglas N, Heringa J.","PMID: 12217922 [PubMed - indexed for MEDLINE]"]
["ring the effect of the amount of among-site-rate-variation, and the degree of sequence divergence on the resulting ancestral states. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://evolu3.ism.ac.jp/~tal/ Contact: tal@ism.ac.jp PMID: 12176835 [PubMed - indexed for MEDLINE]","no","n","11: Bioinformatics. 2002 Aug;18(8):1116-23.","A branch-and-bound algorithm for the inference of ancestral amino-acid sequences","when the replacement rate varies among sites: Application to the evolution of","PMID: 12176835 [PubMed - indexed for MEDLINE]"]
["epository of sequences and population information that is usually dispersed in a variety of other sources. AVAILABILITY: http://www.gen-epi.de/mouse. SUPPLEMENTARY INFORMATION: Documentation and detailed information on population subgroups is available on the homepage: http://www.gen-epi.de/mouse PM","no","n","15: Bioinformatics. 2002 Jun;18(6):890-1.","MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population","genetic markers.","PMID: 12075028 [PubMed - indexed for MEDLINE]"]
["ia coli growth on two carbon sources (acetate and glucose) at all levels of oxygenation, and the resulting optimal metabolic phenotypes were studied. Supplementary information can be downloaded from our website (http://epicurus.che.udel.edu). Copyright 2002 John Wiley & Sons, Inc. PMID: 11745171 [Pu","no","n","24: Biotechnol Bioeng. 2002 Jan 5;77(1):27-36.","Characterizing the metabolic phenotype: a phenotype phase plane analysis.","Edwards JS, Ramakrishna R, Palsson BO.","PMID: 11745171 [PubMed - indexed for MEDLINE]"]
["tains some weakly predictive information with respect to protein complexes, but we show how this prediction can be improved by combining all of them. Supplementary information is available at http:// bioinfo.mbb.yale.edu/integrate/interactions/. PMID: 12836664 [PubMed - indexed for MEDLINE]","yes","n","1: J Struct Funct Genomics. 2002;2(2):71-81.","Integration of genomic datasets to predict protein complexes in yeast.","Jansen R, Lan N, Qian J, Gerstein M.","PMID: 12836664 [PubMed - indexed for MEDLINE]"]
[" supports the graphical comparison of metabolic networks of different organisms. AVAILABILITY: http://www.zbi.uni-saarland.de/chair/projects/BioMiner SUPPLEMENTARY INFORMATION: Additional information on experimental results can be found on our web site. Publication Types: Evaluation Studies PMID: 12","yes","n","2: Bioinformatics. 2002;18 Suppl 2:S219-30.","BioMiner--modeling, analyzing, and visualizing biochemical pathways and","networks.","PMID: 12386006 [PubMed - indexed for MEDLINE]"]
["s that may play a role in determining the protein's structure and function. AVAILABILITY: http://bioinformatics.org/pecop Contact: idoerg@burnham.org SUPPLEMENTARY INFORMATION: http://bioinformatics.org/pecop/about_pecop PMID: 12217925 [PubMed - indexed for MEDLINE]","yes","n","6: Bioinformatics. 2002 Sep;18(9):1276-7.","PeCoP: automatic determination of persistently conserved positions in protein","families.","PMID: 12217925 [PubMed - indexed for MEDLINE]"]
["ta may improve the quality of multiple sequence alignments, this does not add to the ability of the derived profile HMMs to find sequence homologues. SUPPLEMENTARY INFORMATION: A list of HOMSTRAD families used in this study and the corresponding Pfam families is available at http://www.sanger.ac.uk/","yes","n","8: Bioinformatics. 2002 Sep;18(9):1243-9.","The use of structure information to increase alignment accuracy does not aid","homologue detection with profile HMMs.","PMID: 12217916 [PubMed - indexed for MEDLINE]"]
["ILITY: Use of the XEMBL service is free of charge at http://www.ebi.ac.uk/xembl/, and can be accessed via web forms, CGI, and a SOAP-enabled service. SUPPLEMENTARY INFORMATION: Information on the EMBL Nucleotide Sequence Database is available at http://www.ebi.ac.uk/embl/. The EMBL Object Model is a","yes","n","9: Bioinformatics. 2002 Aug;18(8):1147-8.","XEMBL: distributing EMBL data in XML format.","Wang L, Riethoven JJ, Robinson A.","PMID: 12176844 [PubMed - indexed for MEDLINE]"]
["ets thereof, pattern generators, and pattern database interfaces. The modules are interoperable with the BioPerl open source system. AVAILABILITY AND SUPPLEMENTARY INFORMATION: The module package with documentation and example scripts are available at http://forkhead.cgb.ki.se/TFBS/ PMID: 12176838 [","yes","n","10: Bioinformatics. 2002 Aug;18(8):1135-6.","TFBS: Computational framework for transcription factor binding site analysis.","Lenhard B, Wasserman WW.","PMID: 12176838 [PubMed - indexed for MEDLINE]"]
["ers may also encode transframe products. AVAILABILITY: The program is available for download from http://www.gesteland.genetics.utah.edu/freqAnalysis SUPPLEMENTARY INFORMATION: Complete results from the analysis of S. cerevisiae are available on http://www.gesteland.genetics.utah.edu/freqAnalysis PM","yes","n","12: Bioinformatics. 2002 Aug;18(8):1046-53.","Computational identification of putative programmed translational frameshift","sites.","PMID: 12176827 [PubMed - indexed for MEDLINE]"]
[" applicable to the rapid identification of unique sequences in other DNA sequence sets. AVAILABILITY: Freely available upon request from the authors. Supplementary information: Results are available at http://www.sys.uea.ac.uk/~jjw/project/paper PMID: 12117799 [PubMed - indexed for MEDLINE]","yes","n","13: Bioinformatics. 2002 Jul;18(7):1004-10.","Determining a unique defining DNA sequence for yeast species using hashing","techniques.","PMID: 12117799 [PubMed - indexed for MEDLINE]"]
["adeh et al. (2000; Nature, 403, 503-511), our analyses only partially support the conclusions of the original authors. AVAILABILITY: The software and supplementary information are available freely to researchers at academic and non-profit institutions at http://cc.ucsf.edu/jain/public PMID: 12117794","yes","n","14: Bioinformatics. 2002 Jul;18(7):961-70.","Deriving quantitative conclusions from microarray expression data.","Olshen AB, Jain AN.","PMID: 12117794 [PubMed - indexed for MEDLINE]"]
["f raw cDNA microarray data. AVAILABILITY: MS-Windows binaries are freely available for non-profit use at http://www.biologie.ens.fr/yeast-publi.html. SUPPLEMENTARY INFORMATION: Scripts for online creation of Arrayplot files are available at http://transcriptome.ens.fr/lgm_bioinfo/ PMID: 12075027 [Pu","yes","n","16: Bioinformatics. 2002 Jun;18(6):888-9.","Arrayplot for visualization and normalization of cDNA microarray data.","Marc P, Jacq C.","PMID: 12075027 [PubMed - indexed for MEDLINE]"]
["sers in a multi-user/multi-group environment. AVAILABILITY: An AiO specific website, with the possibility to download is at: http://134.99.88.55/aio/ SUPPLEMENTARY INFORMATION: Examples with screen shots- http://134.99.88.55/aio/ : Manual (in PDF format)-http://134.99.88.55/aio/manual.pdf PMID: 1207","yes","n","17: Bioinformatics. 2002 Jun;18(6):884-5.","AiO, combining DNA/protein programs and oligo-management.","Karreman C.","PMID: 12075025 [PubMed - indexed for MEDLINE]"]
[" as well as in windows containing several tyrosine residues. AVAILABILITY: The Sulfinator is accessible at (http://www.expasy.org/tools/sulfinator/). Supplementary information: Sulfinator documentation is accessible at (http://www.expasy.org/tools/sulfinator/sulfinator-doc.html). PMID: 12050077 [Pub","yes","n","18: Bioinformatics. 2002 May;18(5):769-70.","The Sulfinator: predicting tyrosine sulfation sites in protein sequences.","Monigatti F, Gasteiger E, Bairoch A, Jung E.","PMID: 12050077 [PubMed - indexed for MEDLINE]"]
["otein/peptide mass spectra simulations. AVAILABILITY: The massXpert program is free for academic and commercial use at http://frl.lptc.u-bordeaux.fr. SUPPLEMENTARY INFORMATION: The http://frl.lptc.u-bordeaux.frsite contains a tutorial for online perusal or download. PMID: 12016065 [PubMed - indexed ","yes","n","19: Bioinformatics. 2002 Apr;18(4):644-5.","Desktop prediction/analysis of mass spectrometric data in proteomic projects by","using massXpert.","PMID: 12016065 [PubMed - indexed for MEDLINE]"]
[" mouse) studied. Moreover, CpGProD predicts the promoter orientation on the DNA strand. AVAILABILITY: http://pbil.univ-lyon1.fr/software/cpgprod.html SUPPLEMENTARY INFORMATION: http://pbil.univ-lyon1.fr/software/cpgprod.html PMID: 12016061 [PubMed - indexed for MEDLINE]","yes","n","20: Bioinformatics. 2002 Apr;18(4):631-3.","CpGProD: identifying CpG islands associated with transcription start sites in","large genomic mammalian sequences.","PMID: 12016061 [PubMed - indexed for MEDLINE]"]
["ils; (iv) cytoplasmic proteins relative to nuclear ones; and (v) proteins involved in 'protein synthesis,' 'cell structure,' and 'energy production.' SUPPLEMENTARY INFORMATION: http://genecensus.org/expression/translatome PMID: 12016056 [PubMed - indexed for MEDLINE]","yes","n","21: Bioinformatics. 2002 Apr;18(4):585-96.","Analysis of mRNA expression and protein abundance data: an approach for the","comparison of the enrichment of features in the cellular population of proteins","PMID: 12016056 [PubMed - indexed for MEDLINE]"]
["es and the numbers of molecules involved. AVAILABILITY: The software is available at ftp://ibbrain.ibb.waw.pl/stocksand http://www.ibb.waw.pl/stocks. Supplementary information: Parameters of the model of prokaryotic gene expression are available in example files of software distribution. PMID: 11934","yes","n","22: Bioinformatics. 2002 Mar;18(3):470-81.","STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie","algorithm.","PMID: 11934747 [PubMed - indexed for MEDLINE]"]
["ogy-independent structure enables updates of annotation hierarchies during normal database operation without altering the structure. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://www.dkfz.de/tbi/services/mchips PMID: 11934741 [PubMed - indexed for MEDLINE]","yes","n","23: Bioinformatics. 2002 Mar;18(3):423-33.","Microarray data warehouse allowing for inclusion of experiment annotations in","statistical analysis.","PMID: 11934741 [PubMed - indexed for MEDLINE]"]
["terial LipOProteins (DOLOP) is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop along with additional information on the biosynthetic pathway, supplementary material and other related figures. MeSH Terms: Algorithms Bacteria/chemistry Bacteria/genetics Database Management Systems* Databases, ","yes","n","34: Bioinformatics. 2002 Apr;18(4):641-3.","DOLOP--database of bacterial lipoproteins.","Madan Babu M, Sankaran K.","PMID: 12016064 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms","Bacteria/chemistry","Bacteria/genetics","Database Management Systems*","Databases, Protein*","Genome, Bacterial*","Information Storage and Retrieval/methods*","Lipoproteins/chemistry","Lipoproteins/classification*","Lipoproteins/genetics*","Protein Sorting Signals/genetics","Sensitivity and Specificity","Sequence Analysis, Protein/methods","Substances:","Lipoproteins","Protein Sorting Signals"]
["ination chemistry and stability of the native clusters has been investigated through site-directed mutagenesis and spectroscopic analysis. Electronic supplementary material to this paper, containing Mossbauer and UV-visible spectra for mutant Isa1 proteins, can be obtained by using the Springer Link","yes","n","45: J Biol Inorg Chem. 2002 Apr;7(4-5):526-32. Epub 2002 Feb 13.","Iron-sulfur cluster biosynthesis: characterization of Schizosaccharomyces pombe","Isa1.","PMID: 11941510 [PubMed - indexed for MEDLINE]","MeSH Terms:","Alanine","Amino Acid Sequence","Cloning, Molecular","Cross-Linking Reagents/chemistry","Cysteine","DNA-Binding Proteins/chemistry","DNA-Binding Proteins/genetics*","DNA-Binding Proteins/metabolism*","Electron Spin Resonance Spectroscopy","Escherichia coli/chemistry","Ferredoxins/chemistry","Iron-Sulfur Proteins/biosynthesis*","Molecular Sequence Data","Mutation","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Saccharomyces cerevisiae Proteins*","Schizosaccharomyces/genetics","Schizosaccharomyces/metabolism*","Sequence Homology, Amino Acid","Spectroscopy, Mossbauer","Transcription Factors/chemistry","Transcription Factors/genetics*","Transcription Factors/metabolism*","Substances:","Cross-Linking Reagents","DNA-Binding Proteins","Ferredoxins","ISA1 protein, S cerevisiae","Iron-Sulfur Proteins","Saccharomyces cerevisiae Proteins","Transcription Factors","Cysteine","Alanine","Grant Support:","GM08512-03/GM/NIGMS","GM59953/GM/NIGMS"]
["ts. The tool is written in Microsoft Excel 2000 and is available free of charge for use in teaching and research from www.aob.oupjournals.org article supplementary data. PMID: 12324272 [PubMed - indexed for MEDLINE]","yes","y","4: Ann Bot (Lond). 2002 Oct;90(4):485-8.","A modern tool for classical plant growth analysis.","Hunt R, Causton DR, Shipley B, Askew AP.","PMID: 12324272 [PubMed - indexed for MEDLINE]"]
["et allows a safe diagnostic FOB with BAL in patients with hypoxemic ARF, avoiding gas exchange deterioration, and endotracheal intubation. Electronic supplementary material: is available if you access this article at http://dx.doi.org/10.1007/s00134-002-1554-5. On that page (frame on the left side),","yes","y","1: Intensive Care Med. 2003 Jan;29(1):126-9. Epub 2002 Nov 29.","Fiberoptic bronchoscopy during noninvasive positive pressure ventilation","delivered by helmet.","PMID: 12528033 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Aged","Anoxemia/diagnosis","Bronchoalveolar Lavage/methods","Bronchoscopy/methods*","Female","Fiber Optics*","Head Protective Devices*","Humans","Male","Middle Aged","Pneumonia/diagnosis*","Positive-Pressure Respiration/instrumentation*","Prospective Studies","Respiratory Distress Syndrome, Adult/diagnosis*","Statistics, Nonparametric"]
["fter cardiothoracic surgery alters nursing activity; it reduces the time for documentation and increases the time devoted to patient care. Electronic supplementary material: is available if you access this article at http://dx.org/10.1007/s00134-002-1542-9. On that page (frame on the left side), a l","yes","y","2: Intensive Care Med. 2003 Jan;29(1):83-90. Epub 2002 Nov 22.","Intensive care information system reduces documentation time of the nurses after","cardiothoracic surgery.","PMID: 12528027 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Aged","Cardiac Surgical Procedures/nursing","Efficiency, Organizational*","Female","Hospital Information Systems*","Humans","Intensive Care Units*","Male","Middle Aged","Netherlands","Nursing Staff, Hospital/organization & administration*","Thoracic Surgical Procedures/nursing*","Time and Motion Studies"]
["le if you access this article at http://dx.doi.org/10.1007/s00216-002-1595-1. On that page (frame on the left side), a link takes you directly to the supplementary material. PMID: 12474092 [PubMed]","yes","y","3: Anal Bioanal Chem. 2002 Dec;374(7-8):1242-9. Epub 2002 Nov 6.","Comparison of spark OES methods for analysis of inclusions in iron base matters.","Kuss HM, Lungen S, Muller G, Thurmann U.","PMID: 12474092 [PubMed]"]
["le if you access this article at http://dx.doi.org/10.1007/s00114-002-0353-8. On that page (frame on the left side), a link takes you directly to the supplementary material. MeSH Terms: Animals Birds/anatomy & histology* China Environment Fossils* Research Support, Non-U.S. Gov't Trees Vertebrates/a","yes","y","4: Naturwissenschaften. 2002 Sep;89(9):394-8. Epub 2002 Aug 21.","A juvenile coelurosaurian theropod from China indicates arboreal habits.","Zhang F, Zhou Z, Xu X, Wang X.","PMID: 12435090 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Birds/anatomy & histology*","China","Environment","Fossils*","Research Support, Non-U.S. Gov't","Trees","Vertebrates/anatomy & histology*"]
["ling behavior suggests the presence of two pairs of vocal sacs that may contribute to the remarkable call-note complexity in this species. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-002-0335-x. MeSH Te","yes","y","5: Naturwissenschaften. 2002 Aug;89(8):352-6. Epub 2002 Jun 22.","Vocal acrobatics in a Chinese frog, Amolops tormotus.","Feng AS, Narins PM, Xu CH.","PMID: 12435035 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Ranidae/physiology*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Time Factors","Vocalization, Animal*","Grant Support:","R01DC00222/DC/NIDCD","R01DC00663/DC/NIDCD"]
["grees C, 72 h) and in coffee beans after different amounts of roasting. The origin of formation of volatile acidity was also investigated. Electronic supplementary material is available if you access this article at http://dx.doi.org/10.1007/s00216-002-1561-y On that page (frame on the left side) a ","yes","y","6: Anal Bioanal Chem. 2002 Nov;374(5):879-85. Epub 2002 Oct 10.","New procedures for determination of acids in coffee extracts, and observations","on the development of acidity upon ageing.","PMID: 12434245 [PubMed]"]
["libration is a useful tool to characterise the performance of pH electrodes. This is demonstrated with different commercial pH electrodes. ELECTRONIC SUPPLEMENTARY MATERIAL is available if you access this article at http://dx.doi.org/10.1007/s00216-002-1506-5. On that page (frame on the left side), ","yes","y","7: Anal Bioanal Chem. 2002 Nov;374(5):778-86. Epub 2002 Sep 20.","Traceability of pH measurements by glass electrode cells: performance","characteristic of pH electrodes by multi-point calibration.","PMID: 12434231 [PubMed]"]
["nsitivity and specificity of MPSS allowed us to identify a large number of ABA-responsive genes in WT Arabidopsis thaliana. The database given in our supplementary material (http://jcs.biologists.org/supplemental) provides researchers with the opportunity to rapidly assess whether genes of interest ","yes","y","8: J Cell Sci. 2002 Dec 15;115(Pt 24):4891-900.","Genome-wide gene expression profiling in Arabidopsis thaliana reveals new","targets of abscisic acid and largely impaired gene regulation in the abi1-1","PMID: 12432076 [PubMed - indexed for MEDLINE]","MeSH Terms:","Abscisic Acid/pharmacology*","Arabidopsis/genetics*","Base Sequence","DNA Primers","Gene Expression Profiling*","Gene Expression Regulation, Plant/drug effects*","Genome, Plant*","Mutation*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Substances:","DNA Primers","Abscisic Acid","Grant Support:","GM-44640/GM/NIGMS"]
["le if you access this article at http://dx.doi.org/10.1007/s00425-002-0889-z. On that page (frame on the left side), a link takes you directly to the supplementary material. MeSH Terms: 2,4-Dichlorophenoxyacetic Acid/pharmacology ATP-Binding Cassette Transporters/genetics* Abscisic Acid/pharmacology","yes","y","9: Planta. 2002 Nov;216(1):95-106. Epub 2002 Nov 12.","The plant PDR family of ABC transporters.","van den Brule S, Smart CC.","PMID: 12430018 [PubMed - indexed for MEDLINE]","MeSH Terms:","2,4-Dichlorophenoxyacetic Acid/pharmacology","ATP-Binding Cassette Transporters/genetics*","Abscisic Acid/pharmacology","Amino Acid Sequence","Angiosperms/drug effects","Angiosperms/genetics*","Angiosperms/microbiology","Arabidopsis/drug effects","Arabidopsis/genetics","Arabidopsis/microbiology","Cadmium Chloride/pharmacology","Diterpenes/pharmacology*","Drug Resistance/genetics","Fungi/drug effects","Gene Expression Regulation, Plant/drug effects","Molecular Sequence Data","Phylogeny","Plant Diseases/microbiology","Plant Proteins/genetics*","Research Support, Non-U.S. Gov't","Sequence Homology, Amino Acid","Sodium Chloride/pharmacology","Substances:","ATP-Binding Cassette Transporters","Diterpenes","Plant Proteins","TUR2 protein, Spirodela polyrrhiza","Cadmium Chloride","Abscisic Acid","sclareol","Sodium Chloride","2,4-Dichlorophenoxyacetic Acid"]
[" functions as well as diffusion coefficients and are compared with the corresponding findings on clusters of alkanes and perfluoroalkanes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s008940020092y. MeSH Terms","yes","y","10: J Mol Model (Online). 2002 Sep;8(9):266-71. Epub 2002 Sep 4.","Molecular dynamics studies on the aggregation of Y-shaped fluoroalkanes.","Friedemann R, Naumann S, Brickmann J.","PMID: 12415331 [PubMed - indexed for MEDLINE]","MeSH Terms:","Alkanes/chemistry*","Computer Simulation","Diffusion","Fluorocarbons/chemistry*","Models, Molecular*","Molecular Structure","Research Support, Non-U.S. Gov't","Software","Substances:","Alkanes","Fluorocarbons"]
[" the participants was the batch-to-batch variability of commercial Cot1 preparations in their ability to suppress hybridization to repeat sequences. (Supplementary material for this article can be found in the online issue, which is available at http://www.interscience.wiley.com/jpages/0196-4763/sup","yes","y","11: Cytometry. 2002 Oct 1;49(2):43-8.","Comparative analysis of comparative genomic hybridization microarray","technologies: report of a workshop sponsored by the Wellcome Trust.","PMID: 12357458 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Comparative Study","Drosophila/genetics","Education","Female","Genetics, Medical/trends*","Genomics*","Humans","Male","Nucleic Acid Hybridization/immunology","Nucleic Acid Hybridization/methods*","Oligonucleotide Array Sequence Analysis/methods*","Polymerase Chain Reaction","Research Support, Non-U.S. Gov't","Technology Assessment, Biomedical*"]
[" lignans. Furthermore, it appears that, in this species, the hydroxylation of DOP is a rate-limiting point in the pathway leading to PTOX. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/wo.1007/s00425-002-0834-1. MeSH Te","yes","y","12: Planta. 2002 Oct;215(6):1031-9. Epub 2002 Jul 25.","Biosynthesis of podophyllotoxin in Linum album cell cultures.","Seidel V, Windhovel J, Eaton G, Alfermann AW, Arroo RR, Medarde M, Petersen M,","PMID: 12355164 [PubMed - indexed for MEDLINE]","MeSH Terms:","Alcohol Oxidoreductases/metabolism","Aldehyde Oxidoreductases/metabolism","Carbon Isotopes","Cell Division/drug effects","Cells, Cultured","Chromatography, High Pressure Liquid","Cinnamates/chemical synthesis","Cinnamates/pharmacology","Coenzyme A Ligases/metabolism","Coumaric Acids/chemical synthesis","Coumaric Acids/chemistry","Coumaric Acids/metabolism","Coumaric Acids/pharmacology","Flax/cytology","Flax/enzymology","Flax/metabolism*","Hydrogen-Ion Concentration","Lignans/biosynthesis*","Lignans/isolation & purification","Molecular Structure","Phenylalanine Ammonia-Lyase/metabolism","Podophyllotoxin/analogs & derivatives*","Podophyllotoxin/biosynthesis*","Podophyllotoxin/chemistry","Podophyllotoxin/metabolism","Research Support, Non-U.S. Gov't","Spectrum Analysis, Mass","Substances:","Carbon Isotopes","Cinnamates","Coumaric Acids","Lignans","ferulic acid","3-(3,4-dimethoxyphenyl)propenoic acid","Podophyllotoxin","sinapinic acid","deoxypodophyllotoxin","3,4,5-trimethoxycinnamic acid","Alcohol Oxidoreductases","cinnamyl alcohol dehydrogenase","Aldehyde Oxidoreductases","cinnamoyl CoA reductase","Phenylalanine Ammonia-Lyase","Coenzyme A Ligases","hydroxycinnamate-CoA ligase"]
["ity and cell death. In all, our data suggest that NO induces the AOX1a gene and that AOX may participate to counteract the toxicity of NO. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00425-002-0828-z. MeSH Te","yes","y","13: Planta. 2002 Oct;215(6):914-23. Epub 2002 Jul 25.","Nitric oxide induces transcriptional activation of the nitric oxide-tolerant","alternative oxidase in Arabidopsis suspension cells.","PMID: 12355151 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adaptation, Physiological/drug effects","Arabidopsis/cytology","Arabidopsis/enzymology","Arabidopsis/genetics*","Blotting, Northern","Cells, Cultured","Cytochrome c Group/drug effects","Cytochrome c Group/metabolism","Gene Expression Regulation, Enzymologic/drug effects","Isoenzymes/genetics","Nitric Oxide/pharmacology*","Oligonucleotide Array Sequence Analysis","Oxidoreductases/genetics*","Reactive Oxygen Species/metabolism","Research Support, Non-U.S. Gov't","Signal Transduction/drug effects","Time Factors","Trans-Activation (Genetics)/drug effects","Substances:","Cytochrome c Group","Isoenzymes","Reactive Oxygen Species","Nitric Oxide","Oxidoreductases","alternative oxidase"]
["queous solution has been evaluated from the corresponding AM1 thermodynamic parameters. The results agree well with the experimental data. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-002-0094-9 Publicat","yes","y","14: J Mol Model (Online). 2002 Aug;8(8):246-52.","Theoretical investigation of the structure and acid-base properties of potential","2-thiolumazine tautomeric forms using the AM1 semiempirical method.","PMID: 12324801 [PubMed - indexed for MEDLINE]","MeSH Terms:","Empirical Research","Gases/chemistry","Hydrogen-Ion Concentration","Isomerism","Models, Chemical*","Molecular Structure","Pteridines/chemistry*","Research Support, Non-U.S. Gov't","Solvents/chemistry","Thermodynamics","Water/chemistry","Substances:","2-thiolumazine","Gases","Pteridines","Solvents","Water"]
[" the genes for this large family. [The sequence data from this study have been submitted to FlyBase. Annotations for these sequences are available as supplementary material at http://www.genome.org.] MeSH Terms: Amino Acid Sequence Animals Chromosome Mapping Comparative Study Conserved Sequence/gene","yes","y","15: Genome Res. 2002 Sep;12(9):1357-69.","Genome-wide analysis of the odorant-binding protein gene family in Drosophila","melanogaster.","PMID: 12213773 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Animals","Chromosome Mapping","Comparative Study","Conserved Sequence/genetics","Databases, Genetic","Drosophila Proteins/analysis","Drosophila Proteins/genetics","Drosophila melanogaster/genetics*","Gene Duplication","Gene Order/genetics","Genes, Insect/genetics","Genome*","Molecular Sequence Data","Multigene Family/genetics","Olfactory Mucosa/chemistry","Phylogeny","Receptors, Odorant/analysis*","Receptors, Odorant/genetics*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Sequence Alignment/methods","Sequence Analysis, DNA/methods*","Variation (Genetics)/genetics","Substances:","Drosophila Proteins","Receptors, Odorant","odorant-binding protein","Grant Support:","5R01NS31231/NS/NINDS"]
["when they occur simultaneously as complications of breast cancer treatment. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0024-7. MeSH Terms: Breas","yes","y","16: Surg Radiol Anat. 2002 May;24(2):87-90.","The cutaneo-lymph node flap of the superficial circumflex artery.","Assouad J, Becker C, Hidden G, Riquet M.","PMID: 12197025 [PubMed - indexed for MEDLINE]","MeSH Terms:","Breast/surgery","Breast Neoplasms/radiotherapy","Breast Neoplasms/surgery","Cadaver","Feasibility Studies","Female","Humans","Iliac Artery*","Lymph Nodes/blood supply","Lymph Nodes/transplantation*","Lymphedema/etiology","Lymphedema/surgery*","Mammaplasty/methods*","Radiation Injuries/surgery*","Skin/blood supply","Surgical Flaps*/blood supply*"]
["ppears to be that which theoretically leads to the least devascularization. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00276-002-0029-2. MeSH Terms: Arter","yes","y","17: Surg Radiol Anat. 2002 May;24(2):81-6.","Anatomical study of the blood supply of the coxal bone: radiological and","clinical application.","PMID: 12197024 [PubMed - indexed for MEDLINE]","MeSH Terms:","Arteries/anatomy & histology*","Cadaver","Female","Fractures, Bone/classification","Fractures, Bone/surgery","Humans","Osteonecrosis/prevention & control","Pelvic Bones/blood supply*","Pelvic Bones/injuries","Pelvic Bones/radiography","Pelvic Bones/surgery"]
["n the development of the IJV and the lateral branch of the accessory nerve. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0020-y. Publication Types","yes","y","18: Surg Radiol Anat. 2002 May;24(2):129-32.","High duplication of the internal jugular vein: clinical incidence in the adult","and surgical consequences, a report of three clinical cases.","PMID: 12197023 [PubMed - indexed for MEDLINE]","MeSH Terms:","Aged","Carcinoma, Squamous Cell/surgery","Humans","Jugular Veins/anatomy & histology*","Jugular Veins/embryology","Laryngeal Neoplasms/surgery","Lymph Node Excision","Male","Middle Aged"]
["pal artery and an early bifurcation of the second palmar metacarpal artery. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0011. Publication Types: ","yes","y","19: Surg Radiol Anat. 2002 May;24(2):125-8.","Multiple arterial variation of the human upper limb.","Durgun B, Yucel AH, Kizilkanat ED, Dere F.","PMID: 12197022 [PubMed - indexed for MEDLINE]","MeSH Terms:","Axillary Artery/anatomy & histology*","Brachial Artery/anatomy & histology*","Cadaver","Dissection","Humans","Male","Middle Aged","Radial Artery/anatomy & histology*","Ulnar Artery/anatomy & histology*","Upper Extremity/anatomy & histology","Upper Extremity/blood supply*"]
[" localization of the meniscofemoral ligaments should be taken into account. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0023-8. Publication Types","yes","y","20: Surg Radiol Anat. 2002 May;24(2):120-4.","An MRI study of the meniscofemoral and transverse ligaments of the knee.","Erbagci H, Yildirim H, Kizilkan N, Gumusburun E.","PMID: 12197021 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adolescent","Adult","Aged","Aged, 80 and over","Child","Female","Humans","Knee Joint/anatomy & histology*","Ligaments, Articular/anatomy & histology*","Magnetic Resonance Imaging*","Male","Middle Aged"]
["apment and tension from the temporalis muscle and/or the narrow bony canal. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0027-4. MeSH Terms: Cadav","yes","y","21: Surg Radiol Anat. 2002 May;24(2):113-6.","Nervous branch passing through an accessory canal in the sphenozygomatic suture:","the temporal branch of the zygomatic nerve.","PMID: 12197019 [PubMed - indexed for MEDLINE]","MeSH Terms:","Cadaver","Cranial Sutures/anatomy & histology*","Dissection","Facial Pain/etiology","Female","Humans","Male","Nerve Compression Syndromes/etiology","Sphenoid Bone/anatomy & histology*","Zygoma/anatomy & histology*","Zygoma/innervation*"]
["atomical results observed on a small sample of subjects of European origin. The French version of this article is available in the form of electronic supplementary material and can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00276-002-0026-5. MeSH Terms: Arter","yes","y","22: Surg Radiol Anat. 2002 May;24(2):108-12.","Study of the relationship between the suprascapular artery and the brachial","plexus.","PMID: 12197018 [PubMed - indexed for MEDLINE]","MeSH Terms:","Arteries/anatomy & histology","Brachial Plexus/anatomy & histology*","Cadaver","Europe","Female","Humans","Male","Scapula","Shoulder/blood supply*"]
["stocene probably contributed to the isolation of the two taxa described. Aspects of ecology and conservation status are briefly discussed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-002-0320-4. Publica","yes","y","23: Naturwissenschaften. 2002 May;89(5):201-13.","Review of the reticulated python (Python reticulatus Schneider, 1801) with the","description of new subspecies from Indonesia.","PMID: 12135085 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Boidae/anatomy & histology*","Boidae/classification","Indonesia","Phylogeny"]
["sional protrusions enriched in GM1 occur, which may represent a precursor for the formation of micelles budding into the aqueous subphase. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00249-002-0232-4. MeSH Te","yes","y","24: Eur Biophys J. 2002 Jul;31(4):317-22. Epub 2002 Jun 14.","Lateral organization of GM1 in phase-separated monolayers visualized by scanning","force microscopy.","PMID: 12122478 [PubMed - indexed for MEDLINE]","MeSH Terms:","Brain/metabolism","Cholesterol/chemistry*","G(M1) Ganglioside/chemistry*","Lipid Bilayers/chemistry","Lipids/chemistry","Membranes, Artificial","Microscopy, Atomic Force*","Phosphatidylcholines/chemistry*","Sphingomyelins/chemistry*","Substances:","Lipid Bilayers","Lipids","Phosphatidylcholines","Sphingomyelins","G(M1) Ganglioside","Cholesterol","1-palmitoyl-2-oleoylphosphatidylcholine"]
[" Finally, we present results from large-scale simulation of the Rayleigh-Taylor instability and dispersion of colloidal slab in 2D and 3D. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00894-001-0068-3. MeSH Te","yes","y","25: J Mol Model (Online). 2002 Jan;8(1):33-43.","Mesoscopic dynamics of colloids simulated with dissipative particle dynamics and","fluid particle model.","PMID: 12111400 [PubMed - indexed for MEDLINE]","MeSH Terms:","Colloids/chemistry*","Computer Simulation","Crystallization","Hydrophobicity","Micelles","Models, Molecular*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Solvents/chemistry","Substances:","Colloids","Solvents"]
[" (5 min). In validation experiments, both methods gave identical results and the measured sulfhydryls/protein matched the expected values. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00216-002-1347-2. Publica","yes","y","26: Anal Bioanal Chem. 2002 Jul;373(4-5):266-76. Epub 2002 Jun 6.","Quick measurement of protein sulfhydryls with Ellman's reagent and with","4,4'-dithiodipyridine.","PMID: 12110978 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Calibration","Comparative Study","Disulfides","Dithionitrobenzoic Acid","Humans","Muramidase/analysis","Papain/analysis","Proteins/analysis*","Proteins/standards","Pyridines","Reproducibility of Results","Research Support, Non-U.S. Gov't","Sensitivity and Specificity","Serum Albumin, Bovine/analysis","Spectrophotometry, Ultraviolet","Sulfhydryl Compounds/analysis*","Sulfhydryl Compounds/standards","Sulfhydryl Reagents*","Substances:","Disulfides","Proteins","Pyridines","Serum Albumin, Bovine","Sulfhydryl Compounds","Sulfhydryl Reagents","4,4'-dipyridyl disulfide","Dithionitrobenzoic Acid","Muramidase","Papain"]
["t-day paternal lineages within Poland and their distinctiveness from other parts of Europe, at least in respect to their Y-STR haplotypes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00439-002-0728-0. MeSH Te","yes","y","27: Hum Genet. 2002 Jun;110(6):592-600. Epub 2002 May 22.","Homogeneity and distinctiveness of Polish paternal lineages revealed by Y","chromosome microsatellite haplotype analysis.","PMID: 12107446 [PubMed - indexed for MEDLINE]","MeSH Terms:","Alleles","Analysis of Variance","Databases, Nucleic Acid","Europe","Genetics, Population","Haplotypes","Humans","Male","Microsatellite Repeats","Paternity","Poland","Research Support, Non-U.S. Gov't","Y Chromosome/genetics*"]
["ter/coding sequence combinations, as well as to the existence of distinct active-site variants that ultimately influence protein activity. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00438-002-0667-4. MeSH Te","yes","y","28: Mol Genet Genomics. 2002 May;267(3):359-69. Epub 2002 Apr 26.","Combinatorial variation in coding and promoter sequences of genes at the Tri","locus in Pisum sativum accounts for variation in trypsin inhibitor activity in","PMID: 12073038 [PubMed - indexed for MEDLINE]","MeSH Terms:","Genetic Markers","Peas/genetics*","Peas/metabolism","Promoter Regions (Genetics)","Research Support, Non-U.S. Gov't","Seeds/genetics","Seeds/metabolism","Sequence Analysis, DNA","Trypsin/metabolism","Trypsin Inhibitors/genetics*","Trypsin Inhibitors/metabolism","Variation (Genetics)","Substances:","Genetic Markers","Trypsin Inhibitors","Trypsin"]
["terial community as assessed by denaturing gradient gel electrophoresis fingerprinting of PCR amplicons of a portion of the 16S rDNA gene. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-002-0427-1. MeSH Te","yes","y","29: Arch Microbiol. 2002 Jul;178(1):65-70. Epub 2002 Apr 30.","Aciduric Proteobacteria isolated from pH 2.9 soil.","Curtis P, Nakatsu CH, Konopka A.","PMID: 12070771 [PubMed - indexed for MEDLINE]","MeSH Terms:","Culture Media/chemistry","Electrophoresis, Polyacrylamide Gel/methods","Glucose/metabolism","Hydrogen-Ion Concentration","Phylogeny","Proteobacteria/chemistry","Proteobacteria/classification","Proteobacteria/isolation & purification*","Soil Microbiology*","Substrate Specificity","Substances:","Culture Media","Glucose"]
["remendous experimental progress of the past few years is outlined and a number of recent experiments show the current status of the field. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-001-0277-8. PMID: 1","yes","y","30: Naturwissenschaften. 2002 Feb;89(2):47-56.","Bose-Einstein condensation in dilute atomic gases.","Arlt JJ, Bongs K, Sengstock K, Ertmer W.","PMID: 12046620 [PubMed]"]
["cord with the general observation that with increasing temperature, the role of electrostatic interactions in protein stability increases. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-001-0071-8. MeSH Te","yes","y","31: J Mol Model (Online). 2002 Feb;8(2):58-64.","Homology modeling reveals the structural background of the striking difference","in thermal stability between two related [NiFe]hydrogenases.","PMID: 12032599 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acids/analysis","Comparative Study","Electrostatics","Enzyme Stability","Hydrogenase/chemistry*","Models, Molecular*","Protein Subunits","Reproducibility of Results","Research Support, Non-U.S. Gov't","Structural Homology, Protein","Temperature","Thiocapsa roseopersicina/enzymology*","Substances:","Amino Acids","Protein Subunits","nickel-iron hydrogenase","Hydrogenase"]
[" explained by the implementation of several quality assurance procedures in the NICE registry, such as training and automatic data checks. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00134-002-1272-z MeSH Ter","yes","y","32: Intensive Care Med. 2002 May;28(5):656-9. Epub 2002 Apr 13.","Quality of data collected for severity of illness scores in the Dutch National","Intensive Care Evaluation (NICE) registry.","PMID: 12029418 [PubMed - indexed for MEDLINE]","MeSH Terms:","APACHE","Comparative Study","Documentation/standards*","Health Services Research","Humans","Intensive Care Units/standards*","Netherlands","Outcome Assessment (Health Care)","Quality Assurance, Health Care","Registries/standards*","Registries/statistics & numerical data","Severity of Illness Index*","Statistics, Nonparametric"]
["alculated. To visualize the motion of protein domains, movies were generated by similarity ranking of the observed protein configurations. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00249-001-0197-8 MeSH Ter","yes","y","33: Eur Biophys J. 2002 Jun;31(3):172-8. Epub 2002 Jan 29.","Sampling the conformational space of membrane protein surfaces with the AFM.","Scheuring S, Muller DJ, Stahlberg H, Engel HA, Engel A.","PMID: 12029329 [PubMed - indexed for MEDLINE]","MeSH Terms:","Aquaporins/chemistry","Bacteriorhodopsins/chemistry","Escherichia coli Proteins*","Image Enhancement/methods*","Imaging, Three-Dimensional/methods*","Membrane Proteins/chemistry*","Microscopy, Atomic Force/methods*","Motion","Nanotechnology*","Porins/chemistry","Protein Conformation","Research Support, Non-U.S. Gov't","Substances:","Aquaporins","Escherichia coli Proteins","Membrane Proteins","OprF protein, Pseudomonas aeruginosa","Porins","aqpZ protein, E coli","Bacteriorhodopsins"]
["ll the species. This suggests a selective pressure for maintaining the structural and functional configuration of this haplotype in wheat. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s10142-002-0051-9. MeSH Te","yes","y","35: Funct Integr Genomics. 2002 May;2(1-2):40-50. Epub 2002 Apr 9.","Two haplotypes of resistance gene analogs have been conserved during evolution","at the leaf rust resistance locus Lr10in wild and cultivated wheat.","PMID: 12021849 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Blotting, Southern","Chromosomes","Evolution, Molecular","Fungi/pathogenicity*","Haplotypes*","Models, Genetic","Molecular Sequence Data","Phylogeny","Plant Diseases","Selection (Genetics)","Sequence Alignment","Sequence Analysis, DNA","Triticum/genetics","Triticum/microbiology*"]
[". Genes of unknown function may by assigned a hypothetical role based on their patterns of expression resembling well characterized genes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s10142-002-0046-6. MeSH Te","yes","y","36: Funct Integr Genomics. 2002 May;2(1-2):13-27. Epub 2002 Feb 19.","DNA array profiling of gene expression changes during maize embryo development.","Lee JM, Williams ME, Tingey SV, Rafalski JA.","PMID: 12021847 [PubMed - indexed for MEDLINE]","MeSH Terms:","Blotting, Northern","Carbocyanines","Citric Acid Cycle/genetics","DNA Probes","DNA, Complementary","Expressed Sequence Tags","Fatty Acids/biosynthesis","Fatty Acids/metabolism","Gene Expression Profiling*","Gene Expression Regulation, Plant","Gene Frequency","Gene Library","Glycolysis/genetics","Oligonucleotide Array Sequence Analysis*","Plant Leaves/genetics","Plant Roots/genetics","Zea mays/embryology*","Zea mays/genetics","Substances:","Carbocyanines","DNA Probes","DNA, Complementary","Fatty Acids","cyanine dye 3","cyanine dye 5"]
["ll correspond to the ancestral function of these genes. The results are discussed in the light of the evolutionary origin of the mesoderm. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00427-002-0228-1. MeSH Te","yes","y","37: Dev Genes Evol. 2002 May;212(4):186-95. Epub 2002 Apr 18.","Characterisation of two snail genes in the gastropod mollusc Patella vulgata.","Implications for understanding the ancestral function of the snail-related genes","PMID: 12012233 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Animals","Cell Differentiation/genetics","DNA-Binding Proteins/genetics*","Evolution*","Likelihood Functions","Molecular Sequence Data","Multigene Family","Neurons/metabolism","Organ Specificity","Phylogeny","Research Support, Non-U.S. Gov't","Sequence Alignment","Sequence Analysis, Protein","Snails/embryology","Snails/genetics*","Transcription Factors/genetics*","Substances:","DNA-Binding Proteins","Transcription Factors","snail family transcription factors"]
["capability and further suggest that by the Early Cretaceous ecological diversification of early birds was greater than previously assumed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-001-0276-9. MeSH Te","yes","y","38: Naturwissenschaften. 2002 Jan;89(1):34-8.","Largest bird from the Early Cretaceous and its implications for the earliest","avian ecological diversification.","PMID: 12008971 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Birds/anatomy & histology*","Birds/classification*","China","Ecosystem","Paleontology","Phylogeny","Research Support, Non-U.S. Gov't"]
["d in muscle lineages in the ecdysozoan representatives Caenorhabditis elegans or Drosophila; the C. elegansgenome has lost Mox altogether. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00427-002-0223-6. MeSH Te","yes","y","39: Dev Genes Evol. 2002 Apr;212(3):141-4. Epub 2002 Mar 13.","Mox homeobox expression in muscle lineage of the gastropod Haliotis asinina:","evidence for a conserved role in bilaterian myogenesis.","PMID: 11976952 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cell Lineage","Gene Expression Regulation, Developmental*","Homeodomain Proteins/genetics*","In Situ Hybridization","Mollusca/embryology*","Mollusca/genetics*","Muscles/embryology*","Muscles/metabolism*","Phylogeny","RNA, Messenger/genetics","RNA, Messenger/metabolism","Research Support, Non-U.S. Gov't","Substances:","Homeodomain Proteins","RNA, Messenger"]
["l F-box proteins. We conclude that patterning of ppa mRNA could reflect a constraint on ppa function that is not common among F-box genes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00427-002-0222-7. MeSH Te","yes","y","40: Dev Genes Evol. 2002 Apr;212(3):134-40. Epub 2002 Mar 7.","A conserved F-box gene with unusual transcript localization.","Das T, Purkayastha-Mukherjee C, D'Angelo J, Weir M.","PMID: 11976951 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Animals","Carrier Proteins/chemistry*","Carrier Proteins/genetics*","Carrier Proteins/metabolism","Conserved Sequence","Drosophila/genetics*","Drosophila/growth & development","Drosophila Proteins/chemistry","Drosophila Proteins/genetics","Drosophila Proteins/metabolism","Evolution, Molecular","Gene Expression Regulation, Developmental","Humans","Protein Binding","RNA Transport*","RNA, Messenger/genetics","RNA, Messenger/metabolism*","Research Support, Non-U.S. Gov't","Sequence Homology, Amino Acid","Zebrafish/genetics","Zebrafish/growth & development","Zebrafish Proteins/genetics","Zebrafish Proteins/metabolism","Substances:","Carrier Proteins","Drosophila Proteins","RNA, Messenger","Zebrafish Proteins","partner of paired protein, Drosophila"]
["n-containing protrusions and thereby cell adhesive and migratory behaviour could have potential for therapeutic intervention in these conditions. The supplementary material referred to in this section can be found at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/2002/v24.350.html Copyri","yes","y","41: Bioessays. 2002 Apr;24(4):350-61.","Fascins, and their roles in cell structure and function.","Kureishy N, Sapountzi V, Prag S, Anilkumar N, Adams JC.","PMID: 11948621 [PubMed - indexed for MEDLINE]","MeSH Terms:","Actins/physiology*","Animals","Carrier Proteins/chemistry","Carrier Proteins/genetics","Carrier Proteins/physiology*","Cell Adhesion","Cell Movement","Cell Physiology*","Cells/cytology*","Drosophila melanogaster/physiology","Gene Expression Regulation","Humans","Microfilament Proteins/chemistry","Microfilament Proteins/genetics","Microfilament Proteins/physiology*","Models, Molecular","Protein Conformation","Research Support, Non-U.S. Gov't","Substances:","Actins","Carrier Proteins","Microfilament Proteins","fascin"]
["ffinity is reduced only 10-fold. The mechanism of Bi(III)-responsive metalloregulation is discussed, based on the findings presented here. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0336-9. MeSH Te","yes","y","42: J Biol Inorg Chem. 2002 Apr;7(4-5):551-9. Epub 2002 Feb 8.","Characterization of a metalloregulatory bismuth(III) site in Staphylococcus","aureus pI258 CadC repressor.","PMID: 11941514 [PubMed - indexed for MEDLINE]","MeSH Terms:","Bacterial Proteins/chemistry*","Bacterial Proteins/genetics","Bacterial Proteins/metabolism*","Binding Sites","Bismuth/chemistry","Bismuth/metabolism*","Cysteine/genetics","Dimerization","Fluorescence","Gene Expression Regulation, Bacterial","Glycine/genetics","Models, Molecular","Operon","Point Mutation","Promoter Regions (Genetics)","Protein Conformation","Repressor Proteins/chemistry*","Repressor Proteins/metabolism*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Spectrophotometry/methods","Staphylococcus aureus/chemistry*","Substances:","Bacterial Proteins","CadC protein, Bacteria","Repressor Proteins","Cysteine","Glycine","Bismuth","Grant Support:","GM42569/GM/NIGMS"]
["at under physiological condition there is the availability of LIP for catalyzing Fenton-type reactions in close proximity to cellular DNA. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0335-x. MeSH Te","yes","y","43: J Biol Inorg Chem. 2002 Apr;7(4-5):548-50. Epub 2002 Jan 30.","The level of 8-oxo-7,8-dihydro-2'-deoxyguanosine is positively correlated with","the size of the labile iron pool in human lymphocytes.","PMID: 11941513 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Aged","Aged, 80 and over","Ascorbic Acid/blood","Deoxyguanosine/analogs & derivatives","Deoxyguanosine/blood*","Female","Humans","Iron/blood*","Lymphocytes/metabolism*","Male","Middle Aged","Research Support, Non-U.S. Gov't","Substances:","Ascorbic Acid","Iron","8-oxo-7-hydrodeoxyguanosine","Deoxyguanosine"]
["discussed and a comprehensive study of the electronic structure of ligand-cytochrome c complexes and the native protein is also described. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0334-y. MeSH Te","yes","y","44: J Biol Inorg Chem. 2002 Apr;7(4-5):539-47. Epub 2002 Jan 31.","Solution structure of cyanoferricytochrome c: ligand-controlled conformational","flexibility and electronic structure of the heme moiety.","PMID: 11941512 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Comparative Study","Cytochrome c Group/chemistry*","Cytochrome c Group/metabolism","Cytochromes c*","Electrons","Heme/chemistry","Ligands","Magnetic Resonance Spectroscopy","Magnetics","Molecular Sequence Data","Protein Conformation","Research Support, Non-U.S. Gov't","Solutions","Substances:","Cytochrome c Group","Ligands","Solutions","cyanoferricytochrome C","Heme","Cytochromes c"]
["d structure of the catalytic subunit of a carbon monoxide dehydrogenase from Carboxydothermus hydrogenoformans and related dehydrogenases. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0326-y. MeSH Te","yes","y","46: J Biol Inorg Chem. 2002 Apr;7(4-5):514-25. Epub 2002 Jan 23.","Hybrid cluster proteins (HCPs) from Desulfovibrio desulfuricans ATCC 27774 and","Desulfovibrio vulgaris (Hildenborough): X-ray structures at 1.25 A resolution","PMID: 11941509 [PubMed - indexed for MEDLINE]","MeSH Terms:","Aldehyde Oxidoreductases/chemistry","Amino Acid Sequence","Bacterial Proteins/chemistry*","Bacterial Proteins/isolation & purification","Comparative Study","Crystallography, X-Ray","Desulfovibrio/chemistry*","Desulfovibrio vulgaris/chemistry","Electron Spin Resonance Spectroscopy","Iron-Sulfur Proteins/chemistry*","Iron-Sulfur Proteins/isolation & purification","Models, Molecular","Molecular Sequence Data","Multienzyme Complexes/chemistry","Protein Conformation","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Sequence Homology, Amino Acid","Synchrotrons","Substances:","Bacterial Proteins","Iron-Sulfur Proteins","Multienzyme Complexes","prismane protein, Desulfovibrio vulgaris","Aldehyde Oxidoreductases","carbon monoxide dehydrogenase","Secondary Source ID:","PDB/1GN9","PDB/1GNL","PDB/1GNT","Grant Support:","GM5600/GM/NIGMS"]
[" the nickel oxidation states in MCR-ox1, MCR-ox2 and MCR-ox3 and to a possible presence of a second redox active group in the active site. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00775-001-0325-z. MeSH Te","yes","y","47: J Biol Inorg Chem. 2002 Apr;7(4-5):500-13. Epub 2002 Feb 14.","The nickel enzyme methyl-coenzyme M reductase from methanogenic archaea: In","vitro induction of the nickel-based MCR-ox EPR signals from MCR-red2.","PMID: 11941508 [PubMed - indexed for MEDLINE]","MeSH Terms:","Chloroform/chemistry","Citric Acid/chemistry","Electron Spin Resonance Spectroscopy","Euryarchaeota/enzymology*","Hydrogen-Ion Concentration","Light","Metalloporphyrins/chemistry","Nickel","Oxidation-Reduction","Oxidoreductases/chemistry*","Oxidoreductases/metabolism*","Oxygen/chemistry","Phosphothreonine/analogs & derivatives","Phosphothreonine/chemistry","Research Support, Non-U.S. Gov't","Spectrophotometry, Ultraviolet","Sulfides/chemistry","Sulfites/chemistry","Substances:","Metalloporphyrins","Sulfides","Sulfites","titanium citrate","7-mercaptoheptanoylthreonine phosphate","Phosphothreonine","Chloroform","factor F430","Nickel","Citric Acid","Oxygen","polysulfide","Oxidoreductases","methyl coenzyme M reductase"]
["are highly relevant for unraveling the stepwise assembly process of the stromal PsaC, PsaD and PsaE subunits to the PS I core heterodimer. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0321-3. MeSH Te","yes","y","48: J Biol Inorg Chem. 2002 Apr;7(4-5):461-72. Epub 2002 Jan 11.","Solution structure of the unbound, oxidized Photosystem I subunit PsaC,","containing [4Fe-4S] clusters F(A) and F(B): a conformational change occurs upon","PMID: 11941504 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Iron-Sulfur Proteins/chemistry*","Iron-Sulfur Proteins/metabolism","Magnetic Resonance Spectroscopy","Membrane Proteins*","Models, Molecular","Molecular Sequence Data","Oxidation-Reduction","Photosynthetic Reaction Center Complex Proteins/chemistry*","Photosynthetic Reaction Center Complex Proteins/metabolism*","Photosystem I Protein Complex*","Protein Conformation","Protein Subunits","Proteins/chemistry*","Proteins/metabolism*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Substances:","Iron-Sulfur Proteins","Membrane Proteins","Photosynthetic Reaction Center Complex Proteins","Photosystem I Protein Complex","Protein Subunits","Proteins","photosystem I, psaB subunit","Secondary Source ID:","PDB/1K0T"]
["ied. These results suggest that de novo designed peptides may serve as scaffolds for the construction of native bridged sites in proteins. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0320-4. MeSH Te","yes","y","49: J Biol Inorg Chem. 2002 Apr;7(4-5):451-60. Epub 2002 Jan 8.","Stability and nickel binding properties of peptides designed as scaffolds for","the stabilization of Ni(II)-Fe(4)S(4) bridged assemblies.","PMID: 11941503 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Binding Sites","Cysteine/chemistry","Dimerization","Helix-Loop-Helix Motifs","Iron-Sulfur Proteins/chemistry","Iron-Sulfur Proteins/metabolism","Metalloproteins/chemistry","Metalloproteins/metabolism","Models, Chemical","Molecular Sequence Data","Nickel/metabolism*","Peptides/chemistry*","Peptides/metabolism*","Protein Folding","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Substances:","Iron-Sulfur Proteins","Metalloproteins","Peptides","Cysteine","Nickel","Grant Support:","GM28856/GM/NIGMS"]
["[VO(naph-tris)](2)] [where naph-tris is the Schiff base formed between o-hydroxynaphthaldehyde and tris(hydroxymethyl)amine] are reported. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0311-5. MeSH Te","yes","y","50: J Biol Inorg Chem. 2002 Apr;7(4-5):384-96. Epub 2001 Dec 19.","Erratum in:","J Biol Inorg Chem 2002 Jun;7(6):675.","PMID: 11941496 [PubMed - indexed for MEDLINE]","MeSH Terms:","3T3 Cells","Animals","Cells, Cultured","Fibroblasts","Glucose/pharmacokinetics","Humans","Insulin/pharmacology*","Mice","Molecular Mimicry","Reproducibility of Results","Research Support, Non-U.S. Gov't","Toxicity Tests","Vanadium Compounds/chemical synthesis","Vanadium Compounds/chemistry*","Vanadium Compounds/pharmacology*","Substances:","Vanadium Compounds","Insulin","Glucose"]
["tative performance with semi-quantitative results in the concentration predictions of both the standard mixture and the real-world sample. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00216-001-1125-6. PMID: 1","yes","y","51: Anal Bioanal Chem. 2002 Jan;372(1):205-15. Epub 2001 Dec 12.","A laser-induced fluorescence dual-fiber optic array detector applied to the","rapid HPLC separation of polycyclic aromatic hydrocarbons.","PMID: 11939196 [PubMed]"]
["meotic genes has been completely overlooked until recently and awaits further evaluation of its developmental and evolutionary importance. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00438-001-0615-8. MeSH Te","yes","y","52: Mol Genet Genomics. 2002 Feb;266(6):942-50. Epub 2001 Dec 15.","A novel MADS-box gene subfamily with a sister-group relationship to class B","floral homeotic genes.","PMID: 11862488 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Angiosperms/classification","Angiosperms/genetics*","Arabidopsis/genetics","Cloning, Molecular","DNA, Complementary/chemistry","DNA, Complementary/genetics","Gene Expression Regulation, Plant","Genes, Plant/genetics*","In Situ Hybridization","MADS Domain Proteins/genetics*","Molecular Sequence Data","Phylogeny","Research Support, Non-U.S. Gov't","Sequence Alignment","Sequence Analysis, DNA","Sequence Homology, Amino Acid","Zea mays/genetics","Substances:","DNA, Complementary","MADS Domain Proteins","Secondary Source ID:","GENBANK/AJ271208","GENBANK/AJ307056","GENBANK/AJ318098"]
["tween amoC and amoA is variable in length and may be used to profile the community of ammonia-oxidizing bacteria in environmental samples. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-001-0369-z. MeSH Te","yes","y","53: Arch Microbiol. 2002 Feb;177(2):139-49. Epub 2001 Dec 6.","Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing","bacteria.","PMID: 11807563 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Ammonia/metabolism*","Betaproteobacteria/classification","Betaproteobacteria/enzymology","Betaproteobacteria/genetics*","Chromatiaceae/classification","Chromatiaceae/enzymology","Chromatiaceae/genetics","Comparative Study","Environmental Microbiology","Gammaproteobacteria/classification","Gammaproteobacteria/enzymology","Gammaproteobacteria/genetics*","Gene Dosage","Molecular Sequence Data","Nitrosomonas/classification","Nitrosomonas/enzymology","Nitrosomonas/genetics","Operon","Oxidoreductases/genetics*","Protein Structure, Secondary","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Sequence Homology, Amino Acid","Variation (Genetics)","Substances:","Ammonia","Oxidoreductases","ammonia monooxygenase"]
["ransformation and strengthens the role of Src in the development and progression of human colon cancer. Supportive Supplemental Data can be viewed at http://pga.tigr.org/PGApubs.shtml. MeSH Terms: Animals Cell Line, Transformed Cell Transformation, Neoplastic* Cluster Analysis Colonic Neoplasms/gene","yes","n","1: Oncogene. 2002 Oct 17;21(47):7256-65.","Identification of Src transformation fingerprint in human colon cancer.","Malek RL, Irby RB, Guo QM, Lee K, Wong S, He M, Tsai J, Frank B, Liu ET,","PMID: 12370817 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cell Line, Transformed","Cell Transformation, Neoplastic*","Cluster Analysis","Colonic Neoplasms/genetics*","Gene Expression Profiling","Gene Expression Regulation, Neoplastic","Genes, src*","Humans","Pyridones/pharmacology","Pyrimidines/pharmacology","Rats","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Reverse Transcriptase Polymerase Chain Reaction","Up-Regulation","Substances:","PD 180970","Pyridones","Pyrimidines","Grant Support:","6120-119-L0-A/PHS","CA77049-02/CA/NCI","CA85052-A1/CA/NCI","CA85429-01/CA/NCI","HL59781/HL/NHLBI"]

{"sheet":"2003","index":7,"n_rows":87,"n_cols":33,"rows_kept":87,"flags":["formulas_cached_only"]}
["Reference","Live?","Journal?"]
["ty. AVAILABILITY: Academic users should send their request for the perl program for calculating likelihood probabilities at jack.cao@astrazeneca.com. SUPPLEMENTARY INFORMATION: The materials can be viewed at http://www.astrazeneca-montreal.com/AZRDM_info/supporting_info.pdf. Publication Types: Evalu","No","n","64: Bioinformatics. 2003 Jan 22;19(2):234-40.","A naive Bayes model to predict coupling between seven transmembrane domain","receptors and G-proteins.","PMID: 12538244 [PubMed - indexed for MEDLINE]"]
["mber of classes in data (cancerous and normal). AVAILABILITY: JAVA software of dynamic SOM tree algorithm is available upon request for academic use. SUPPLEMENTARY INFORMATION: A comparison of rectangular and hexagonal topologies for GSOM is available from http://www.mame.mu.oz.au/mechatronics/journ","no","n","18: Bioinformatics. 2003 Nov 1;19(16):2131-40.","An unsupervised hierarchical dynamic self-organizing approach to cancer class","discovery and marker gene identification in microarray data.","PMID: 14594719 [PubMed - indexed for MEDLINE]"]
["ss data. Their capability of predicting protein functions generally falls between that of the Y2H data and that of the MIPS protein complex data. The supplementary information is available at the following Web site: http://www-hto.usc.edu/-msms/AssessInteraction/. PMID: 12603024 [PubMed - indexed fo","no","n","55: Pac Symp Biocomput. 2003;:140-51.","Assessment of the reliability of protein-protein interactions and protein","function prediction.","PMID: 12603024 [PubMed - indexed for MEDLINE]"]
["omparable classification accuracy shown in the applications and its flexibility render the MSVM a viable alternative to other classification methods. SUPPLEMENTARY INFORMATION: http://www.stat.ohio-state.edu/~yklee/msvm.htm Publication Types: Evaluation Studies Validation Studies PMID: 12801874 [Pub","no","n","44: Bioinformatics. 2003 Jun 12;19(9):1132-9.","Classification of multiple cancer types by multicategory support vector machines","using gene expression data.","PMID: 12801874 [PubMed - indexed for MEDLINE]"]
[" ones to functionally annotate novel protein sequences from genomic projects. AVAILABILITY: MASIA WEB site: http://www.scsb.utmb.edu/masia/masia.html SUPPLEMENTARY INFORMATION: The dendrogram of 42 APE sequences used to derive motifs is available on http://www.scsb.utmb.edu/comp_biol.html/DNA_repair","No","n","37: Bioinformatics. 2003 Jul 22;19(11):1381-90.","Identifying property based sequence motifs in protein families and","superfamilies: application to DNase-1 related endonucleases.","PMID: 12874050 [PubMed - indexed for MEDLINE]"]
["ation is available at http://www.pathogenomics.sfu.ca/islandpath and the source code is freely available, under GNU public licence, from the authors. SUPPLEMENTARY INFORMATION: An online help file, which includes analyses of the utility of IslandPath, can be found at http://www.pathogenomics.sfu.ca/","no","n","57: Bioinformatics. 2003 Feb 12;19(3):418-20.","IslandPath: aiding detection of genomic islands in prokaryotes.","Hsiao W, Wan I, Jones SJ, Brinkman FS.","PMID: 12584130 [PubMed - indexed for MEDLINE]"]
["ures estimation, statistical significance test and extent prediction. AVAILABILITY: The software is available at: http://www.chgb.org.cn/lda/lda.htm. SUPPLEMENTARY INFORMATION: Detailed tutorials, LDA help system and examples are distributed within LDA software. For Macintosh OS X user, the Jre vers","NO","n","15: Bioinformatics. 2003 Nov 1;19(16):2147-8.","LDA--a java-based linkage disequilibrium analyzer.","Ding K, Zhou K, He F, Shen Y.","PMID: 14594722 [PubMed - indexed for MEDLINE]"]
["interactions among gene products. Further, it integrates the capability of conducting both deterministic and stochastic simulations. AVAILABILITY AND SUPPLEMENTARY INFORMATION: Dynetica 1.0, example models, and the user's guide are available at http://www.its.caltech.edu/~you/Dynetica/Dynetica_page.","no","n","56: Bioinformatics. 2003 Feb 12;19(3):435-6.","Modeling biological systems using Dynetica--a simulator of dynamic networks.","You L, Hoonlor A, Yin J.","PMID: 12584138 [PubMed - indexed for MEDLINE]"]
["dy subjects. AVAILABILITY: Information on obtaining the executable code, example data, example analysis, and documentation is available upon request. SUPPLEMENTARY INFORMATION: All supplementary information can be found at http://phg.mc.vanderbilt.edu/Software/MDR. PMID: 12584123 [PubMed - indexed f","no","n","59: Bioinformatics. 2003 Feb 12;19(3):376-82.","Multifactor dimensionality reduction software for detecting gene-gene and","gene-environment interactions.","PMID: 12584123 [PubMed - indexed for MEDLINE]"]
["ces (MIPS, mips.gsf.de). We show that our approach outperforms other available methods for function prediction based on protein interaction data. The supplementary data is available at www-hto.usc.edu/~msms/ProteinFunction. PMID: 14980019 [PubMed - indexed for MEDLINE]","no","n","1: J Comput Biol. 2003;10(6):947-60.","Prediction of protein function using protein-protein interaction data.","Deng M, Zhang K, Mehta S, Chen T, Sun F.","PMID: 14980019 [PubMed - indexed for MEDLINE]"]
["2). The option to directly submit probe sequences to the probe match tool of the Ribosomal Database Project II (RDP-II) further allows one to extract supplementary information on probe specificities. The two main features of probeBase, 'search probeBase' and 'find probe set', help researchers to fin","no","n","66: Nucleic Acids Res. 2003 Jan 1;31(1):514-6.","probeBase: an online resource for rRNA-targeted oligonucleotide probes.","Loy A, Horn M, Wagner M.","PMID: 12520066 [PubMed - indexed for MEDLINE]"]
["s available at http://www.imtech.res.in/raghava/propred1/. Mirror site of this server is available at http://bioinformatics.uams.edu/mirror/propred1/ Supplementary information: Matrices and document on server are available at http://www.imtech.res.in/raghava/propred1/page2.html Publication Types: Ev","No","n","50: Bioinformatics. 2003 May 22;19(8):1009-14.","ProPred1: prediction of promiscuous MHC Class-I binding sites.","Singh H, Raghava GP.","PMID: 12761064 [PubMed - indexed for MEDLINE]"]
["clear receptor proteins, which took 11 min on a DEC Alpha 6100 computer Availability: RASCAL is available at ftp://ftp-igbmc.u-strasbg.fr/pub/RASCAL. SUPPLEMENTARY INFORMATION: http://bioinfo-igbmc.u-strasbourg.fr/BioInfo/RASCAL/paper/rascal_supp.html Publication Types: Evaluation Studies Validation","No","n","42: Bioinformatics. 2003 Jun 12;19(9):1155-61.","RASCAL: rapid scanning and correction of multiple sequence alignments.","Thompson JD, Thierry JC, Poch O.","PMID: 12801878 [PubMed - indexed for MEDLINE]"]
["names or the correct closest spelling for a query compound name, if it exists. AVAILABILITY: Web-based interface available at http://ibb.uab.es/snow/ SUPPLEMENTARY INFORMATION: http://ibb.uab.es/snow/snow_moreinfo.html Publication Types: Evaluation Studies Validation Studies PMID: 14668242 [PubMed -","no","n","4: Bioinformatics. 2003 Dec 12;19(18):2492-3.","SNOW: standard nomenclature wizard to help searching for (bio) chemical","standardized names.","PMID: 14668242 [PubMed - indexed for MEDLINE]"]
[" disease phenotype due to the expansion potential of repeats present in them. The list of genes and other details of analysis are given in the online supplementary data (http://www.ingenovis.com/tripletrepeats). PMID: 12651711 [PubMed - indexed for MEDLINE]","no","n","53: Bioinformatics. 2003 Mar 22;19(5):549-52.","Triplet repeats in human genome: distribution and their association with genes","and other genomic regions.","PMID: 12651711 [PubMed - indexed for MEDLINE]"]
["this information novel biological hypotheses may be addressed. AVAILABILITY: Venn Mapper is freely available on http://www.erasmusmc.nl/gatcplatform. SUPPLEMENTARY INFORMATION: http://www.erasmusmc.nl/gatcplatform/vennmapper.html. Publication Types: Evaluation Studies Validation Studies PMID: 145947","no","n","20: Bioinformatics. 2003 Nov 1;19(16):2065-71.","Venn Mapping: clustering of heterologous microarray data based on the number of","co-occurring differentially expressed genes.","PMID: 14594711 [PubMed - indexed for MEDLINE]"]
["rotocols. AVAILABILITY: The 3D-Jury system is available via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/) to the academic community. SUPPLEMENTARY INFORMATION: 3D-Jury is coupled to the continuous online server evaluation program, LiveBench (http://BioInfo.PL/LiveBench/) Publication","yes","n","49: Bioinformatics. 2003 May 22;19(8):1015-8.","3D-Jury: a simple approach to improve protein structure predictions.","Ginalski K, Elofsson A, Fischer D, Rychlewski L.","PMID: 12761065 [PubMed - indexed for MEDLINE]"]
["plete data normalization methods is available as part of the R package Affy, which is a part of the Bioconductor project http://www.bioconductor.org. SUPPLEMENTARY INFORMATION: Additional figures may be found at http://www.stat.berkeley.edu/~bolstad/normalize/index.html Publication Types: Evaluation","yes","n","65: Bioinformatics. 2003 Jan 22;19(2):185-93.","A comparison of normalization methods for high density oligonucleotide array","data based on variance and bias.","PMID: 12538238 [PubMed - indexed for MEDLINE]"]
["intensity, background noise, and bleeding. We conclude that Bayesian networks are a reliable and useful model for microarray spot quality assessment. SUPPLEMENTARY INFORMATION: http://sigwww.cs.tut.fi/TICSP/SpotQuality/. Publication Types: Evaluation Studies Validation Studies PMID: 14594707 [PubMed","yes","n","21: Bioinformatics. 2003 Nov 1;19(16):2031-8.","A novel strategy for microarray quality control using Bayesian networks.","Hautaniemi S, Edgren H, Vesanen P, Wolf M, Jarvinen AK, Yli-Harja O, Astola J,","PMID: 14594707 [PubMed - indexed for MEDLINE]"]
["he rate of false positives. AVAILABILITY: This method is incorporated into BRB-ArrayTools version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). SUPPLEMENTARY MATERIAL: ftp://linus.nci.nih.gov/pub/techreport/RVM_supplement.pdf Publication Types: Evaluation Studies Validation Studies MeSH Terms:","yes","n","1: Bioinformatics. 2003 Dec 12;19(18):2448-55.","A random variance model for detection of differential gene expression in small","microarray experiments.","PMID: 14668230 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Analysis of Variance","Comparative Study","False Positive Reactions","Gene Expression Profiling/methods*","Models, Genetic*","Models, Statistical*","Oligonucleotide Array Sequence Analysis/methods*","Reproducibility of Results","Sample Size","Sensitivity and Specificity","Sequence Analysis, DNA/methods*","Variation (Genetics)"]
["th the literature. AVAILABILITY: The implementation of this algorithm is available at the site http://guppy.mpe.nus.edu.sg/~mpessk/SparseLOGREG.shtml Supplementary Information: Supplementary material is available at the site http://guppy.mpe.nus.edu.sg/~mpessk/SparseLOGREG.shtml Publication Types: E","yes","n","14: Bioinformatics. 2003 Nov 22;19(17):2246-53.","A simple and efficient algorithm for gene selection using sparse logistic","regression.","PMID: 14630653 [PubMed - indexed for MEDLINE]"]
["sults. The programs are designed primarily for Arabidopsis thaliana researchers, but can be adapted readily for other model systems. Availability and Supplementary information: http://www.personal.psu.edu/nhs109/Programs/ PMID: 14512358 [PubMed - indexed for MEDLINE]","yes","n","31: Bioinformatics. 2003 Sep 22;19(14):1846-8.","A tool-kit for cDNA microarray and promoter analysis.","Shah NH, King DC, Shah PN, Fedoroff NV.","PMID: 14512358 [PubMed - indexed for MEDLINE]"]
["publicly available data of TIGR (The Institute for Genomic Research). 1744 distinct RGAs were identified, 597 of which belonged to the NBS-LRR class. Supplementary data (sequences and annotations) is available on the web site http:/gkoczyk.bioinfo.pl/CMBL. PMID: 14668919 [PubMed - indexed for MEDLIN","yes","n","2: Cell Mol Biol Lett. 2003;8(4):963-72.","An assessment of the resistance gene analogues of Oryza sativa ssp. japonica:","their presence and structure.","PMID: 14668919 [PubMed - indexed for MEDLINE]"]
["reely available from http://www.bio.vu.nl/microb/research/tumor.html provided one adheres to the end-user license agreement in the associated manual. SUPPLEMENTARY INFORMATION: Above website also supplies the in- and output files used in the example run. PMID: 14555635 [PubMed - indexed for MEDLINE]","yes","n","23: Bioinformatics. 2003 Oct 12;19(15):2000-1.","Analysing gene expressions with GRANK.","de Boer WP, Oudejans JJ, Meijer CJ, Lankelma J.","PMID: 14555635 [PubMed - indexed for MEDLINE]"]
[" can be trained on relatively small data sets to provide prediction more accurate than those based on previously published methods or on MHC binding. SUPPLEMENTARY INFORMATION: Data for 203 synthesized peptides is available at http://linus.nci.nih.gov/Data/LAU203_Peptide.pdf Publication Types: Evalu","yes","n","24: Bioinformatics. 2003 Oct 12;19(15):1978-84.","Application of support vector machines for T-cell epitopes prediction.","Zhao Y, Pinilla C, Valmori D, Martin R, Simon R.","PMID: 14555632 [PubMed - indexed for MEDLINE]"]
["on of signals) we have shown that the novel system for comparative analysis of the properties of information-bearing biomolecules works as in theory. SUPPLEMENTARY INFORMATION: http://genome.gbf.de/wavepaper. Publication Types: Evaluation Studies Validation Studies PMID: 14594705 [PubMed - indexed f","yes","n","22: Bioinformatics. 2003 Nov 1;19(16):2016-21.","Applying signal theory to the analysis of biomolecules.","Kauer G, Blocker H.","PMID: 14594705 [PubMed - indexed for MEDLINE]"]
["ion of the analysed experimental data to the databases. AVAILABILITY: ARIA 1.2 is available from: http://www.pasteur.fr/recherche/unites/Binfs/aria/. SUPPLEMENTARY INFORMATION: XML DTDs (for chemical shifts and NOE crosspeaks), Python scripts for the conversion of various NMR data formats and the re","yes","n","60: Bioinformatics. 2003 Jan 22;19(2):315-6.","ARIA: automated NOE assignment and NMR structure calculation.","Linge JP, Habeck M, Rieping W, Nilges M.","PMID: 12538267 [PubMed - indexed for MEDLINE]"]
["(or 1 760 000 grid points total) was about 10 s. AVAILABILITY: The test implementation of the algorithm will be available upon request for academics. Supplementary information: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf Publication Types: Evaluation Studies Validation Studies PMID: 1451","yes","n","33: Bioinformatics. 2003 Sep 22;19(14):1824-31.","Automatic registration of microarray images. I. Rectangular grid.","Galinsky VL.","PMID: 14512354 [PubMed - indexed for MEDLINE]"]
["s less than a second. For images with high expression rates ( approximately 90%) the registration time is even smaller, around a quarter of a second. Supplementary information: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf PMID: 14512355 [PubMed - indexed for MEDLINE]","yes","n","32: Bioinformatics. 2003 Sep 22;19(14):1832-6.","Automatic registration of microarray images. II. Hexagonal grid.","Galinsky VL.","PMID: 14512355 [PubMed - indexed for MEDLINE]"]
["d background model alleviates the drawbacks of MAP (maximum a posteriori log likelihood) scores. AVAILABILITY: Available on request from the authors. SUPPLEMENTARY INFORMATION: Data and the results presented in this paper are available on the web at http://compbio.ornl.gov/mira/index.html Publicatio","yes","n","25: Bioinformatics. 2003 Oct 12;19(15):1952-63.","Background rareness-based iterative multiple sequence alignment algorithm for","regulatory element detection.","PMID: 14555629 [PubMed - indexed for MEDLINE]"]
[" by-product of bagged clustering are the cluster votes which can be used to assess the confidence of cluster assignments for individual observations. SUPPLEMENTARY INFORMATION: For supplementary information on datasets, analyses, and software, consult http://www.stat.berkeley.edu/~sandrine and http:","yes","n","46: Bioinformatics. 2003 Jun 12;19(9):1090-9.","Bagging to improve the accuracy of a clustering procedure.","Dudoit S, Fridlyand J.","PMID: 12801869 [PubMed - indexed for MEDLINE]"]
[" each of the K queries, but BLAST++ completes the processing in a much shorter time. AVAILABILITY: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++ Supplementary information: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++ Publication Types: Evaluation Studies Validation Studies PMID: 14630666 ","yes","n","12: Bioinformatics. 2003 Nov 22;19(17):2323-4.","BLAST++: BLASTing queries in batches.","Wang H, Ooi BC, Tan KL, Ong TH, Zhou L.","PMID: 14630666 [PubMed - indexed for MEDLINE]"]
["lary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. SUPPLEMENTARY INFORMATION: http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide","yes","n","10: Bioinformatics. 2003 Dec 12;19(18):2404-12.","caCORE: a common infrastructure for cancer informatics.","Covitz PA, Hartel F, Schaefer C, De Coronado S, Fragoso G, Sahni H, Gustafson S,","PMID: 14668224 [PubMed - indexed for MEDLINE]"]
["equences for over 70% of the predicted genes in the Arabidopsis thaliana genome as well as primer sequences for GST amplification and a wide range of supplementary information. All CATMA GST sequences are specific to the gene for which they were designed, and all gene models were predicted from a co","yes","n","67: Nucleic Acids Res. 2003 Jan 1;31(1):156-8.","CATMA: a complete Arabidopsis GST database.","Crowe ML, Serizet C, Thareau V, Aubourg S, Rouze P, Hilson P, Beynon J, Weisbeek","PMID: 12519971 [PubMed - indexed for MEDLINE]"]
["1 and samples of input data sets on Windows PC are available at http://www.clab.kwansei.ac.jp/mining/discas/discas.html upon request from the author. SUPPLEMENTARY INFORMATION: Summary of prediction results and cross validations is accessible via http://www.clab.kwansei.ac.jp/~okada/BIJ/BIJsupple.ht","yes","n","40: Bioinformatics. 2003 Jul 1;19(10):1208-15.","Characteristic substructures and properties in chemical carcinogens studied by","the cascade model.","PMID: 12835263 [PubMed - indexed for MEDLINE]"]
["or high-throughput characterization of functional regions in proteins. AVAILABILITY: The ConSurf web server is available at:http://consurf.tau.ac.il. SUPPLEMENTARY INFORMATION: A set of examples is available at http://consurf.tau.ac.il under 'GALLERY'. PMID: 12499312 [PubMed - indexed for MEDLINE]","yes","n","68: Bioinformatics. 2003 Jan;19(1):163-4.","ConSurf: identification of functional regions in proteins by surface-mapping of","phylogenetic information.","PMID: 12499312 [PubMed - indexed for MEDLINE]"]
["d breast cancer, that we are able to identify partitions that elude standard clustering analysis. AVAILABILITY: Free, at http://ctwc.weizmann.ac.il.. SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/bioinfo2/ Publication Types: Evaluation Studies Validation Studies PMID:","yes","n","47: Bioinformatics. 2003 Jun 12;19(9):1079-89.","Coupled two-way clustering analysis of breast cancer and colon cancer gene","expression data.","PMID: 12801868 [PubMed - indexed for MEDLINE]"]
["nts Coupled Two Way Clustering (Getz et al., 2000), a method designed to mine gene expression data Availability: Free, at http://ctwc.weizmann.ac.il. SUPPLEMENTARY INFORMATION: The site has a link to an example which provides figures and detailed explanations PMID: 12801877 [PubMed - indexed for MED","yes","n","43: Bioinformatics. 2003 Jun 12;19(9):1153-4.","Coupled two-way clustering server.","Getz G, Domany E.","PMID: 12801877 [PubMed - indexed for MEDLINE]"]
["ods are available from http://www.ncbs.res.in/~faculty/mini/ddbase/ddbase.html Supplementary information: http://www.ncbs.res.in/~faculty/mini/ddbase/supplementary/supplementary.html Publication Types: Evaluation Studies Validation Studies PMID: 14512346 [PubMed - indexed for MEDLINE]","yes","n","34: Bioinformatics. 2003 Sep 22;19(14):1760-4.","DDBASE2.0: updated domain database with improved identification of structural","domains.","PMID: 14512346 [PubMed - indexed for MEDLINE]"]
["dels. In addition to accuracy, our method also provides comprehensible rules to help elucidate the translation between raw data and useful knowledge. Supplementary information: http://sdmc.i2r.a-star.edu.sg/GEDatasets/supplementaldata/eccb2003/ECCB2003.html . Contact: jinyan@i2r.a-star.edu.sg PMID: ","yes","n","27: Bioinformatics. 2003 Oct;19 Suppl 2:II93-II102.","Discovery of significant rules for classifying cancer diagnosis data.","Li J, Liu H, Ng SK, Wong L.","PMID: 14534178 [PubMed - in process]"]
["B files including modeled disulfides. Validation demonstrates a high level of accuracy for the algorithm. AVAILABILITY: http://www.ehscenter.org/dbd/ Supplementary information: http://www.ehscenter.org/dbd/ Publication Types: Evaluation Studies Validation Studies PMID: 14512360 [PubMed - indexed for","yes","n","30: Bioinformatics. 2003 Sep 22;19(14):1852-3.","Disulfide by Design: a computational method for the rational design of disulfide","bonds in proteins.","PMID: 14512360 [PubMed - indexed for MEDLINE]"]
["Upon request from the corresponding author. Free for academic users (license agreement). Special contracts are available for industrial corporations. SUPPLEMENTARY INFORMATION: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer. Publication Types: Evaluation Studies PMID: 12538248 [PubMed - index","yes","n","63: Bioinformatics. 2003 Jan 22;19(2):261-9.","FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic","networks on interactive flux maps.","PMID: 12538248 [PubMed - indexed for MEDLINE]"]
[" and binary Matlab.dll files which require Matlab to run can be downloaded for free by academic institutions at http://www.chip.org/~ge/gedihome.html Supplementary information: http://www.chip.org/~ge/gedihome.html PMID: 14630665 [PubMed - indexed for MEDLINE]","yes","n","13: Bioinformatics. 2003 Nov 22;19(17):2321-2.","Gene Expression Dynamics Inspector (GEDI): for integrative analysis of","expression profiles.","PMID: 14630665 [PubMed - indexed for MEDLINE]"]
["at the same time being more specific. Availability: A web interface for AUGUSTUS and the executable program are located at http://augustus.gobics.de. Supplementary Information: The datasets used for testing and training are available at http://augustus.gobics.de/datasets/ Contact: mstanke@gwdg.de PM","yes","n","26: Bioinformatics. 2003 Oct;19 Suppl 2:II215-II225.","Gene prediction with a hidden Markov model and a new intron submodel.","Stanke M, Waack S.","PMID: 14534192 [PubMed - in process]"]
["sition to breast cancer, and the method is used to identify a set of significant genes. The method is also applied successfully to the leukemia data. SUPPLEMENTARY INFORMATION: http://stat.tamu.edu/people/faculty/bmallick.html. Publication Types: Evaluation Studies Validation Studies PMID: 12499298 ","Yes","n","69: Bioinformatics. 2003 Jan;19(1):90-7.","Gene selection: a Bayesian variable selection approach.","Lee KE, Sha N, Dougherty ER, Vannucci M, Mallick BK.","PMID: 12499298 [PubMed - indexed for MEDLINE]"]
["red so as to be easily modified for viewing data from any database that stores gene structures. AVAILABILITY: The GeneComber public web interface and supplementary information is located at http://bioinformatics.ubc.ca/genecomber The source code is released under the GNU General Public License and i","yes","n","38: Bioinformatics. 2003 Jul 1;19(10):1296-7.","GeneComber: combining outputs of gene prediction programs for improved results.","Shah SP, McVicker GP, Mackworth AK, Rogic S, Ouellette BF.","PMID: 12835277 [PubMed - indexed for MEDLINE]"]
["lso provides an explanation mechanism that traces every finding to the pertinent data. AVAILABILITY: GenePath can be accessed at http://genepath.org. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://genepath.org/bi-.supp. Publication Types: Evaluation Studies PMID: 12584124 [","yes","n","58: Bioinformatics. 2003 Feb 12;19(3):383-9.","GenePath: a system for automated construction of genetic networks from mutant","data.","PMID: 12584124 [PubMed - indexed for MEDLINE]"]
["that GA-based algorithms may represent a powerful new tool in the analysis and exploration of complex multi-class gene expression data. AVAILABILITY: Supplementary information, data sets and source codes are available at http://www.omniarray.com/bioinformatics/GA. Publication Types: Evaluation Studi","yes","n","71: Bioinformatics. 2003 Jan;19(1):37-44.","Genetic algorithms applied to multi-class prediction for the analysis of gene","expression data.","PMID: 12499291 [PubMed - indexed for MEDLINE]"]
["sequence analysis. AVAILABILITY: gff2aplot is freely available under the GNU software licence and can be downloaded from the address specified below. Supplementary information: http://genome.imim.es/software/gfftools/GFF2APLOT.html Publication Types: Evaluation Studies PMID: 14668236 [PubMed - index","yes","n","5: Bioinformatics. 2003 Dec 12;19(18):2477-9.","gff2aplot: Plotting sequence comparisons.","Abril JF, Guigo R, Wiehe T.","PMID: 14668236 [PubMed - indexed for MEDLINE]"]
["work integrities. Such difference between different experimental methods can provide insight into the systematic bias present among these techniques. SUPPLEMENTARY INFORMATION: The full list of our results can be found in the supplemental web site http://www.nas.nasa.gov/Groups/SciTech/nano/msamanta","yes","n","9: Bioinformatics. 2003 Dec 12;19(18):2413-9.","Global snapshot of a protein interaction network-a percolation based approach.","Chin CS, Samanta MP.","PMID: 14668225 [PubMed - indexed for MEDLINE]"]
["th operons of E.coli shows that low-level clusters are reflected in genome organization and gene regulation. AVAILABILITY: Source code, data sets and supplementary information are available at http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html Publication Types: Evaluation Studies Va","yes","n","48: Bioinformatics. 2003 May 22;19(8):1027-34.","Hierarchical analysis of dependency in metabolic networks.","Gagneur J, Jackson DB, Casari G.","PMID: 12761067 [PubMed - indexed for MEDLINE]"]
["thod outperforms existing methods for numerical data. Availability: Programs transforming input data into LP format files are available upon request. Supplementary information: http://sunflower.kuicr.kyoto-u.ac.jp/~morihiro/protint/supplement.html Contact: akutsu@kuicr.kyoto-u.ac.jp PMID: 14534173 [","yes","n","28: Bioinformatics. 2003 Oct;19 Suppl 2:II58-II65.","Inferring strengths of protein-protein interactions from experimental data using","linear programming.","PMID: 14534173 [PubMed - in process]"]
["idea when combined with a learning algorithm, such as the support vector machine that does not suffer from the curse of dimensionality. AVAILABILITY: Supplementary data at www.cs.columbia.edu/compbio/hiclust. Software source code available by request. Publication Types: Evaluation Studies Validation","yes","n","19: Bioinformatics. 2003 Nov 1;19(16):2097-104.","Kernel hierarchical gene clustering from microarray expression data.","Qin J, Lewis DP, Noble WS.","PMID: 14594715 [PubMed - indexed for MEDLINE]"]
["ously published by Cho et al. (Nat. Genet., 27, 48-54, 2001). AVAILABILITY: The Rosetta system is available at http://www.idi.ntnu.no/~aleks/rosetta. SUPPLEMENTARY INFORMATION: http://www.lcb.uu.se/~hvidsten/bioinf_cho/ Publication Types: Evaluation Studies Validation Studies PMID: 12801872 [PubMed ","yes","n","45: Bioinformatics. 2003 Jun 12;19(9):1116-23.","Learning rule-based models of biological process from gene expression time","profiles using gene ontology.","PMID: 12801872 [PubMed - indexed for MEDLINE]"]
["d if the bias is rational. AVAILABILITY: Java code of the algorithm can be found at http://www.csse.monash.edu.au/~lloyd/tildeProgLang/Java2/Biased/. SUPPLEMENTARY INFORMATION: Examples of applications to Plasmodium falciparum genomic DNA can be found at the above URL. PMID: 12835276 [PubMed - index","yes","n","39: Bioinformatics. 2003 Jul 1;19(10):1294-5.","Longest biased interval and longest non-negative sum interval.","Allison L.","PMID: 12835276 [PubMed - indexed for MEDLINE]"]
[" clusters obtained. AVAILABILITY: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html SUPPLEMENTARY INFORMATION: http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html Publication Types: Evaluation Studies Validation Studies PMID: 14668243 ","yes","n","3: Bioinformatics. 2003 Dec 12;19(18):2494-5.","Machaon CVE: cluster validation for gene expression data.","Bolshakova N, Azuaje F.","PMID: 14668243 [PubMed - indexed for MEDLINE]"]
["in viewer mode at http://www.patronov.net/sciencevr/mnv/indexview.html or in constructor mode at http://www.patronov.net/sciencevr/mnv/indexmake.html SUPPLEMENTARY INFORMATION: The figures for the paper as well as the Appendices may be found at http://www.patronov.net/sciencevr/mnv/screenshots.html ","yes","n","7: Bioinformatics. 2003 Dec 12;19(18):2436-41.","Metabolic pathways in three dimensions.","Rojdestvenski I.","PMID: 14668228 [PubMed - indexed for MEDLINE]"]
["ains having different genotypes under various environmental conditions, and automated pathway layout creation. AVAILABILITY: http://mbel.kaist.ac.kr/ Supplementary information: A manual for MetaFluxNet is available as PDF file. PMID: 14594721 [PubMed - indexed for MEDLINE]","yes","n","16: Bioinformatics. 2003 Nov 1;19(16):2144-6.","MetaFluxNet: the management of metabolic reaction information and quantitative","metabolic flux analysis.","PMID: 14594721 [PubMed - indexed for MEDLINE]"]
["of multiple reporters per gene, use of replicate experiments, and sample referencing schemes in measurements based on expression change. AVAILABILITY/SUPPLEMENTARY INFORMATION: Expression data and supplementary information are available at http://www.rii.com/publications/2003/HE_SDS.htm Publication ","Yes","n","51: Bioinformatics. 2003 May 22;19(8):956-65.","Microarray standard data set and figures of merit for comparing data processing","methods and experiment designs.","PMID: 12761058 [PubMed - indexed for MEDLINE]"]
["environment Availability: Available on request to the authors. The software itself is free for scientific purposes but requires commercial libraries. SUPPLEMENTARY INFORMATION: http://www.mpi-magdeburg.mpg.de/projects/promot PMID: 12801880 [PubMed - indexed for MEDLINE]","yes","n","41: Bioinformatics. 2003 Jun 12;19(9):1169-76.","Modular modeling of cellular systems with ProMoT/Diva.","Ginkel M, Kremling A, Nutsch T, Rehner R, Gilles ED.","PMID: 12801880 [PubMed - indexed for MEDLINE]"]
[" allows for ranking of their predicted functional consequences based on conservation in multiple sequence alignments. AVAILABILITY: http://mutdb.org/ Supplementary information: http://mutdb.org/about/about.html PMID: 14512363 [PubMed - indexed for MEDLINE]","yes","n","29: Bioinformatics. 2003 Sep 22;19(14):1858-60.","MutDB: annotating human variation with functionally relevant data.","Mooney SD, Altman RB.","PMID: 14512363 [PubMed - indexed for MEDLINE]"]
[" newly developed software. AVAILABILITY: The NCL is freely available under the GNU General Public License from http://hydrodictyon.eeb.uconn.edu/ncl/ Supplementary information: Documentation for the NCL (general information and source code documentation) is available in HTML format at http://hydrodi","yes","n","11: Bioinformatics. 2003 Nov 22;19(17):2330-1.","NCL: a C++ class library for interpreting data files in NEXUS format.","Lewis PO.","PMID: 14630669 [PubMed - indexed for MEDLINE]"]
["Our program provides an optimal method for performing this task. AVAILABILITY: The software is available, free of charge, on request from Oxagen Ltd. SUPPLEMENTARY INFORMATION: http://www.oxagen.co.uk PMID: 12538255 [PubMed - indexed for MEDLINE]","yes","n","61: Bioinformatics. 2003 Jan 22;19(2):291-2.","Pedstrip: extracting a maximal subset of available, unrelated individuals from a","pedigree.","PMID: 12538255 [PubMed - indexed for MEDLINE]"]
["her database systems over the network, and it represents a complete solution for the management of the entire manufacturing process. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://www.dkfz-heidelberg.de/kompl_genome/Other/QuickLims/index.html PMID: 12538251 [PubMed - indexed for MEDLINE]","yes","n","62: Bioinformatics. 2003 Jan 22;19(2):283-4.","QuickLIMS: facilitating the data management for DNA-microarray fabrication.","Kokocinski F, Wrobel G, Hahn M, Lichter P.","PMID: 12538251 [PubMed - indexed for MEDLINE]"]
["tware for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from http://www.dq.fct.unl.pt/qoa/jas/seqrep. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002 Publication Types: Evaluation Stu","yes","n","72: Bioinformatics. 2003 Jan;19(1):30-6.","Representation of DNA sequences with virtual potentials and their processing by","(SEQREP) Kohonen self-organizing maps.","PMID: 12499290 [PubMed - indexed for MEDLINE]"]
["another independent data sets are also presented to show the strength of our method. AVAILABILITY: Under http://sdmc.lit.org.sg/GEDatasets/, click on Supplementary Information. Publication Types: Evaluation Studies Validation Studies PMID: 12499295 [PubMed - indexed for MEDLINE]","Yes","n","70: Bioinformatics. 2003 Jan;19(1):71-8.","Simple rules underlying gene expression profiles of more than six subtypes of","acute lymphoblastic leukemia (ALL) patients.","PMID: 12499295 [PubMed - indexed for MEDLINE]"]
["at lies within a given distance of a real SNP. AVAILABILITY: The software is available, free of charge, for academic use on request from the authors. SUPPLEMENTARY INFORMATION: www.oxagen.co.uk PMID: 14594720 [PubMed - indexed for MEDLINE]","yes","n","17: Bioinformatics. 2003 Nov 1;19(16):2141-3.","SNP cherry picker: maximizing the chance of finding an association with a","disease SNP.","PMID: 14594720 [PubMed - indexed for MEDLINE]"]
["Y: An academic version of the algorithm (full source listing in standard C language) can be freely downloaded (http://www.caspur.it/~castri/STRING/). SUPPLEMENTARY INFORMATION: Some illustrative figures and some sample results are provided as supplementary material at: http://www.caspur.it/~castri/S","yes","n","35: Bioinformatics. 2003 Sep 22;19(14):1733-8.","STRING: finding tandem repeats in DNA sequences.","Parisi V, De Fonzo V, Aluffi-Pentini F.","PMID: 14512342 [PubMed - indexed for MEDLINE]"]
["ABILITY: An implementation of our algorithm and other programs for analyzing the data is available from http://www.tp.umu.se/forskning/networks/meta/ SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.tp.umu.se/forskning/networks/meta/ Publication Types: Evaluation Studies ","yes","n","54: Bioinformatics. 2003 Mar 1;19(4):532-8.","Subnetwork hierarchies of biochemical pathways.","Holme P, Huss M, Jeong H.","PMID: 12611809 [PubMed - indexed for MEDLINE]"]
["provides good approximations to the responses of this complex system. AVAILABILITY: FUNDER is available from http://bbm1.ucm.es/torralba/funder/down/ SUPPLEMENTARY INFORMATION: http://bbm1.ucm.es/torralba/funder/ Publication Types: Evaluation Studies Validation Studies PMID: 14668227 [PubMed - index","yes","n","8: Bioinformatics. 2003 Dec 12;19(18):2428-35.","Susceptibility of non-linear systems as an approach to metabolic responses.","Torralba AS.","PMID: 14668227 [PubMed - indexed for MEDLINE]"]
[" have a high reliability and separating them from tags that carry an inherent ambiguity in their capacity to discriminate between genes. To this end, supplementary information in the form of a web companion to this paper is located at http:// biobase.biotech.kth.se/tagseq. PMID: 12682372 [PubMed - i","Yes","n","52: Nucleic Acids Res. 2003 Apr 15;31(8):2217-26.","Transcript identification by analysis of short sequence tags--influence of tag","length, restriction site and transcript database.","PMID: 12682372 [PubMed - indexed for MEDLINE]"]
[" intervals. AVAILABILITY: The model is implemented in R statistical language script and is available under GNU/GLP copyleft at supplemental web site. SUPPLEMENTARY INFORMATION: http://www.ime.usp.br/~rvencio/SAGEci/ Publication Types: Evaluation Studies Validation Studies PMID: 14668232 [PubMed - in","yes","n","6: Bioinformatics. 2003 Dec 12;19(18):2461-4.","Using credibility intervals instead of hypothesis tests in SAGE analysis.","Vencio RZ, Brentani H, Pereira CA.","PMID: 14668232 [PubMed - indexed for MEDLINE]"]
["icle if you access the article at http://dx.doi.org/10.1007/s00894-003-0118-0. A link in the frame on the left on that page takes you directly to the supplementary material. Figure Structure 1 of the N15m cluster, showing bond distances in A and bond angles in degrees PMID: 12707803 [PubMed - in pro","yes","y","12: J Mol Model (Online). 2003 Apr;9(2):99-107. Epub 2003 Mar 12.","A computer-aided quantum chemical study of the N(15)(-) cluster.","Cheng L, Li Q, Xu W, Zhang S.","PMID: 12707803 [PubMed - in process]"]
["le if you access this article at http://dx.doi.org/10.1007/s00122-002-1182-z. On that page (frame on the left side), a link takes you directly to the supplementary material. MeSH Terms: Animals Diptera/physiology* Genes, Plant* Poaceae/genetics* Polyploidy* Research Support, Non-U.S. Gov't Transfect","yes","y","11: Theor Appl Genet. 2003 May;106(7):1248-55. Epub 2003 Jan 23.","A new Hessian fly resistance gene (H30) transferred from the wild grass Aegilops","triuncialis to hexaploid wheat.","PMID: 12748776 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Diptera/physiology*","Genes, Plant*","Poaceae/genetics*","Polyploidy*","Research Support, Non-U.S. Gov't","Transfection*","Triticum/genetics*"]
["surements of positions of cells in 3D matrices by eliminating the need to perform optical sectioning and can be used with any brightfield microscope. Supplementary material for this article can be found at http://www.interscience.wiley.com/jpages/0196-4763/suppmat/54_2/v54.125.html Copyright 2003 Wi","yes","y","8: Cytometry A. 2003 Aug;54(2):125-31.","An aperture-shifting light-microscopic method for rapidly quantifying positions","of cells in 3D matrices.","PMID: 12879459 [PubMed - indexed for MEDLINE]","MeSH Terms:","Calibration","Cell Line, Tumor","Cells/cytology*","Collagen/chemistry","Humans","Image Processing, Computer-Assisted","Microscopy/methods*","Microscopy, Fluorescence/methods","Microscopy, Video","Research Support, U.S. Gov't, P.H.S.","Substances:","Collagen","Grant Support:","R24-CA-56591/CA/NCI"]
["his report presents two new cases of CPLS, and suggests that the CPLS phenotype may represent the mild end of the Fryns syndrome phenotypic spectrum. Supplementary material for this article can be found on the Birth Defects Research (Part A) website (http://www.interscience.wiley.com/ jpages/1542-07","yes","y","7: Birth Defects Res A Clin Mol Teratol. 2003 Jun;67(6):460-6.","Cleft-palate lateral synechia syndrome: insight into the phenotypic spectrum of","Fryns syndrome?","PMID: 12962292 [PubMed - indexed for MEDLINE]","MeSH Terms:","Abnormalities, Multiple/genetics","Abnormalities, Multiple/pathology*","Adhesions/congenital","Adhesions/genetics","Adhesions/pathology","Alveolar Process/abnormalities","Cleft Palate/genetics","Cleft Palate/pathology*","DNA/analysis","Diseases in Twins*","Face/abnormalities","Fatal Outcome","Female","Humans","Infant, Newborn","Minisatellite Repeats/genetics","Mouth Abnormalities/genetics","Mouth Abnormalities/pathology*","Polymerase Chain Reaction","Research Support, Non-U.S. Gov't","Syndrome","Twins, Monozygotic/genetics","Substances:","DNA"]
[" transcriptionally active cell responsive to environmental stimuli and capable of a complex series of both early and late changes in gene expression. Supplementary material for this article can be found on the Journal of Cellular Biochemistry website (http://jws-edci.interscience.wiley.com:8998/jpag","yes","y","9: J Cell Biochem. 2003 Jul 1;89(4):848-61.","Erratum in:","J Cell Biochem. 2003 Aug 15;89(6):1302.","PMID: 12858349 [PubMed - indexed for MEDLINE]","MeSH Terms:","Cluster Analysis","Comparative Study","Escherichia coli/chemistry","Gene Expression/drug effects","Gene Expression Profiling/methods","Humans","Lipopolysaccharides/pharmacology*","Multigene Family","Neutrophil Activation/drug effects","Neutrophil Activation/physiology*","Neutrophils/drug effects*","Neutrophils/physiology","Oligonucleotide Array Sequence Analysis","RNA/analysis","RNA/genetics","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Substances:","Lipopolysaccharides","RNA","Grant Support:","R01-DK54369/DK/NIDDK"]
["et allows a safe diagnostic FOB with BAL in patients with hypoxemic ARF, avoiding gas exchange deterioration, and endotracheal intubation. Electronic supplementary material: is available if you access this article at http://dx.doi.org/10.1007/s00134-002-1554-5. On that page (frame on the left side),","yes","y","16: Intensive Care Med. 2003 Jan;29(1):126-9. Epub 2002 Nov 29.","Fiberoptic bronchoscopy during noninvasive positive pressure ventilation","delivered by helmet.","PMID: 12528033 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Aged","Anoxemia/diagnosis","Bronchoalveolar Lavage/methods","Bronchoscopy/methods*","Female","Fiber Optics*","Head Protective Devices*","Humans","Male","Middle Aged","Pneumonia/diagnosis*","Positive-Pressure Respiration/instrumentation*","Prospective Studies","Respiratory Distress Syndrome, Adult/diagnosis*","Statistics, Nonparametric"]
["fter cardiothoracic surgery alters nursing activity; it reduces the time for documentation and increases the time devoted to patient care. Electronic supplementary material: is available if you access this article at http://dx.org/10.1007/s00134-002-1542-9. On that page (frame on the left side), a l","yes","y","17: Intensive Care Med. 2003 Jan;29(1):83-90. Epub 2002 Nov 22.","Intensive care information system reduces documentation time of the nurses after","cardiothoracic surgery.","PMID: 12528027 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Aged","Cardiac Surgical Procedures/nursing","Efficiency, Organizational*","Female","Hospital Information Systems*","Humans","Intensive Care Units*","Male","Middle Aged","Netherlands","Nursing Staff, Hospital/organization & administration*","Thoracic Surgical Procedures/nursing*","Time and Motion Studies"]
["icle if you access the article at http://dx.doi.org/10.1007/s00894-003-0116-2. A link in the frame on the left on that page takes you directly to the supplementary material. PMID: 12838399 [PubMed - in process]","yes","y","10: J Mol Model (Online). 2003 Aug;9(4):207-16. Epub 2003 Jul 1.","Molecular crystals: the crystal field effect on molecular electronic structure.","Yatsenko AV.","PMID: 12838399 [PubMed - in process]"]
["icle if you access the article at http://dx.doi.org/10.1007/s00894-002-0114-9. A link in the frame on the left on that page takes you directly to the supplementary material. Figure Docking structures of1 and2 binding with oligonucleotide: l-Ser-Hism.5'-TpTpdC-3'(left), d-Ser-Hism.5'-TpTpdC-3'(right)","yes","y","13: J Mol Model (Online). 2003 Apr;9(2):84-7. Epub 2003 Feb 21.","Molecular modeling of diastereoisomeric aggregates of l/d ser/histamine amide","with 5'-TpTpdC-3'.","PMID: 12707801 [PubMed - in process]"]
["cific expression, genomic organization and evolutionary conservation of the different PAD isotypes will be discussed in detail. This article contains supplementary material which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/2003/25/v25.1106.htm","yes","y","5: Bioessays. 2003 Nov;25(11):1106-18.","PAD, a growing family of citrullinating enzymes: genes, features and involvement","in disease.","PMID: 14579251 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Animals","Arthritis, Rheumatoid/enzymology","Humans","Hydrolases/classification","Hydrolases/genetics*","Hydrolases/metabolism*","Isoenzymes/classification","Isoenzymes/genetics*","Isoenzymes/metabolism*","Molecular Sequence Data","Multigene Family","Multiple Sclerosis/enzymology","Phylogeny","Protein Conformation","Psoriasis/enzymology","Sequence Alignment","Substances:","Isoenzymes","Hydrolases","protein-arginine deiminase"]
["work properties shed new light on the basis of human cognitive diseases including schizophrenia, autism, Huntington's disease and mental retardation. Supplementary material for this article can be found on the BioEssays website http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html. C","yes","y","2: Bioessays. 2003 Dec;25(12):1229-35.","Synapse signalling complexes and networks: machines underlying cognition.","Grant SG.","PMID: 14635258 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Humans","Models, Biological","Models, Theoretical","Nerve Net*","Neurons/physiology*","Protein Binding","Receptors, N-Methyl-D-Aspartate/physiology","Research Support, Non-U.S. Gov't","Signal Transduction*","Synapses/physiology*","Substances:","Receptors, N-Methyl-D-Aspartate"]
["es well with the average path length of the GSC and is a useful parameter for a system-level comparison of metabolic networks of different organisms. SUPPLEMENTARY INFORMATION: http://genome.gbf.de/bioinformatics/ Publication Types: Evaluation Studies PMID: 12874056 [PubMed - indexed for MEDLINE]","yes","y","36: Bioinformatics. 2003 Jul 22;19(11):1423-30.","The connectivity structure, giant strong component and centrality of metabolic","networks.","PMID: 12874056 [PubMed - indexed for MEDLINE]"]
["istalsis was demonstrated on cine MR using ultrafast MRI. Direction and frequency of peristaltic waves are closely related to menstrual cycle phases. Supplementary material for this article can be found on the JMRI website at http://www.interscience.wiley.com/jpages/1053-1807/suppmat/index.html. Cop","yes","y","3: J Magn Reson Imaging. 2003 Dec;18(6):726-33.","Uterine peristalsis shown on cine MR imaging using ultrafast sequence.","Nakai A, Togashi K, Yamaoka T, Fujiwara T, Ueda H, Koyama T, Kobayashi H,","PMID: 14635158 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Female","Humans","Image Processing, Computer-Assisted","Magnetic Resonance Imaging, Cine/methods*","Menstrual Cycle/physiology*","Uterine Contraction/physiology*"]
["of W3110 in the absence of MgCl(2). The expression ratios of a total of 232 genes were <0.75 in all three strains (the supplemental data are shown at http://www.nara.kindai.ac.jp/nogei/seiken/array.html), suggesting that the PhoP/PhoQ system is involved directly or indirectly in the transcription of","no","n","1: J Bacteriol. 2003 Jul;185(13):3696-702.","Identification and molecular characterization of the Mg2+ stimulon of","Escherichia coli.","PMID: 12813061 [PubMed - indexed for MEDLINE]","MeSH Terms:","Bacterial Proteins/genetics","Bacterial Proteins/metabolism","Base Sequence","DNA Footprinting","Deoxyribonucleases/metabolism","Escherichia coli/genetics","Escherichia coli/metabolism*","Escherichia coli Proteins/genetics","Escherichia coli Proteins/metabolism*","Gene Expression Profiling","Gene Expression Regulation, Bacterial*","Magnesium/pharmacology*","Molecular Sequence Data","Oligonucleotide Array Sequence Analysis/methods*","Promoter Regions (Genetics)","Research Support, Non-U.S. Gov't","Signal Transduction*","Transcription, Genetic","Substances:","Bacterial Proteins","Escherichia coli Proteins","PhoQ protein, Bacteria","PhoP protein, Bacteria","Magnesium","Deoxyribonucleases"]

{"sheet":"2004","index":8,"n_rows":173,"n_cols":56,"rows_kept":173,"flags":["formulas_cached_only"]}
["Reference",null,"Live?","Journal?"]
[" interface at http://systemsbiology.northwestern.edu/BNICE (site under construction). CONTACT: vassily@northwestern.edu or broadbelt@northwestern.edu SUPPLEMENTARY INFORMATION: http://systemsbiology.northwestern.edu/BNICE/publications. Publication Types: Evaluation Studies PMID: 15613400 [PubMed - i","1: Bioinformatics. 2005 Apr 15;21(8):1603-9. Epub 2004 Dec 21.","n/a","n","Hatzimanikatis V, Li C, Ionita JA, Henry CS, Jankowski MD, Broadbelt LJ.","PMID: 15613400 [PubMed - indexed for MEDLINE]"]
["sting programs (ADHoRe and LineUp) for chromosomal homology detection and found that in general CloseUp compares favorably. AVAILABILITY: CloseUp and supplementary information are available at http://www.igb.uci.edu/servers/cgss.html CONTACT: pfbaldi@ics.uci.edu. Publication Types: Evaluation Studie","10: Bioinformatics. 2005 Apr 15;21(8):1339-48. Epub 2004 Dec 7.","no","n","Hampson SE, Gaut BS, Baldi P.","PMID: 15585535 [PubMed - indexed for MEDLINE]"]
["gnments. In all experiments, the sample temperature was 120 degrees C, to ensure a homogeneous solution and sufficient molecular mobility. Electronic Supplementary Material: Supplementary material (1D 13C NMR spectra of the 13C-labeled and unlabeled polymers) is available in the online version of th","100: Anal Bioanal Chem. 2004 Mar;378(6):1414-27.","no","n","acrylate-co-carbon monoxide-co-ethylene) by isotopic labeling and two","PMID: 15214405 [PubMed - indexed for MEDLINE]","MeSH Terms:","Acrylates/chemistry*","Carbon Isotopes/chemistry","Carbon Monoxide/chemistry*","Ethylenes/chemistry*","Isotope Labeling","Magnetic Resonance Spectroscopy/methods","Molecular Structure","Polymers/analysis*","Polymers/chemistry*","Research Support, Non-U.S. Gov't","Substances:","Acrylates","Carbon Isotopes","Ethylenes","Polymers","n-butyl acrylate","Carbon Monoxide","ethylene"]
["ed gene order from annotated genomes. AVAILABILITY: Available free of charge for Unix/Linux/Cygwin platforms at ftp://159.149.110.11/pub/GeneSyn_1.0/ SUPPLEMENTARY INFORMATION: ftp://159.149.110.11/pub/GeneSyn_1.0/ Publication Types: Evaluation Studies PMID: 14976031 [PubMed - indexed for MEDLINE]","100: Bioinformatics. 2004 Jun 12;20(9):1472-4. Epub 2004 Feb 19.","No","n","Pavesi G, Mauri G, Iannelli F, Gissi C, Pesole G.","PMID: 14976031 [PubMed - indexed for MEDLINE]"]
["tally testable hypotheses. AVAILABILITY: Supplementary data and Matlab computer source code will be made available on the web at the URL given below. SUPPLEMENTARY INFORMATION: http://public.kgi.edu/~wild/LDS/index.htm Publication Types: Evaluation Studies Validation Studies PMID: 14962938 [PubMed -","101: Bioinformatics. 2004 Jun 12;20(9):1361-72. Epub 2004 Feb 12.","no","n","models.","PMID: 14962938 [PubMed - indexed for MEDLINE]"]
["rogression of cancer. Although some genetic changes were associated only with the 8p pathway, most secondary genetic changes appear in both pathways. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","101: Int J Cancer. 2004 Jul 20;110(6):850-6.","no","n","of allelotyping data.","PMID: 15170667 [PubMed - indexed for MEDLINE]","MeSH Terms:","Alleles","Bayes Theorem","Chromosome Aberrations*","Chromosomes, Human/genetics*","Chromosomes, Human, Pair 9","Cyclin-Dependent Kinase Inhibitor p16/genetics","Genes, p16","Genotype","Humans","Loss of Heterozygosity","Microsatellite Repeats/genetics","Neural Networks (Computer)","Research Support, Non-U.S. Gov't","Urologic Neoplasms/genetics*","Substances:","Cyclin-Dependent Kinase Inhibitor p16"]
["gene transcripts, and assigns sensitivity and specificity scores to each probeset/gene pair. AVAILABILITY: http://genecards.weizmann.ac.il/geneannot/ SUPPLEMENTARY INFORMATION: Program description and statistics http://genecards.weizmann.ac.il/geneannot/DOC/index.html Publication Types: Evaluation S","102: Bioinformatics. 2004 Jun 12;20(9):1457-8. Epub 2004 Feb 12.","no","n","and GeneCards genes.","PMID: 14962929 [PubMed - indexed for MEDLINE]"]
["n for arbitrary natural and random sequences. AVAILABILITY: paRNAss is available as a Web service at http://bibiserv.techfak.uni-bielefeld.de/parnass SUPPLEMENTARY INFORMATION: Detailed information on the analyses summarized in Table 1 can be found at http://bibiserv.techfak.uni-bielefeld.de/parnass","103: Bioinformatics. 2004 Jul 10;20(10):1573-82. Epub 2004 Feb 12.","No","n","Voss B, Meyer C, Giegerich R.","PMID: 14962925 [PubMed - indexed for MEDLINE]"]
["biology and differentiation-specific expression patterns and gives important clues related to the possible cellular origin of these pediatric tumors. Supplementary material for this article is available at the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","103: Int J Cancer. 2004 Jul 10;110(5):687-94.","No","n","rhabdomyosarcoma and Ewing's sarcoma.","PMID: 15146558 [PubMed - indexed for MEDLINE]","MeSH Terms:","Cell Differentiation","Cell Line, Tumor","Child","Cyclin D1/biosynthesis","DNA Primers/pharmacology","DNA-Binding Proteins/biosynthesis","Disease Progression","Fibroblasts/metabolism","Gene Expression Regulation, Neoplastic*","Genetic Markers","Heparan Sulfate Proteoglycan/biosynthesis","Humans","Lipid Metabolism","Models, Statistical","Oligonucleotide Array Sequence Analysis","RNA, Complementary/metabolism","RNA, Messenger/metabolism*","Repressor Proteins/biosynthesis","Research Support, Non-U.S. Gov't","Reverse Transcriptase Polymerase Chain Reaction","Rhabdomyosarcoma/genetics*","Sarcoma, Ewing's/genetics*","Trans-Activators/biosynthesis","Tumor Markers, Biological","Substances:","CITED2 protein, human","DNA Primers","DNA-Binding Proteins","Genetic Markers","Heparan Sulfate Proteoglycan","RNA, Complementary","RNA, Messenger","Repressor Proteins","Trans-Activators","Tumor Markers, Biological","glypican 3","Cyclin D1"]
["strate that our method has improved power in finding physically close residues in crystal structures, compared to that of Ranganathan and colleagues. SUPPLEMENTARY INFORMATION: www.afodor.net/bioinfosup.html Publication Types: Evaluation Studies Validation Studies PMID: 14962924 [PubMed - indexed fo","104: Bioinformatics. 2004 Jul 10;20(10):1565-72. Epub 2004 Feb 12.","no","n","co-variance in multiple sequence alignments.","PMID: 14962924 [PubMed - indexed for MEDLINE]"]
["or the late and continuous evolution of the nucleolus in early eukaryotes and argue against an endosymbiotic origin of the nucleolus and the nucleus. Supplementary material for this article can be found on the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html","105: Bioessays. 2004 May;26(5):567-81.","no","n","Bioessays. 2004 Oct;26(10):1144-5; author reply 1145-7.","PMID: 15112237 [PubMed - indexed for MEDLINE]","MeSH Terms:","Archaeal Proteins/metabolism","Bacterial Proteins/metabolism","Cell Nucleolus*/chemistry","Cell Nucleolus*/metabolism","Databases, Factual","Evolution*","Models, Biological","Nuclear Proteins/chemistry*","Nuclear Proteins/classification*","Nuclear Proteins/genetics","Nuclear Proteins/metabolism","Phylogeny","Protein Structure, Tertiary","Proteome/analysis","Ribosomal Proteins","Ribosomes/metabolism","Substances:","Archaeal Proteins","Bacterial Proteins","Nuclear Proteins","Proteome","Ribosomal Proteins"]
["h E-Cell2 simulation system, which can be downloaded from http://www.e-cell.org. CD-ROMs are also available and are distributed at major conferences. SUPPLEMENTARY INFORMATION: All the kinetic data are available via http://www.e-cell.org PMID: 14962921 [PubMed - indexed for MEDLINE]","105: Bioinformatics. 2004 Jul 22;20(11):1795-6. Epub 2004 Feb 12.","no","n","scale.","PMID: 14962921 [PubMed - indexed for MEDLINE]"]
["parison of individuals with NS and individuals with VCFS, a correct identification rate of 95% was achieved for both syndromes. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","106: Am J Med Genet A. 2004 May 1;126(4):339-48.","no","n","Hammond P, Hutton TJ, Allanson JE, Campbell LE, Hennekam RC, Holden S, Patton","PMID: 15098232 [PubMed - indexed for MEDLINE]","MeSH Terms:","Abnormalities, Multiple/pathology*","Adolescent","Adult","Child","Child, Preschool","Comparative Study","Craniofacial Abnormalities/pathology","Face/pathology*","Heart Defects, Congenital/pathology","Humans","Imaging, Three-Dimensional/instrumentation","Imaging, Three-Dimensional/methods*","Infant","Infant, Newborn","Middle Aged","Models, Anatomic","Noonan Syndrome/pathology*","Research Support, Non-U.S. Gov't","Syndrome","Velopharyngeal Insufficiency/pathology"]
["ible methods, log ratio values and a list of genes showing significant variations between conditions. AVAILABILITY: http://www.bionet.espci.fr/varan/ SUPPLEMENTARY INFORMATION: http://www.bionet.espci.fr/varan/help.html PMID: 14962915 [PubMed - indexed for MEDLINE]","106: Bioinformatics. 2004 Jul 10;20(10):1641-3. Epub 2004 Feb 12.","Yes","n","Golfier G, Dang MT, Dauphinot L, Graison E, Rossier J, Potier MC.","PMID: 14962915 [PubMed - indexed for MEDLINE]"]
["mportant results. AVAILABILITY: The software module dChipSNP implementing these methods is available at http://biosun1.harvard.edu/complab/dchip/snp/ SUPPLEMENTARY INFORMATION: The breast cancer data are provided by Andrea L. Richardson, Zhigang C. Wang and James D. Iglehart. Publication Types: Eval","107: Bioinformatics. 2004 May 22;20(8):1233-40. Epub 2004 Feb 10.","yes","n","loss-of-heterozygosity data.","PMID: 14871870 [PubMed - indexed for MEDLINE]"]
["esidues that have potential structural or functional importance. AVAILABILITY: The ConSeq web server is available at http://conseq.bioinfo.tau.ac.il/ SUPPLEMENTARY INFORMATION: The ConSeq methodology, a description of its performance in a set of five well-documented proteins, a comparison to other m","108: Bioinformatics. 2004 May 22;20(8):1322-4. Epub 2004 Feb 10.","yes","n","in protein sequences.","PMID: 14871869 [PubMed - indexed for MEDLINE]"]
[" and the characteristics of the subgraphs resulting from the application of our software to the revised datasets. AVAILABILITY: Complete datasets and supplementary material may be downloaded from http://helix.ex.ac.uk/metabolism. The software for the creation of enzyme-centric graphs from reaction d","108: Bioinformatics. 2004 Sep 1;20(13):2050-5. Epub 2004 Apr 8.","yes","n","Horne AB, Hodgman TC, Spence HD, Dalby AR.","PMID: 15073012 [PubMed - indexed for MEDLINE]","MeSH Terms:","Computer Simulation","Databases, Protein*","Enzymes/chemistry*","Enzymes/metabolism*","Metabolism/physiology*","Models, Biological*","Multienzyme Complexes/chemistry","Multienzyme Complexes/metabolism","Protein Interaction Mapping/methods*","Research Support, Non-U.S. Gov't","Signal Transduction/physiology*","Substances:","Enzymes","Multienzyme Complexes"]
["monline.unibas.ch/; http://germonline.igh.cnrs.fr/), Japan (http://germonline.biochem.s.u-tokyo.ac.jp/) and USA (http://germonline.yeastgenome.org/). SUPPLEMENTARY INFORMATION: Extended documentation of the database is available through the link 'About GermOnline' at the websites. PMID: 14751982 [Pu","109: Bioinformatics. 2004 Mar 22;20(5):808-11. Epub 2004 Jan 29.","yes","n","community annotation knowledgebase on germ cell differentiation.","PMID: 14751982 [PubMed - indexed for MEDLINE]"]
[" needed to bring under control the tobacco-related lung cancer epidemic in European women before it reaches the high level observed in North America. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","109: Int J Cancer. 2004 Jun 10;110(2):155-69.","yes","n","Int J Cancer. 2004 Oct 10;111(6):981.","PMID: 15069676 [PubMed - indexed for MEDLINE]","MeSH Terms:","Europe/epidemiology","Female","Humans","Male","Neoplasms/mortality*","Research Support, Non-U.S. Gov't","Time Factors"]
["bly information. Results are output in spreadsheets containing information that facilitates manual validation. AVAILABILITY: The TERMINUS package and supplementary information can be downloaded from http://www.genome.kbrin.uky.edu/fungi_tel/terminus/ CONTACT: farman@uky.edu. PMID: 15585532 [PubMed -","11: Bioinformatics. 2005 Apr 15;21(8):1695-8. Epub 2004 Dec 7.","yes","n","Li W, Rehmeyer CJ, Staben C, Farman ML.","PMID: 15585532 [PubMed - indexed for MEDLINE]"]
["d adapted by groups working on diverse EST sequencing projects. AVAILABILITY: The system and source code are available upon request from the authors. Supplementary information: http://EST-PAGE.binf.gmu.edu PMID: 14734326 [PubMed - indexed for MEDLINE]","110: Bioinformatics. 2004 Jan 22;20(2):286-8.","yes","n","Matukumalli LK, Grefenstette JJ, Sonstegard TS, Van Tassell CP.","PMID: 14734326 [PubMed - indexed for MEDLINE]"]
["mining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. SUPPLEMENTARY INFORMATION: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena","111: Bioinformatics. 2004 Jan 22;20(2):279-81.","yes","n","Brodie R, Roper RL, Upton C.","PMID: 14734323 [PubMed - indexed for MEDLINE]"]
["ted annealing heuristic. LVB runs fast and gives high quality results. AVAILABILITY: The software is available at http://www.rubic.reading.ac.uk/lvb/ Supplementary information: Supplementary information may be downloaded from http://www.rubic.reading.ac.uk/~daniel/ Publication Types: Evaluation Stud","112: Bioinformatics. 2004 Jan 22;20(2):274-5.","yes","n","Barker D.","PMID: 14734321 [PubMed - indexed for MEDLINE]"]
["f the probe set. AVAILABILITY: The program is available on the internet. Sources are freely available, for non-profit use, on request to the authors. Supplementary information: http://pbil.univ-lyon1.fr/roso Publication Types: Evaluation Studies Validation Studies PMID: 14734320 [PubMed - indexed fo","113: Bioinformatics. 2004 Jan 22;20(2):271-3.","yes","n","Reymond N, Charles H, Duret L, Calevro F, Beslon G, Fayard JM.","PMID: 14734320 [PubMed - indexed for MEDLINE]"]
[" found by other clustering methods. AVAILABILITY: The complete result of our algorithm for all the human proteins in SWISS-PROT and TrEMBL, and other supplementary information are available at http://motif.ics.es.osaka-u.ac.jp/Ncut-KL/ Publication Types: Evaluation Studies Validation Studies PMID: 1","114: Bioinformatics. 2004 Jan 22;20(2):243-52.","yes","n","protein sequences.","PMID: 14734316 [PubMed - indexed for MEDLINE]"]
[" as some novel genes. AVAILABILITY: R code for the empirical Bayes adjustment and step-down P-value calculation via resampling are available from the supplementary web-site. Supplementary information: http://www.mathstat.gsu.edu/~matsnd/EB/supp.htm Publication Types: Evaluation Studies Validation St","115: Bioinformatics. 2004 Jan 22;20(2):235-42.","yes","n","differentially expressed genes in microarray experiments.","PMID: 14734315 [PubMed - indexed for MEDLINE]"]
["emonstrate the feasibility of using automated microscopy as a high-throughput screen for identifying modulators of large-scale chromatin folding. The Supplementary Material referred to in this article can be found at the CYTO Part A website (http://www.interscience.wiley.com/jpages/0196-4763/suppmat","115: Cytometry A. 2004 Apr;58(2):157-66.","yes","n","chromatin structure unfolding activity.","PMID: 15057969 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Automation","CHO Cells","Chromatin/chemistry*","Chromatin/genetics","Chromatin/metabolism*","Chromatin Assembly and Disassembly*","Cricetinae","Estrogen Receptor alpha/chemistry*","Estrogen Receptor alpha/genetics","Estrogen Receptor alpha/metabolism*","Microscopy, Fluorescence/instrumentation","Microscopy, Fluorescence/methods*","Protein Structure, Tertiary","Recombinant Fusion Proteins/chemistry","Recombinant Fusion Proteins/genetics","Recombinant Fusion Proteins/metabolism","Reproducibility of Results","Research Support, U.S. Gov't, P.H.S.","Sequence Deletion/genetics","Time Factors","Substances:","Chromatin","Estrogen Receptor alpha","Recombinant Fusion Proteins","Grant Support:","R01-GM42516/GM/NIGMS","R01-GM58460/GM/NIGMS"]
["ional feature of the FluxAnalyzer (freely available for academic users upon request, special contracts for industrial companies; see web page below). Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer Publication Types: Evaluation Studies Validation Studies PMID: 147343","116: Bioinformatics. 2004 Jan 22;20(2):226-34.","yes","n","Klamt S, Gilles ED.","PMID: 14734314 [PubMed - indexed for MEDLINE]"]
["ical pieces of evidence to be considered in order to enhance the therapeutic benefit of a strategy that is currently being tested in clinical trials. Supplementary Material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","116: Int J Cancer. 2004 May 20;110(1):51-60.","yes","n","murine colon cancer with anti-CD137 monoclonal antibodies and alloantigens.","PMID: 15054868 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adenoviridae/genetics","Animals","Antibodies, Monoclonal/therapeutic use*","Antigens, CD","Cell Movement","Colonic Neoplasms/therapy*","Dendritic Cells/immunology*","Gene Therapy*","Interferon Type II/biosynthesis","Interleukin-12/genetics*","Interleukin-12/physiology","Isoantigens/immunology*","Mice","Mice, Inbred BALB C","Mice, Inbred C57BL","Receptors, Nerve Growth Factor/antagonists & inhibitors","Receptors, Nerve Growth Factor/immunology*","Receptors, Tumor Necrosis Factor/antagonists & inhibitors","Receptors, Tumor Necrosis Factor/immunology*","Research Support, Non-U.S. Gov't","Transfection","Substances:","Antibodies, Monoclonal","Antigens, CD","CD137 antigen","Isoantigens","Receptors, Nerve Growth Factor","Receptors, Tumor Necrosis Factor","Interleukin-12","Interferon Type II"]
["VAILABILITY: The program has been implemented in ANSI C and is freely available for academic use at http://www.cse.wustl.edu/~zhang/projects/rna/ilm/ Supplementary information: http://www.cse.wustl.edu/~zhang/projects/rna/ilm/ Publication Types: Evaluation Studies Validation Studies PMID: 14693809 [","117: Bioinformatics. 2004 Jan 1;20(1):58-66.","yes","n","with pseudoknots.","PMID: 14693809 [PubMed - indexed for MEDLINE]"]
["ces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Oryza sativa, Arabidopsis thaliana and a subset of all human proteins. AVAILABILITY: Supplementary information and subcellular location annotations for eukaryotes are available at http://166.111.30.65/hying/fuzzy_loc.htm Publication Ty","118: Bioinformatics. 2004 Jan 1;20(1):21-8.","yes","n","Huang Y, Li Y.","PMID: 14693804 [PubMed - indexed for MEDLINE]"]
["els of disulphide-rich short polypeptides. The database can be accessed from http://www.ncbs.res.in/ approximately faculty/mini/dsdbase/dsdbase.html. Supplementary information can be accessed from http://www.ncbs.res.in/ approximately faculty/mini/dsdbase/nar/suppl.htm. PMID: 14681394 [PubMed - inde","119: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D200-2.","yes","n","Vinayagam A, Pugalenthi G, Rajesh R, Sowdhamini R.","PMID: 14681394 [PubMed - indexed for MEDLINE]"]
["classification. AVAILABILITY: The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm CONTACT: wyh@cs.dartmouth.edu SUPPLEMENTARY INFORMATION: Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm. Publication Types: ","12: Bioinformatics. 2005 Apr 15;21(8):1530-7. Epub 2004 Dec 7.","yes","n","classification using microarray gene expression data.","PMID: 15585531 [PubMed - indexed for MEDLINE]"]
["classification. AVAILABILITY: The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm CONTACT: wyh@cs.dartmouth.edu SUPPLEMENTARY INFORMATION: Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm. Publication Types: ","12: Bioinformatics. 2005 Apr 15;21(8):1530-7. Epub 2004 Dec 7.","yes","n","classification using microarray gene expression data.","PMID: 15585531 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Cluster Analysis","Computer Simulation","Gene Expression Profiling/methods*","Genetic Markers/genetics*","Models, Genetic*","Oligonucleotide Array Sequence Analysis/methods*","Pattern Recognition, Automated/methods*","Phenotype*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Software*","Substances:","Genetic Markers"]
["e proposed for data normalized using methods established in the field of proteomics. AVAILABILITY: Software is available on request from the authors. SUPPLEMENTARY INFORMATION: There is supplementary material available online at http://www.flychip.org.uk/kreil/pub/2dgels/ Publication Types: Evaluati","123: Bioinformatics. 2004 Sep 1;20(13):2026-34. Epub 2004 Mar 25.","yes","n","expression analysis of 2D difference gel electrophoresis results.","PMID: 15044229 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Bayes Theorem","Comparative Study","Computer Simulation","Data Interpretation, Statistical","Electrophoresis, Gel, Two-Dimensional/methods*","Electrophoresis, Gel, Two-Dimensional/standards","Gene Expression Profiling/methods*","Gene Expression Profiling/standards","Models, Genetic","Models, Statistical","Oligonucleotide Array Sequence Analysis/methods*","Oligonucleotide Array Sequence Analysis/standards","Research Support, Non-U.S. Gov't","Sensitivity and Specificity","Sequence Alignment/methods*","Sequence Alignment/standards","Sequence Analysis, DNA/methods*","Sequence Analysis, DNA/standards"]
["o SFTPC mutation from interstitial lung disease to PAP. Notably, the reported mutations do not appear to be dominant negatives. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","124: Am J Med Genet A. 2004 Apr 1;126(1):18-26.","yes","n","fibrosing lung disease.","PMID: 15039969 [PubMed - indexed for MEDLINE]","MeSH Terms:","Bronchoalveolar Lavage Fluid/chemistry","Child, Preschool","Cohort Studies","Comparative Study","Female","Humans","Infant","Infant, Newborn","Lung Diseases, Interstitial/genetics*","Lung Diseases, Interstitial/metabolism","Male","Mutation*","Pedigree","Peptides*","Phenotype","Pulmonary Alveolar Proteinosis/congenital*","Pulmonary Alveolar Proteinosis/diagnosis","Pulmonary Alveolar Proteinosis/genetics*","Pulmonary Fibrosis/genetics*","Pulmonary Fibrosis/metabolism","Pulmonary Surfactant-Associated Protein C/analogs & derivatives*","Pulmonary Surfactant-Associated Protein C/genetics*","Pulmonary Surfactant-Associated Protein C/metabolism","Research Support, Non-U.S. Gov't","Substances:","Peptides","Pulmonary Surfactant-Associated Protein C","SFTPC protein, human","Secondary Source ID:","OMIM/178620"]
["methods we propose are capable of deducing and quantifying functional interactions within and across cellular gene, signaling and metabolic networks. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.dbi.tju.edu/bioinformatics2004.pdf Publication Types: Evaluation Studies ","125: Bioinformatics. 2004 Aug 12;20(12):1877-86. Epub 2004 Mar 22.","yes","n","expression, protein and metabolite data.","PMID: 15037511 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Cell Physiology*","Computer Graphics","Computer Simulation","Gene Expression Profiling/methods*","Gene Expression Regulation/physiology*","Models, Biological*","Multienzyme Complexes/metabolism","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Signal Transduction/physiology*","Time Factors","User-Computer Interface*","Substances:","Multienzyme Complexes","Grant Support:","AA08714/AA/NIAAA","GM59570/GM/NIGMS","P20-GM64375/GM/NIGMS"]
["e use of a variety of score matrices for different subclasses of glycans due to their complexity is also discussed. CONTACT: mami@kuicr.kyoto-u.ac.jp SUPPLEMENTARY INFORMATION: The glycan score matrix can be downloaded from http://kanehisa.kuicr.kyoto-u.ac.jp/Paper/kcam/glycanMatrix0.1.txt. Publicat","13: Bioinformatics. 2005 Apr 15;21(8):1457-63. Epub 2004 Dec 7.","yes","n","Aoki KF, Mamitsuka H, Akutsu T, Kanehisa M.","PMID: 15585530 [PubMed - indexed for MEDLINE]"]
["ion, standardized exercise testing and training programs appear to be underused in German CF centers, despite a high degree of interest in the topic. Supplementary material for this article can be found on the Pediatric Pulmonology website (http//www.interscience.wiley.com/jpages/8755-6863/suppmat).","131: Pediatr Pulmonol. 2004 Apr;37(4):351-5.","yes","n","Barker M, Hebestreit A, Gruber W, Hebestreit H.","PMID: 15022132 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Attitude of Health Personnel","Child","Cystic Fibrosis/physiopathology*","Cystic Fibrosis/rehabilitation*","Exercise Test/methods","Exercise Test/statistics & numerical data*","Germany","Health Services Needs and Demand","Health Surveys","Humans","Physical Education and Training/methods","Physical Education and Training/statistics & numerical data*","Questionnaires","Research Support, Non-U.S. Gov't"]
["matic change in the gene expression program during the transition of fetal liver progenitor cells from an undifferentiated to a differentiated state. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me","133: Hepatology. 2004 Mar;39(3):617-27.","yes","n","development using complementary DNA microarrays.","PMID: 14999680 [PubMed - indexed for MEDLINE]","MeSH Terms:","Aging/genetics*","Animals","Animals, Newborn/growth & development","Animals, Newborn/physiology","Embryonic and Fetal Development","Fetus/physiology","Gene Expression*","Liver/embryology*","Liver/physiology*","Oligonucleotide Array Sequence Analysis","Rats*","Research Support, U.S. Gov't, P.H.S.","Stem Cells/physiology*","Grant Support:","P30 DK 41296/DK/NIDDK","P30 DK 56496/DK/NIDDK","R01 DK 17609/DK/NIDDK","R01 DK 59321/DK/NIDDK","U24 DK 058768/DK/NIDDK"]
["r these loci. However, the differences between the two populations suggest that population specific locus heterogeneity exists. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","137: Am J Med Genet A. 2004 Mar 1;125(2):135-44.","yes","n","Antioquia-Colombia and Ohio.","PMID: 14981713 [PubMed - indexed for MEDLINE]","MeSH Terms:","Cleft Lip/genetics*","Cleft Lip/pathology","Cleft Palate/genetics*","Cleft Palate/pathology","Colombia","Comparative Study","Family Health","Female","Genes, Dominant","Genes, Recessive","Genetic Markers*","Genetic Predisposition to Disease/genetics*","Genotype","Humans","Linkage (Genetics)/genetics*","Lod Score","Male","Microsatellite Repeats","Ohio","Pedigree","Prevalence","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Substances:","Genetic Markers","Grant Support:","P60 DE13076/DE/NIDCR","R01 DE 14677/DE/NIDCR"]
["ted in cancer. Our results have provided further insight into the roles of TERT and ATM by identifying genes likely to be involved in their function. Supplementary material for this article can be found on the Genes, Chromosomes and Cancer website at http://www.interscience.wiley.com/jpages/1045-225","138: Genes Chromosomes Cancer. 2004 Apr;39(4):298-310.","yes","n","Baross A, Schertzer M, Zuyderduyn SD, Jones SJ, Marra MA, Lansdorp PM.","PMID: 14978791 [PubMed - indexed for MEDLINE]","MeSH Terms:","Ataxia Telangiectasia/genetics","Cell Cycle Proteins","Cells, Cultured","Child","Comparative Study","DNA-Binding Proteins","Expressed Sequence Tags","Fibroblasts/chemistry*","Fibroblasts/metabolism*","Fibroblasts/pathology","Gene Expression Profiling/methods*","Gene Expression Regulation/genetics*","Gene Expression Regulation/physiology","Gene Library","Genes/genetics","Genes/physiology","Humans","Infant, Newborn","Male","Protein-Serine-Threonine Kinases/genetics*","Research Support, Non-U.S. Gov't","Retroviridae/genetics","Skin/cytology","Skin/pathology","Telomerase/genetics*","Telomere/enzymology","Telomere/genetics","Transduction, Genetic/methods","Tumor Suppressor Proteins","Substances:","Cell Cycle Proteins","DNA-Binding Proteins","Tumor Suppressor Proteins","Protein-Serine-Threonine Kinases","ataxia telangiectasia mutated protein","Telomerase","telomerase reverse transcriptase"]
["downloaded from http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN. It underlies the GPL version 2. CONTACT: m.futschik@biologie.hu-berlin.de SUPPLEMENTARY INFORMATION: Further information about the methods used in the OLIN software package can be found at http://itb.biologie.hu-berlin.de/~f","14: Bioinformatics. 2005 Apr 15;21(8):1724-6. Epub 2004 Dec 7.","yes","n","microarray data.","PMID: 15585527 [PubMed - indexed for MEDLINE]"]
[" it possible to target most of the known HLA alleles with known specificities using only a few peptides, and may be used in construction of vaccines. Supplementary material is available at http://www.cbs.dtu.dk/researchgroups/immunology/supertypes.html. MeSH Terms: Amino Acid Motifs Cluster Analysis","141: Immunogenetics. 2004 Mar;55(12):797-810. Epub 2004 Feb 13.","yes","n","matrices.","PMID: 14963618 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Motifs","Cluster Analysis","Histocompatibility Antigens Class I/classification*","Histocompatibility Antigens Class II/classification*","Humans","Markov Chains","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Substances:","Histocompatibility Antigens Class I","Histocompatibility Antigens Class II","Grant Support:","AI49213-02/AI/NIAID"]
["Gene Ontology database. AVAILABILITY: VennMaster is platform-independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/ven","15: Bioinformatics. 2005 Apr 15;21(8):1592-5. Epub 2004 Nov 30.","yes","n","relations.","PMID: 15572472 [PubMed - indexed for MEDLINE]"]
[" two established recombination detection methods: Recpars and the DSS (difference of sum of squares) method. AVAILABILITY: Software, data and further supplementary material are available at the following website: http://www.bioss.sari.ac.uk/~dirk/Supplements/ Publication Types: Evaluation Studies Me","15: Bioinformatics. 2005 May 1;21(9):1797-806. Epub 2004 Nov 30.","yes","n","measure.","PMID: 15572473 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Cluster Analysis","DNA Mutational Analysis/methods","Evolution, Molecular","Models, Genetic*","Models, Statistical","Pattern Recognition, Automated/methods*","Phylogeny","Recombination, Genetic/genetics*","Research Support, Non-U.S. Gov't","Sequence Alignment/methods*","Sequence Analysis, DNA/methods*","Variation (Genetics)/genetics*"]
["ich may be used as candidate markers for diagnosing the early onset of HCC in high-risk populations and may guide new strategies for chemoprevention. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me","150: Hepatology. 2004 Feb;39(2):518-27.","yes","n","cirrhosis.","PMID: 14768006 [PubMed - indexed for MEDLINE]","MeSH Terms:","Antigens, Neoplasm/genetics","Carcinoma, Hepatocellular/epidemiology","Carcinoma, Hepatocellular/genetics*","Cell Adhesion Molecules/genetics","Gene Expression Regulation, Neoplastic","Humans","Liver Cirrhosis/epidemiology","Liver Cirrhosis/etiology","Liver Cirrhosis/genetics*","Liver Neoplasms/epidemiology","Liver Neoplasms/genetics*","Oligonucleotide Array Sequence Analysis*","Research Support, U.S. Gov't, P.H.S.","Risk Factors","Substances:","Antigens, Neoplasm","Cell Adhesion Molecules","tumor-associated antigen GA733"]
[" mRNA levels, controlling most, if not all, intracellular events from early signaling to the final secretion of proteins involved in innate immunity. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me","151: Hepatology. 2004 Feb;39(2):353-64.","yes","n","coverage of the human liver transcriptome.","PMID: 14767988 [PubMed - indexed for MEDLINE]","MeSH Terms:","Acute Disease","Adult","Aged","Aged, 80 and over","Cytokines/genetics","Databases, Genetic","Female","Gene Expression","Genetic Markers","Hepatitis/genetics*","Hepatitis/immunology","Hepatitis/physiopathology","Hepatocytes/immunology","Hepatocytes/physiology","Humans","Male","Middle Aged","Oligonucleotide Array Sequence Analysis/methods*","Promoter Regions (Genetics)","RNA, Messenger/analysis","Research Support, Non-U.S. Gov't","Signal Transduction/genetics","Substances:","Cytokines","Genetic Markers","RNA, Messenger"]
[" to a better understanding of the clinical evolution of familial adenomatous polyposis and to finding of new prophylactic and therapeutic approaches. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","153: Int J Cancer. 2004 Mar 20;109(2):200-6.","Yes","n","De Giovanni C, Landuzzi L, Nicoletti G, Astolfi A, Croci S, Micaroni M, Nanni P,","PMID: 14750170 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adenomatous Polyposis Coli/genetics*","Adenomatous Polyposis Coli/metabolism","Adenomatous Polyposis Coli/pathology","Adenomatous Polyposis Coli Protein/metabolism","Animals","Cell Differentiation","Cytoskeletal Proteins/genetics","Cytoskeletal Proteins/metabolism","Female","Gene Expression Profiling","Genes, APC*","Heterozygote*","Intestinal Neoplasms/genetics*","Intestinal Neoplasms/metabolism","Intestinal Neoplasms/pathology","Mice","Mice, Inbred C57BL","Mice, Nude","Oligonucleotide Array Sequence Analysis","Proto-Oncogene Proteins/metabolism","RNA, Neoplasm/metabolism","Research Support, Non-U.S. Gov't","Transcription Factors/genetics","Transcription Factors/metabolism","Tumor Cells, Cultured","Wnt Proteins","Zebrafish Proteins*","Substances:","Adenomatous Polyposis Coli Protein","Cytoskeletal Proteins","Proto-Oncogene Proteins","RNA, Neoplasm","Transcription Factors","Wnt Proteins","Zebrafish Proteins","wnt8b protein, zebrafish"]
["cuss these issues and some methodological approaches that can detect multilocus effects, using hypertension as a model disease. This article contains supplementary material, which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html. Copyrig","154: Bioessays. 2004 Feb;26(2):170-9.","yes","n","equal or why do so many human studies fail to replicate animal findings?","PMID: 14745835 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Disease*","Disease Models, Animal*","Epistasis, Genetic","Genetic Predisposition to Disease","Humans","Hypertension/genetics","Hypertension/physiopathology","Linkage (Genetics)","Phenotype"]
["est possible mechanisms of action of the core elements in the promoters with multiple transcription start sites. CONTACT: ioschikhes-1@medctr.osu.edu SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bmi.osu.edu/~ilya/synergy/Gershenzon_SuppMat-R.pdf. Publication Types: Eva","16: Bioinformatics. 2005 Apr 15;21(8):1295-300. Epub 2004 Nov 30.","yes","n","analysis.","PMID: 15572469 [PubMed - indexed for MEDLINE]"]
[" membrane, trachea and mouth parts during insect development, and possibly for other roles including chitin synthesis. AVAILABILITY: Perl program and supplementary material are available at http://www.ksu.edu/bioinformatics/supplementary.htm Publication Types: Evaluation Studies Validation Studies M","162: Bioinformatics. 2004 Jan 22;20(2):161-9.","yes","n","melanogaster genome.","PMID: 14734306 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Animals","Chitinase/chemistry*","Chitinase/classification","Chitinase/genetics*","Databases, Protein","Drosophila melanogaster/enzymology*","Drosophila melanogaster/genetics*","Gene Expression Profiling/methods","Genome*","Models, Molecular*","Molecular Sequence Data","Phylogeny","Protein Conformation","Protein Structure, Tertiary","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Sequence Alignment/methods*","Sequence Analysis, Protein/methods*","Sequence Homology, Amino Acid","Structure-Activity Relationship","Substances:","Chitinase","Grant Support:","P20 RR16475/RR/NCRR"]
["d that the salivary proteins are less conserved than the housekeeping proteins, and therefore are changing at a faster evolutionary rate. Tabular and supplementary material containing the cDNA sequences and annotations are available at http://www.ncbi.nlm.nih.gov/projects/Mosquito/A_darlingi_sialome","163: Insect Mol Biol. 2004 Feb;13(1):73-88.","yes","n","Calvo E, Andersen J, Francischetti IM, deL  Capurro M, deBianchi AG, James AA,","PMID: 14728669 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Anopheles/genetics*","Brazil","Comparative Study","DNA, Complementary/classification*","Databases, Genetic","Electrophoresis, Polyacrylamide Gel","Gene Library*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Saliva/chemistry*","Salivary Glands/secretion*","Sequence Analysis, DNA","Substances:","DNA, Complementary","Grant Support:","AI29746/AI/NIAID"]
["data set on acute lymphocytic leukemia. AVAILABILITY: The R-package MACAT can be obtained from http://www.compdiag.molgen.mpg.de/software/macat.shtml SUPPLEMENTARY INFORMATION: http://www.compdiag.molgen.mpg.de/software/macat.shtml. Publication Types: Evaluation Studies PMID: 15572464 [PubMed - inde","17: Bioinformatics. 2005 May 1;21(9):2112-3. Epub 2004 Nov 30.","yes","n","Toedling J, Schmeier S, Heinig M, Georgi B, Roepcke S.","PMID: 15572464 [PubMed - indexed for MEDLINE]"]
["ults demonstrate that mammalian viral genome types differ in their amino acid preference. AVAILABILITY: The tools used to format and analyze data and supplementary material are available at http://www.cse.sc.edu/~rose/aminoPreference/index.html CONTACT: rose@cse.sc.edu. Publication Types: Evaluation","18: Bioinformatics. 2005 Apr 15;21(8):1349-57. Epub 2004 Nov 30.","yes","n","Rose JR, Turkett WH Jr, Oroian IC, Laegreid WW, Keele J.","PMID: 15572467 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Amino Acid Sequence","Animals","Base Sequence","Chromosome Mapping/methods*","Comparative Study","DNA, Viral/genetics*","Genome, Viral*","Mammals","Models, Genetic","Molecular Sequence Data","Research Support, U.S. Gov't, Non-P.H.S.","Sequence Alignment/methods*","Sequence Analysis, DNA/methods*","Species Specificity","Statistics","Viral Proteins/genetics*","Substances:","DNA, Viral","Viral Proteins"]
["ILABILITY: The software is publicly available under the GNU general public licence from http://www.cs.may.ie/distributed CONTACT: tom.naughton@may.ie SUPPLEMENTARY INFORMATION: Full documentation and a user manual is available from http://www.cs.may.ie/distributed. Publication Types: Evaluation Stud","18: Bioinformatics. 2005 Apr 15;21(8):1705-6. Epub 2004 Nov 25.","yes","n","Keane TM, Naughton TJ.","PMID: 15564297 [PubMed - indexed for MEDLINE]"]
["f signal pathway databases. AVAILABILITY: The pipeline software components are freely available on request to the authors. CONTACT: dstates@umich.edu SUPPLEMENTARY INFORMATION: http://stateslab.bioinformatics.med.umich.edu/software.html. PMID: 15564295 [PubMed - indexed for MEDLINE]","19: Bioinformatics. 2005 Apr 15;21(8):1653-8. Epub 2004 Nov 25.","yes","n","statistical methods with partial and full parse for knowledge extraction.","PMID: 15564295 [PubMed - indexed for MEDLINE]"]
["mes are 30-40% faster for M-ZDOCK. AVAILABILITY: M-ZDOCK is freely available to academic users at http://zlab.bu.edu/m-zdock/ CONTACT: zhiping@bu.edu SUPPLEMENTARY INFORMATION: http://zlab.bu.edu/m-zdock. Publication Types: Evaluation Studies PMID: 15613396 [PubMed - indexed for MEDLINE]","2: Bioinformatics. 2005 Apr 15;21(8):1472-8. Epub 2004 Dec 21.","yes","n","Pierce B, Tong W, Weng Z.","PMID: 15613396 [PubMed - indexed for MEDLINE]"]
[" were written in PERL and are freely available at http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html CONTACT: nelsonrt@iastate.edu SUPPLEMENTARY INFORMATION: Figures and dataset can be obtained from: http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html. Publicatio","20: Bioinformatics. 2005 Mar 1;21(5):691-3. Epub 2004 Nov 5.","yes","n","Nelson RT, Grant D, Shoemaker RC.","PMID: 15531616 [PubMed - indexed for MEDLINE]"]
[" provide a coherent framework for functional genomic datamining. AVAILABILITY: Free availability over the Internet. CONTACT: f.c.p.holstege@med.uu.nl SUPPLEMENTARY INFORMATION: http://www.genomics.med.uu.nl/pub/pk/comb_gen_network. Publication Types: Evaluation Studies Validation Studies PMID: 15531","21: Bioinformatics. 2005 Apr 15;21(8):1644-52. Epub 2004 Nov 5.","yes","n","high-throughput data.","PMID: 15531615 [PubMed - indexed for MEDLINE]"]
["ic interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/. MeSH Terms: Adaptation, Physiolo","22: Arch Microbiol. 2005 Jan;183(1):27-36. Epub 2004 Nov 13.","Yes","n","strain EbN1.","PMID: 15551059 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adaptation, Physiological/genetics","Aerobiosis","Anaerobiosis","Azoarcus/genetics","Bacterial Proteins/genetics","Betaproteobacteria/classification","Betaproteobacteria/genetics*","Betaproteobacteria/metabolism*","Biodegradation","Chromosomes, Bacterial/genetics","DNA, Bacterial/chemistry","Evolution, Molecular","Gene Expression Regulation, Bacterial","Gene Transfer, Horizontal","Genes, Bacterial","Genome, Bacterial*","Hydrocarbons, Aromatic/metabolism*","Interspersed Repetitive Sequences","Molecular Sequence Data","Multigene Family","Nitrogen Fixation/genetics","Open Reading Frames","Plasmids/genetics","Research Support, Non-U.S. Gov't","Sequence Analysis, DNA*","Sequence Homology","Substances:","Bacterial Proteins","DNA, Bacterial","Hydrocarbons, Aromatic","Plasmids","Secondary Source ID:","GENBANK/CR555306","GENBANK/CR555307","GENBANK/CR555308"]
["ring of microarray signals. AVAILABILITY: LabArray is available at http://www.eng.nus.edu.sg/civil/Labarray/labarray.htm CONTACT: cveliuwt@nus.edu.sg SUPPLEMENTARY INFORMATION: Screenshots and instructions for use are available at the above website. Publication Types: Evaluation Studies PMID: 155095","22: Bioinformatics. 2005 Mar 1;21(5):689-90. Epub 2004 Oct 27.","yes","n","Ng JK, Liu WT.","PMID: 15509598 [PubMed - indexed for MEDLINE]"]
["quence data, with the emphasis on studies of rates and patterns of sequence evolution. AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org. PMID: 15509596 [PubMed - indexed for MEDLINE]","23: Bioinformatics. 2005 Mar 1;21(5):676-9. Epub 2004 Oct 27.","yes","n","Pond SL, Frost SD, Muse SV.","PMID: 15509596 [PubMed - indexed for MEDLINE]"]
["www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. CONTACT: psort-mail@sfu.ca, brinkman@sfu.ca SUPPLEMENTARY INFORMATION: http://www.psort.org/psortb/supplementaryinfo.html. Publication Types: Evaluation Studies PMID: 15501914 [PubMed - indexed ","24: Bioinformatics. 2005 Mar 1;21(5):617-23. Epub 2004 Oct 22.","yes","n","and insights gained from comparative proteome analysis.","PMID: 15501914 [PubMed - indexed for MEDLINE]"]
["vel follow-up analysis. AVAILABILITY: The R package arrayMagic is available with BSD license at http://www.bioconductor.org CONTACT: a.buness@dkfz.de SUPPLEMENTARY INFORMATION: The package contains documentation in the form of manual pages and a vignette with a guided tour of a typical workflow. PMI","25: Bioinformatics. 2005 Feb 15;21(4):554-6. Epub 2004 Sep 28.","yes","n","Buness A, Huber W, Steiner K, Sultmann H, Poustka A.","PMID: 15454413 [PubMed - indexed for MEDLINE]"]
["automated assignment program. AVAILABILITY: APART is available from http://sir.lanl.gov/NMR/APART.htm CONTACT: npawley@lanl.gov; rmichalczyk@lanl.gov SUPPLEMENTARY INFORMATION: Manual pages with installation instructions, procedures and screen shots can also be found at http://sir.lanl.gov/NMR/APART","26: Bioinformatics. 2005 Mar 1;21(5):680-2. Epub 2004 Sep 23.","yes","n","Pawley NH, Gans JD, Michalczyk R.","PMID: 15388520 [PubMed - indexed for MEDLINE]"]
["blically available at the GeneNote website, http://genecards.weizmann.ac.il/genenote/ and, GEO accession GSE803. CONTACT: doron.lancet@weizmann.ac.il SUPPLEMENTARY INFORMATION: Four tables available at the above site. Publication Types: Evaluation Studies PMID: 15388519 [PubMed - indexed for MEDLINE","27: Bioinformatics. 2005 Mar 1;21(5):650-9. Epub 2004 Sep 23.","yes","n","relationships in human tissue specification.","PMID: 15388519 [PubMed - indexed for MEDLINE]"]
["atabase of Interacting Proteins. The validity of our approach is successfully tested against other available techniques. CONTACT: leone@isiosf.isi.it SUPPLEMENTARY INFORMATION: http://isiosf.isi.it/~pagnani Publication Types: Evaluation Studies Validation Studies PMID: 15377508 [PubMed - indexed for","28: Bioinformatics. 2005 Jan 15;21(2):239-47. Epub 2004 Sep 17.","yes","n","Leone M, Pagnani A.","PMID: 15377508 [PubMed - indexed for MEDLINE]"]
["ntal plate and paraxial mesoderm. Deducing the mechanical influences on cell behavior is critical, if we are to understand vertebral axis patterning. Supplementary material for this article is available online at http://www.mrw.interscience.wiley.com/suppmat/1542-975X/suppmat/72/v72.266.html. (c) 20","28: Birth Defects Res C Embryo Today. 2004 Sep;72(3):267-76.","yes","n","vertebral axis patterning.","PMID: 15495182 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Body Patterning/physiology*","Cell Movement/physiology*","Cell Physiology*","Chick Embryo","Extracellular Matrix/physiology*","Microscopy, Interference/methods*","Photomicrography/methods*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Grant Support:","R01 HL68855/HL/NHLBI","R01 HL73700-03/HL/NHLBI"]
["e drawing methods. AVAILABILITY: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html) CONTACT: darren@science.uct.ac.za SUPPLEMENTARY INFORMATION: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded fro","29: Bioinformatics. 2005 Jan 15;21(2):260-2. Epub 2004 Sep 17.","yes","n","Martin DP, Williamson C, Posada D.","PMID: 15377507 [PubMed - indexed for MEDLINE]"]
["retin (through cAMP) and adrenergic receptor agonist activation (through Ca(2+)/PKC) induces maximal ductal bicarbonate secretion in liver diseases. (Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me","29: Hepatology. 2004 Nov;40(5):1116-27.","Yes","n","Ca(2+)- and PKC-dependent stimulation of cAMP.","PMID: 15486932 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adrenergic alpha-Agonists/pharmacology","Animals","Bicarbonates/metabolism","Bile/secretion","Bile Ducts/cytology","Bile Ducts/metabolism*","Bile Ducts/secretion","Bile Ducts, Intrahepatic/metabolism","Biological Transport","Calcium/physiology*","Cell Membrane","Cyclic AMP/metabolism*","Cyclic AMP-Dependent Protein Kinases/metabolism","Drug Synergism","Isoenzymes/metabolism","Ligation","Male","Phenylephrine/pharmacology","Protein Isoforms/metabolism","Protein Kinase C/metabolism","Protein Kinase C/physiology*","Rats","Rats, Inbred F344","Receptors, Adrenergic, alpha-1/agonists*","Receptors, Adrenergic, alpha-1/metabolism","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Secretin/pharmacology","Up-Regulation","Substances:","Adrenergic alpha-Agonists","Bicarbonates","Isoenzymes","Protein Isoforms","Receptors, Adrenergic, alpha-1","Secretin","Phenylephrine","Cyclic AMP","Calcium","Cyclic AMP-Dependent Protein Kinases","Protein Kinase C","Grant Support:","DK 54208/DK/NIDDK","DK58411/DK/NIDDK"]
["ee MIAME compliance. AVAILABILITY: The application is available from the author at http://www.ansorge-group.embl.de/bloader CONTACT: schwager@embl.de SUPPLEMENTARY INFORMATION: For more details on BLoader visit the above web page. PMID: 15613394 [PubMed - indexed for MEDLINE]","3: Bioinformatics. 2005 Apr 15;21(8):1727-9. Epub 2004 Dec 21.","yes","n","Schwager C, Blake J.","PMID: 15613394 [PubMed - indexed for MEDLINE]"]
["scribed below. A PhenomicDB implementation differing in some technical details has been set up for the public at Metalife AG http://www.phenomicDB.de SUPPLEMENTARY INFORMATION: database model, semantic mapping table. PMID: 15374875 [PubMed - indexed for MEDLINE]","30: Bioinformatics. 2005 Feb 1;21(3):418-20. Epub 2004 Sep 16.","yes","n","phenomics.","PMID: 15374875 [PubMed - indexed for MEDLINE]"]
["intosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Clann has been written in the C programming language. Source code is available on request. PMID: 15374874 [PubMed - indexed","31: Bioinformatics. 2005 Feb 1;21(3):390-2. Epub 2004 Sep 16.","yes","n","Creevey CJ, McInerney JO.","PMID: 15374874 [PubMed - indexed for MEDLINE]"]
["LITY: The R package is freely available at http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html CONTACT: delmar@inapg.inra.fr SUPPLEMENTARY INFORMATION: http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html. Publication Types: Evaluation Studies PMID: 1","32: Bioinformatics. 2005 Feb 15;21(4):502-8. Epub 2004 Sep 16.","yes","n","replicated gene expression data.","PMID: 15374871 [PubMed - indexed for MEDLINE]"]
["ion on time-lagged co-regulation between genes/gene clusters. AVAILABILITY: The software is available upon request. CONTACT: jiliping@comp.nus.edu.sg SUPPLEMENTARY INFORMATION: Supplementary tables and figures for this paper can be found at http://www.comp.nus.edu.sg/~jiliping/p2.htm. Publication Ty","33: Bioinformatics. 2005 Feb 15;21(4):509-16. Epub 2004 Sep 16.","yes","n","Ji L, Tan KL.","PMID: 15374868 [PubMed - indexed for MEDLINE]"]
["ion but also on its own mechanism of regulation: genes in the same altered region responded very differently to the gain or loss of genetic material. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience.wiley.com/jpages/1045-22","33: Genes Chromosomes Cancer. 2004 Dec;41(4):353-65.","yes","n","material detected by comparative genomic hybridization.","PMID: 15382261 [PubMed - indexed for MEDLINE]","MeSH Terms:","Chromosomes, Human, Pair 13/genetics*","Chromosomes, Human, Pair 19/genetics*","Chromosomes, Human, Pair 6/genetics*","Expressed Sequence Tags","Gene Dosage*","Gene Expression Profiling","Humans","In Situ Hybridization, Fluorescence","Lymphoma, T-Cell/genetics*","Nucleic Acid Hybridization","Oligonucleotide Array Sequence Analysis","Research Support, Non-U.S. Gov't"]
["n sequences. AVAILABILITY: The program is freely available for non-profit organizations, upon request to the authors. CONTACT: giorgio.valle@unipd.it SUPPLEMENTARY INFORMATION: The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analys","34: Bioinformatics. 2005 Mar 1;21(5):582-8. Epub 2004 Sep 16.","yes","n","whole genomes.","PMID: 15374857 [PubMed - indexed for MEDLINE]"]
["s against random patterns. Wet-experimentally discovered motifs reported in the literature were also used to confirm the effectiveness of our method. SUPPLEMENTARY INFORMATION: http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs. Publication Types: Evaluation Studies Validation Studies PMID: 15374856 [P","35: Bioinformatics. 2005 Feb 1;21(3):314-24. Epub 2004 Sep 16.","yes","n","protein interaction datasets.","PMID: 15374856 [PubMed - indexed for MEDLINE]"]
["nsional functional genomics datasets, VizRank can systematically find relevant biological patterns. AVAILABILITY: http://www.ailab.si/supp/bi-vizrank SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-vizrank. PMID: 15358614 [PubMed - indexed for MEDLINE]","36: Bioinformatics. 2005 Feb 1;21(3):413-4. Epub 2004 Sep 9.","Yes","n","learning.","PMID: 15358614 [PubMed - indexed for MEDLINE]"]
[". These mechanisms are key for clonal expansion and for controlling the long term behavior (e.g. programmed cell death) of these cells. AVAILABILITY: Supplementary data is available at http://public.kgi.edu/wild/index.htm and Matlab source code for variational Bayesian learning of SSMs is available ","37: Bioinformatics. 2005 Feb 1;21(3):349-56. Epub 2004 Sep 7.","yes","n","factors.","PMID: 15353451 [PubMed - indexed for MEDLINE]"]
["AILABILITY: A CRC card template, XML representation and XML schema are freely available at http://people.musc.edu/~zhengw/CRCCard/CRC_Card_Index.html SUPPLEMENTARY INFORMATION: Supplemental Figures 1-4. PMID: 15353449 [PubMed - indexed for MEDLINE]","38: Bioinformatics. 2005 Feb 1;21(3):415-7. Epub 2004 Sep 7.","yes","n","Shegogue D, Zheng WJ.","PMID: 15353449 [PubMed - indexed for MEDLINE]"]
[" downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset. SUPPLEMENTARY INFORMATION: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu. PMID: 1535344","39: Bioinformatics. 2005 Feb 1;21(3):402-4. Epub 2004 Sep 7.","yes","n","Price EW, Carbone I.","PMID: 15353448 [PubMed - indexed for MEDLINE]"]
["d improve metabolomics by multidisciplinary cooperation. AVAILABILITY: http://csbdb.mpimp-golm.mpg.de/gmd.html CONTACT: Steinhauser@mpimp-golm.mpg.de SUPPLEMENTARY INFORMATION: http://csbdb.mpimp-golm.mpg.de/ PMID: 15613389 [PubMed - indexed for MEDLINE]","4: Bioinformatics. 2005 Apr 15;21(8):1635-8. Epub 2004 Dec 21.","yes","n","Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmuller E, Dormann P,","PMID: 15613389 [PubMed - indexed for MEDLINE]"]
["of uncharacterized proteins, or relationships among properties. AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl. Publication Types: Evaluation Studies PMID: 1534757","40: Bioinformatics. 2005 Feb 1;21(3):293-306. Epub 2004 Sep 3.","yes","n","for microbiology, genome annotation and comparative genomics.","PMID: 15347579 [PubMed - indexed for MEDLINE]"]
["D scores, NPL scores, P-values and other parameters. AVAILABILITY: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.ht m SUPPLEMENTARY INFORMATION: Supplementary information is available on the website. PMID: 15347576 [PubMed - indexed for MEDLINE]","41: Bioinformatics. 2005 Feb 1;21(3):405-7. Epub 2004 Sep 3.","yes","n","analyses.","PMID: 15347576 [PubMed - indexed for MEDLINE]"]
["he reported patients appear to have the same condition as the family reported by Kantaputra [2002: Am J Med Genet 111:420-428]. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","42: Am J Med Genet A. 2004 Oct 1;130(2):181-90.","yes","n","Am J Med Genet A. 2005 May 15;135(1):114; author reply 115.","PMID: 15372530 [PubMed - indexed for MEDLINE]","MeSH Terms:","Abnormalities, Multiple/genetics","Abnormalities, Multiple/pathology*","Child","Dwarfism/pathology*","Family Health","Female","Humans","Male","Microcephaly/pathology","Osteochondrodysplasias/pathology","Pedigree","Research Support, Non-U.S. Gov't","Skin Abnormalities*","Syndrome","Tooth Abnormalities*"]
["prove useful for detecting novel overlapping genes--especially short coding ORFs in viruses. AVAILABILITY: Programs may be obtained from the authors. SUPPLEMENTARY INFORMATION: http://biochem.otago.ac.nz/double.html. Publication Types: Evaluation Studies PMID: 15347574 [PubMed - indexed for MEDLINE]","42: Bioinformatics. 2005 Feb 1;21(3):282-92. Epub 2004 Sep 3.","yes","n","Firth AE, Brown CM.","PMID: 15347574 [PubMed - indexed for MEDLINE]"]
["plain the phenotype observed in the family. Thus, the exon skipping resulted from a nonsense-associated altered splicing (NAS). This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","43: Am J Med Genet A. 2004 Oct 1;130(2):160-4.","yes","n","Stickler syndrome.","PMID: 15372529 [PubMed - indexed for MEDLINE]","MeSH Terms:","Abnormalities, Multiple/genetics*","Abnormalities, Multiple/pathology","Base Sequence","Child, Preschool","Codon, Nonsense/genetics*","Collagen Type XI/genetics*","DNA Mutational Analysis","Exons/genetics*","Face/abnormalities","Family Health","Female","Hearing Loss, Sensorineural/pathology","Humans","Knee Joint/pathology","Male","Molecular Sequence Data","Pedigree","Proteins/genetics","Research Support, Non-U.S. Gov't","Syndrome","Substances:","COL11A2 protein, human","Codon, Nonsense","Collagen Type XI","Proteins"]
["or factorial experiment design and template loading methods to ease the submission process for large experiments. AVAILABILITY: http://barleybase.org SUPPLEMENTARY INFORMATION: BarleyExpress Users Manual. PMID: 15347571 [PubMed - indexed for MEDLINE]","43: Bioinformatics. 2005 Feb 1;21(3):399-401. Epub 2004 Sep 3.","yes","n","annotations.","PMID: 15347571 [PubMed - indexed for MEDLINE]"]
["COL6A2, and/or COL18A genes located on the distal portion of chromosome 21q, which are lost when the ring chromosome is formed. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","44: Am J Med Genet A. 2004 Oct 1;130(2):191-5.","yes","n","Rope AF, Hinton RB, Spicer RL, Blough-Pfau R, Saal HM.","PMID: 15372526 [PubMed - indexed for MEDLINE]","MeSH Terms:","Abnormalities, Multiple/genetics*","Abnormalities, Multiple/pathology","Aorta/abnormalities*","Chromosomes, Human, Pair 21/genetics*","Humans","In Situ Hybridization, Fluorescence","Infant","Karyotyping","Male","Ring Chromosomes*","Syndrome"]
["pare and query libraries of frequency matrices for TFBSs. AVAILABILITY: Software is available to use over the Web at http://rulai.cshl.edu/MatCompare SUPPLEMENTARY INFORMATION: Database and clustering statistics, matrix families and representatives are available at http://rulai.cshl.edu/MatCompare/S","44: Bioinformatics. 2005 Feb 1;21(3):307-13. Epub 2004 Aug 19.","yes","n","sites.","PMID: 15319260 [PubMed - indexed for MEDLINE]"]
["ns; (3) PS affects more males than females; and 4) the published diagnostic criteria are useful for clinical care and research. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","45: Am J Med Genet A. 2004 Oct 1;130(2):111-22.","yes","n","criteria to published cases.","PMID: 15372514 [PubMed - indexed for MEDLINE]","MeSH Terms:","Diagnosis, Differential","Female","Humans","Kidney Diseases/complications","Male","Proteus Syndrome/complications","Proteus Syndrome/diagnosis*","Urologic Diseases/complications"]
[" simulation package Dizzy. It is available for download at http://labs.systemsbiology.net/bolouri/software/Dizzy/ CONTACT: dorrell@systemsbiology.org SUPPLEMENTARY INFORMATION: A conceptual model of the regulatory part of the galactose utilization pathway in yeast, used as an example in the paper, i","45: Bioinformatics. 2005 Jan 15;21(2):208-17. Epub 2004 Aug 19.","yes","n","Orrell D, Ramsey S, de Atauri P, Bolouri H.","PMID: 15319259 [PubMed - indexed for MEDLINE]"]
[" phenotypes of Cx45(-/-) mice. Our results indicate that Cx45 is an essential connexin for coordinated conduction through early cardiac myocytes. The Supplementary Material referred to in this article can be found at the Anatomical Record website (http://www.interscience.wiley.com/jpages/0003-276X/s","46: Anat Rec A Discov Mol Cell Evol Biol. 2004 Oct;280(2):973-9.","yes","n","stem cell-derived cardiac myocytes.","PMID: 15372487 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Calcium/metabolism","Cell Differentiation","Comparative Study","Connexins/genetics","Connexins/physiology*","Electrophysiology","Gap Junctions/metabolism*","Heart Conduction System/metabolism*","Mice/embryology*","Myocytes, Cardiac/metabolism*","Myocytes, Cardiac/pathology","Phenotype","Research Support, Non-U.S. Gov't","Stem Cells/cytology*","Stem Cells/metabolism","Substances:","Connexins","connexin 45","Calcium"]
["ta flow and to customize their analyses by combining common data analysis tools to fit their needs. AVAILABILITY: http://www.ailab.si/supp/bi-visprog SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-visprog. PMID: 15308546 [PubMed - indexed for MEDLINE]","46: Bioinformatics. 2005 Feb 1;21(3):396-8. Epub 2004 Aug 12.","yes","n","Curk T, Demsar J, Xu Q, Leban G, Petrovic U, Bratko I, Shaulsky G, Zupan B.","PMID: 15308546 [PubMed - indexed for MEDLINE]"]
["f techniques to capture both morphological and functional data from the CPCS will further improve with continued interdisciplinary collaboration. The Supplementary Material referred to in this article can be found at the Anatomical Record website (http://www.interscience.wiley.com/jpages/0003-276X/s","47: Anat Rec A Discov Mol Cell Evol Biol. 2004 Oct;280(2):980-9.","yes","n","over the past 150 years: technologies to overcome the challenges.","PMID: 15372434 [PubMed - indexed for MEDLINE]","MeSH Terms:","Action Potentials","Animals","Embryo*/cytology","Embryo*/innervation","Embryo*/metabolism","Heart Conduction System/cytology","Heart Conduction System/embryology*","Heart Conduction System/physiology","History, 20th Century","History, 21st Century","Humans","Pacemaker, Artificial*/history"]
["easured over different subsets of patients. A possible biological explanation for these properties is discussed. CONTACT: eytan.domany@weizmann.ac.il SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/downloads/liate/ Publication Types: Evaluation Studies Validation Studie","47: Bioinformatics. 2005 Jan 15;21(2):171-8. Epub 2004 Aug 12.","yes","n","Ein-Dor L, Kela I, Getz G, Givol D, Domany E.","PMID: 15308542 [PubMed - indexed for MEDLINE]"]
[" oculo-palato-cerebral syndrome, supporting autosomal recessive inheritance, and a detailed comparison with the previous cases. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","48: Am J Med Genet A. 2004 Sep 15;130(1):92-5.","yes","n","inheritance.","PMID: 15368502 [PubMed - indexed for MEDLINE]","MeSH Terms:","Abnormalities, Multiple/genetics*","Cleft Palate/genetics*","Consanguinity*","Craniofacial Abnormalities/genetics","Dwarfism/genetics","Eye Abnormalities/genetics*","Female","Genes, Recessive","Humans","Infant","Inheritance Patterns*","Microcephaly/genetics*","Pedigree"]
["ve full control of their tools. AVAILABILITY: The described software tools are available from the Halmstad University website www.hh.se/staff/bioinf/ SUPPLEMENTARY INFORMATION: Details of the algorithms are described in supporting information available from the Halmstad University website www.hh.se/","48: Bioinformatics. 2004 Dec 12;20(18):3628-35. Epub 2004 Aug 5.","yes","n","mass fingerprinting.","PMID: 15297302 [PubMed - indexed for MEDLINE]"]
["e TXNIP gene, based on its intronic, exonic, and 5' UTR sequences, is not involved as a major contributor to the FCH phenotype. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299/","49: Am J Med Genet A. 2004 Sep 15;130(1):73-5.","yes","n","hyperlipidemia.","PMID: 15368498 [PubMed - indexed for MEDLINE]","MeSH Terms:","5' Untranslated Regions","Adult","Aged","Animals","Carrier Proteins/genetics*","Exons","Female","Humans","Hyperlipidemia, Familial Combined/genetics*","Introns","Male","Mice","Middle Aged","Netherlands","Phenotype","Sequence Analysis, DNA","Thioredoxin/genetics*","Substances:","5' Untranslated Regions","Carrier Proteins","TXNIP protein, human","Thioredoxin"]
["ork models fit the PPI networks. We show that the structure of PPI networks is better modeled by a geometric random graph than by a scale-free model. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://www.cs.utoronto.ca/~juris/data/data/ppiGRG04/ Publication Types: Evaluatio","49: Bioinformatics. 2004 Dec 12;20(18):3508-15. Epub 2004 Jul 29.","Yes","n","Przulj N, Corneil DG, Jurisica I.","PMID: 15284103 [PubMed - indexed for MEDLINE]"]
["atics.leeds.ac.uk/ppi_pred. The dataset of 180 proteins used in this study is also available via the same web site. CONTACT: westhead@bmb.leeds.ac.uk SUPPLEMENTARY INFORMATION: http://www.bioinformatics.leeds.ac.uk/ppi-pred/supp-material. Publication Types: Evaluation Studies PMID: 15613384 [PubMed ","5: Bioinformatics. 2005 Apr 15;21(8):1487-94. Epub 2004 Dec 21.","yes","n","machines approach.","PMID: 15613384 [PubMed - indexed for MEDLINE]"]
["lying zeroth, first, second and third order partial correlation analysis can be downloaded at: http://mendes.vbi.vt.edu/tiki-index.php?page=Software. SUPPLEMENTARY INFORMATION: Supplementary information can be found at: URL to be decided. Publication Types: Evaluation Studies PMID: 15284096 [PubMed ","50: Bioinformatics. 2004 Dec 12;20(18):3565-74. Epub 2004 Jul 29.","yes","n","coefficients.","PMID: 15284096 [PubMed - indexed for MEDLINE]"]
["mmatory stimuli and support the possibility that the phenomenon of jaundice of sepsis\" represents an adaptive physiological response to endotoxemia. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Co\"","50: Hepatology. 2004 Aug;40(2):424-33.","yes","n","rats.","PMID: 15368447 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Bilirubin/pharmacology","Bilirubin/physiology*","Carrageenan","Cell Line","Cytoprotection","Endotoxemia/blood","Endotoxins/pharmacology*","Enzyme Inhibitors/metabolism","Enzyme Inhibitors/pharmacology","Heme Oxygenase (Decyclizing)/metabolism","Heme Oxygenase-1","Hindlimb","Inflammation/chemically induced","Lipopolysaccharides/pharmacology","Male","Nitric Oxide/antagonists & inhibitors*","Nitric Oxide/biosynthesis","Nitric Oxide/blood","Nitric Oxide Synthase/antagonists & inhibitors*","Nitric Oxide Synthase/genetics","Nitric Oxide Synthase/metabolism","Nitric Oxide Synthase Type II","Oxidoreductases Acting on CH-CH Group Donors/metabolism","Prostaglandin-Endoperoxide Synthases/metabolism","Rats","Rats, Sprague-Dawley","Research Support, U.S. Gov't, P.H.S.","Transcription, Genetic/drug effects","Substances:","Endotoxins","Enzyme Inhibitors","Lipopolysaccharides","Nitric Oxide","Bilirubin","Carrageenan","Nitric Oxide Synthase","Nitric Oxide Synthase Type II","Nos2 protein, rat","Prostaglandin-Endoperoxide Synthases","Heme Oxygenase (Decyclizing)","Heme Oxygenase-1","Oxidoreductases Acting on CH-CH Group Donors","biliverdin reductase","Grant Support:","DK063954/DK/NIDDK","DK51679/DK/NIDDK","DK62628/DK/NIDDK","OK07727/PHS"]
["ective in recovering biological networks from experimentally collected data. AVAILABILITY: Source code and simulated data are available upon request. SUPPLEMENTARY INFORMATION: http://www.jarvislab.net/Bioinformatics/BNAdvances/ Publication Types: Evaluation Studies Validation Studies PMID: 15284094","51: Bioinformatics. 2004 Dec 12;20(18):3594-603. Epub 2004 Jul 29.","yes","n","observational biological data.","PMID: 15284094 [PubMed - indexed for MEDLINE]"]
["ly stages of liver development, and the extracellular matrix components may play important roles in biliary differentiation and vascular development. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Co","51: Hepatology. 2004 Aug;40(2):346-55.","yes","n","liver development.","PMID: 15368439 [PubMed - indexed for MEDLINE]","MeSH Terms:","Aging/metabolism*","Animals","Animals, Newborn/growth & development","Animals, Newborn/metabolism*","Bile Ducts, Extrahepatic/embryology","Bile Ducts, Extrahepatic/growth & development","Bile Ducts, Extrahepatic/metabolism","Bile Ducts, Intrahepatic/embryology","Bile Ducts, Intrahepatic/growth & development","Bile Ducts, Intrahepatic/metabolism","Blood Vessels/growth & development","Blood Vessels/metabolism","Cell Aging","Embryo/metabolism","Extracellular Matrix Proteins/metabolism*","Hepatocytes/metabolism","Hepatocytes/physiology","Immunohistochemistry","Integrins/metabolism*","Liver/cytology","Liver/embryology*","Liver/growth & development","Liver/metabolism*","Liver Circulation","Mice","Mice, Inbred C3H","Receptors, Cell Surface/metabolism*","Research Support, Non-U.S. Gov't","Substances:","Extracellular Matrix Proteins","Integrins","Receptors, Cell Surface","extracellular matrix receptor"]
["b web-site offers a database of NMR raw datasets, ordered by spectral characteristics. AVAILABILITY: NMRb is available from: http://nmrb.cbs.cnrs.fr. SUPPLEMENTARY INFORMATION: General organization of NMRb figure, relational model organization, and XML structure files are available from http://nmrb.","52: Bioinformatics. 2004 Dec 12;20(18):3707-9. Epub 2004 Jul 29.","yes","n","Pons JL, Malliavin TE, Tramesel D, Delsuc MA.","PMID: 15284093 [PubMed - indexed for MEDLINE]"]
["the AE. Random reactivation of the original HBV pool, rather than a sequential evolution of one strain, also contributes to the onset of repeated AE. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Co","52: Hepatology. 2004 Aug;40(2):310-17.","yes","n","the liver and from other exacerbation.","PMID: 15368435 [PubMed - indexed for MEDLINE]","MeSH Terms:","Acute Disease","Adult","Base Sequence","Carrier State","Comparative Study","Female","Genome, Viral","Hepatitis B e Antigens","Hepatitis B virus/genetics","Hepatitis B, Chronic/physiopathology*","Hepatitis B, Chronic/virology*","Humans","Liver/virology*","Male","Middle Aged","Phylogeny","Research Support, Non-U.S. Gov't","Severity of Illness Index","Species Specificity","Viremia*","Substances:","Hepatitis B e Antigens"]
["am runs relatively fast and is suitable for analyzing alignments containing large number of sequences. AVAILABILITY: ftp://iole.swmed.edu/pub/PCOAT/. SUPPLEMENTARY INFORMATION: The PCOAT ftp site contains a detailed description of the program, and the results of PCOAT analysis on C2H2 alignment and ","53: Bioinformatics. 2004 Dec 12;20(18):3697-9. Epub 2004 Jul 22.","yes","n","Qi Y, Grishin NV.","PMID: 15271785 [PubMed - indexed for MEDLINE]"]
["l tool to characterize protein families and to optimize the alignments for comparative modelling. AVAILABILITY: http://bioserv.cbs.cnrs.fr/VITO/DOC/. SUPPLEMENTARY INFORMATION: http://bioserv.cbs.cnrs.fr/VITO/DOC/index.html. PMID: 15271783 [PubMed - indexed for MEDLINE]","54: Bioinformatics. 2004 Dec 12;20(18):3694-6. Epub 2004 Jul 22.","yes","n","Catherinot V, Labesse G.","PMID: 15271783 [PubMed - indexed for MEDLINE]"]
[" network allowing biologists to explore gene relationships at the system level. AVAILABILITY: Download from http://genenetwork.sbl.bc.sinica.edu.tw/. SUPPLEMENTARY INFORMATION: Supplement documentation of algorithms for the four approaches is downloadable at the above location. PMID: 15271782 [PubMe","55: Bioinformatics. 2004 Dec 12;20(18):3691-3. Epub 2004 Jul 22.","Yes","n","microarray data.","PMID: 15271782 [PubMed - indexed for MEDLINE]"]
["ers previously determined by manual searching. AVAILABILITY: ORFcurator and all associated scripts are freely available as supplementary information. SUPPLEMENTARY INFORMATION: http://www.genomecurator.org/ORFcurator/ Publication Types: Evaluation Studies PMID: 15271781 [PubMed - indexed for MEDLINE","56: Bioinformatics. 2004 Dec 12;20(18):3462-5. Epub 2004 Jul 22.","yes","n","organisms.","PMID: 15271781 [PubMed - indexed for MEDLINE]"]
["ical analysis of both empirical data and methods designed to detect natural selection. AVAILABILITY: http://www.stats.ox.ac.uk/mathgen/software.html. SUPPLEMENTARY INFORMATION: http://www.stats.ox.ac.uk/mathgen/software.html. PMID: 15271777 [PubMed - indexed for MEDLINE]","57: Bioinformatics. 2004 Dec 12;20(18):3673-5. Epub 2004 Jul 22.","yes","n","recombination.","PMID: 15271777 [PubMed - indexed for MEDLINE]"]
["ated up-regulation of gene expression. In conclusion, this study suggests a role of NS5A and NF-kappaB in HCV pathogenesis and related liver disease. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Co","57: Hepatology. 2004 Sep;40(3):708-18.","yes","n","microarray and comparative promoter analyses.","PMID: 15349911 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Binding Sites","Calcium/metabolism","Carcinoma, Hepatocellular/genetics","Carrier Proteins/physiology","Gene Expression Profiling","Gene Expression Regulation, Viral*","Hepatitis C/etiology*","Humans","Interferon-alpha/therapeutic use","Interleukin-1/physiology","Intracellular Signaling Peptides and Proteins*","Lipid Metabolism","Liver Neoplasms/genetics","Molecular Sequence Data","NF-kappa B/metabolism","Oligonucleotide Array Sequence Analysis*","Promoter Regions (Genetics)*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Signal Transduction/physiology*","Transforming Growth Factor beta/physiology","Viral Nonstructural Proteins/physiology*","Substances:","Carrier Proteins","Interferon-alpha","Interleukin-1","Intracellular Signaling Peptides and Proteins","NF-kappa B","NS-5 protein, hepatitis C virus","Transforming Growth Factor beta","Viral Nonstructural Proteins","latent TGF-beta binding protein","transforming growth factor beta1","Calcium","Grant Support:","2 P30 DK34933/DK/NIDDK","DK59771/DK/NIDDK"]
["ts. The success of the predictions is validated by examining the predictions in the context of the three-dimensional structures of protein complexes. SUPPLEMENTARY INFORMATION: http://www.public.iastate.edu/~chhyan/ISMB2004/list.html PMID: 15262822 [PubMed - in process]","58: Bioinformatics. 2004 Aug 4;20 Suppl 1:I371-I378.","yes","n","Yan C, Dobbs D, Honavar V.","PMID: 15262822 [PubMed - in process]"]
[" HCC subclasses should provide an attractive source for the development of therapeutic targets (e.g., HIF1a) for selective treatment of HCC patients. Supplementary material for this article can be found on the HEPATOLOGY Web site (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html) Co","58: Hepatology. 2004 Sep;40(3):667-76.","yes","n","Hepatology. 2004 Sep;40(3):521-3.","PMID: 15349906 [PubMed - indexed for MEDLINE]","MeSH Terms:","Carcinoma, Hepatocellular/classification*","Carcinoma, Hepatocellular/genetics","Carcinoma, Hepatocellular/mortality","Gene Expression Profiling*","Humans","Liver/metabolism","Liver Neoplasms/classification*","Liver Neoplasms/genetics","Liver Neoplasms/mortality"]
["stead of years, and uncover homologs missed by heuristic techniques to speed CM searches. AVAILABILITY: Software in development; contact the authors. SUPPLEMENTARY INFORMATION: http://bio.cs.washington.edu/supplements/zasha-ISMB-2004 (Additional technical details on the method; predicted homologs.) ","59: Bioinformatics. 2004 Aug 4;20 Suppl 1:I334-I341.","yes","n","loss of accuracy.","PMID: 15262817 [PubMed - in process]"]
["cells resistant to TNFalpha-mediated apoptosis and acquisition of sensitivity to death stimuli is an implicit feature of the differentiation process. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Co","59: Hepatology. 2004 Sep;40(3):590-9.","yes","n","sensitization to TNFalpha-mediated apoptosis.","PMID: 15349897 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Apoptosis/drug effects*","Cell Differentiation","Cell Line","Cell Lineage","Glutathione/physiology","Liver/cytology*","Liver/drug effects","Mitochondria, Liver/drug effects","Oxidative Stress","Rats","Reactive Oxygen Species","Stem Cells/cytology*","Tumor Necrosis Factor-alpha/pharmacology*","Substances:","Reactive Oxygen Species","Tumor Necrosis Factor-alpha","Glutathione"]
["s on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values. Availability SUPPLEMENTARY INFORMATION: RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http:","6: Bioinformatics. 2005 Feb 15;21(4):456-63. Epub 2004 Dec 17.","yes","n","phylogenetic trees.","PMID: 15608047 [PubMed - indexed for MEDLINE]"]
["lable. AVAILABILITY: A software package implementing our method is freely available under the GNU general public license (GPL) at http://ghmm.org/gql SUPPLEMENTARY INFORMATION: Supplemental material can be found at http://algorithmics.molgen.mpg.de/ExpMix PMID: 15262810 [PubMed - in process]","60: Bioinformatics. 2004 Aug 4;20 Suppl 1:I283-I289.","yes","n","HMMs.","PMID: 15262810 [PubMed - in process]"]
["has been significantly perturbed across the conditions of the expression dataset used. AVAILABILITY: Freely available (in Supplementary information). SUPPLEMENTARY INFORMATION: Available at the following URL http://arep.med.harvard.edu/kharchenko/mep/supplements.html PMID: 15262797 [PubMed - in proc","61: Bioinformatics. 2004 Aug 4;20 Suppl 1:I178-I185.","yes","n","Kharchenko P, Vitkup D, Church GM.","PMID: 15262797 [PubMed - in process]"]
["causal networks affecting the traits in a multigenic manner. AVAILABILITY: TraitMap database and GPS are accessible at http://omicspace.riken.jp/gps/ SUPPLEMENTARY INFORMATION: See http://omicspace.riken.jp/info/traitmap.html PMID: 15262794 [PubMed - in process]","62: Bioinformatics. 2004 Aug 4;20 Suppl 1:I152-I160.","yes","n","biomolecular networks.","PMID: 15262794 [PubMed - in process]"]
[" is a suitable tool for detecting putative cell cycle regulators in the realm of known human transcription factors. AVAILABILITY: Further details and supplementary data can be obtained from http://corg.molgen.mpg.de/cellcycle PMID: 15262788 [PubMed - in process]","63: Bioinformatics. 2004 Aug 4;20 Suppl 1:I109-I115.","Yes","n","transcription factor binding sites.","PMID: 15262788 [PubMed - in process]"]
["increases. We apply the method to the identification of splice sites, and further evaluate its effect within the context of exon and gene prediction. SUPPLEMENTARY INFORMATION: The datasets built specifically for this paper as well as the full set of results are available at http://genome.imim.es/da","64: Bioinformatics. 2004 Aug 4;20 Suppl 1:I69-I76.","yes","n","Castelo R, Guigo R.","PMID: 15262783 [PubMed - in process]"]
["Demonstration web server and software download, subject to the Virginia Tech Noncommercial License are available at http://gaia.biotech.vt.edu/goat/. SUPPLEMENTARY INFORMATION: Updates, installation and configuration information are available at http://gaia.biotech.vt.edu/goat. PMID: 15256414 [PubMe","65: Bioinformatics. 2004 Dec 12;20(18):3662-4. Epub 2004 Jul 15.","yes","n","Kaluszka A, Gibas C.","PMID: 15256414 [PubMed - indexed for MEDLINE]"]
["pare and query libraries of frequency matrices for TFBSs. AVAILABILITY: Software is available to use over the Web at http://rulai.cshl.edu/MatCompare SUPPLEMENTARY INFORMATION: Database and clustering statistics, matrix families and representatives are available at http://rulai.cshl.edu/MatCompare/S","65: Bioinformatics. 2005 Feb 1;21(3):307-13. Epub 2004 Aug 19.","yes","n","sites.","PMID: 15319260 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Binding Sites","Comparative Study","Protein Binding","Research Support, U.S. Gov't, Non-P.H.S.","Sequence Alignment/methods*","Sequence Analysis, Protein/methods*","Transcription Factors/analysis","Transcription Factors/chemistry*","Substances:","Transcription Factors"]
["al preferences for ubiquitin ligation to target proteins, and compartment-specific amino acid patterns in close proximity to the modified side chain. SUPPLEMENTARY INFORMATION: http://www.people.fas.harvard.edu/~catic. PMID: 15256413 [PubMed - indexed for MEDLINE]","66: Bioinformatics. 2004 Dec 12;20(18):3302-7. Epub 2004 Jul 15.","yes","n","Catic A, Collins C, Church GM, Ploegh HL.","PMID: 15256413 [PubMed - indexed for MEDLINE]"]
["y, it suggests multiple options for storage and queries of the dog RH database. AVAILABILITY: http://idefix.univ-rennes1.fr:8080/Dogs/rh-server.html. SUPPLEMENTARY INFORMATION: All information is available at http://idefix.univ-rennes1.fr:8080/Dogs/help_rh-server.html. PMID: 15256409 [PubMed - index","67: Bioinformatics. 2004 Dec 12;20(18):3665-7. Epub 2004 Jul 15.","yes","n","canine genome.","PMID: 15256409 [PubMed - indexed for MEDLINE]"]
["n the predicted risk groups and the receiver operator characteristics analysis. AVAILABILITY: R programs are available upon request from the authors. SUPPLEMENTARY INFORMATION: http://dna.ucdavis.edu/~hli/bioinfo-surv-supp.pdf. Publication Types: Evaluation Studies Validation Studies PMID: 15256406 ","68: Bioinformatics. 2004 Dec 12;20(18):3406-12. Epub 2004 Jul 15.","yes","n","survival data.","PMID: 15256406 [PubMed - indexed for MEDLINE]"]
["numerous independent experiments as well as by the analysis of spike-in data. AVAILABILITY: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html. SUPPLEMENTARY INFORMATION: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html. PMID: 15256405 [PubMed - indexed for MEDLINE]","69: Bioinformatics. 2004 Dec 12;20(18):3670-2. Epub 2004 Jul 15.","yes","n","Finocchiaro G, Parise P, Minardi SP, Alcalay M, Muller H.","PMID: 15256405 [PubMed - indexed for MEDLINE]"]
["analysis results and R functions for the proposed methods can be found at http://www.biostat.umn.edu/~baolin/research CONTACT: baolin@biostat.umn.edu SUPPLEMENTARY INFORMATION: http://www.biostat.umn.edu/~baolin/research. Publication Types: Evaluation Studies Validation Studies PMID: 15598833 [PubMe","7: Bioinformatics. 2005 Apr 15;21(8):1565-71. Epub 2004 Dec 14.","yes","n","the improved SAM statistics.","PMID: 15598833 [PubMed - indexed for MEDLINE]"]
["o simulate the parameters from the posteriors. The method is applied to leukemia data from a previous study and a published dataset on breast cancer. SUPPLEMENTARY INFORMATION: http://stat.tamu.edu/people/faculty/bmallick.html. Publication Types: Evaluation Studies Validation Studies PMID: 15256404 ","70: Bioinformatics. 2004 Dec 12;20(18):3423-30. Epub 2004 Jul 15.","yes","n","Bae K, Mallick BK.","PMID: 15256404 [PubMed - indexed for MEDLINE]"]
["BILITY: A web based user interface which is dynamically linked to the Genome Atlas Database can be accessed via www.cbs.dtu.dk/services/GenomeAtlas/. SUPPLEMENTARY INFORMATION: This paper has a supplemental information page which links to the examples presented: www.cbs.dtu.dk/services/GenomeAtlas/s","71: Bioinformatics. 2004 Dec 12;20(18):3682-6. Epub 2004 Jul 15.","yes","n","sequence data.","PMID: 15256401 [PubMed - indexed for MEDLINE]"]
["ay outweigh the benefit of saving on microarray cost. The microarray data from both platforms show that the major assumption of pooling may not hold. SUPPLEMENTARY INFORMATION: Supplementary material referenced in the text is available at http://linus.nci.nih.gov/brb/TechReport.htm. Publication Type","72: Bioinformatics. 2004 Dec 12;20(18):3318-25. Epub 2004 Jul 9.","yes","y","Shih JH, Michalowska AM, Dobbin K, Ye Y, Qiu TH, Green JE.","PMID: 15247103 [PubMed - indexed for MEDLINE]"]
["tech.res.in/raghava/gpcrpred/. We have also suggested subfamilies for 42 sequences which were previously identified as unclassified ClassA GPCRs. The supplementary information is available at http://www.imtech.res.in/raghava/gpcrpred/info.html. Publication Types: Evaluation Studies PMID: 15215416 [P","73: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W383-9.","yes","y","G-protein coupled receptors.","PMID: 15215416 [PubMed - indexed for MEDLINE]"]
["agnostic scan time, expand the target population, improve patient comfort, and facilitate targeted, interventional treatment of infarcted myocardium. Supplementary material for this article can be found on the MRM website at http://www.interscience.wiley.com/jpages/0740-3194/suppmat/index.html. MeSH","74: Magn Reson Med. 2004 Aug;52(2):354-61.","yes","y","interactive MRI without ECG-gating or breath-holding.","PMID: 15282818 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Computer Simulation","Contrast Media/administration & dosage","Humans","Magnetic Resonance Imaging/methods*","Myocardial Infarction/diagnosis*","Swine","Substances:","Contrast Media"]
[" of transcription regulatory regions in eukaryotes and can be directly applied to clusters of co-expressed genes obtained in gene expression studies. Supplementary information is available at http://www.mit.edu/ approximately kreiman/resources/cisregul/. Publication Types: Evaluation Studies PMID: 1","74: Nucleic Acids Res. 2004 May 20;32(9):2889-900. Print 2004.","yes","y","sets of co-expressed genes.","PMID: 15155858 [PubMed - indexed for MEDLINE]"]
["ns--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data. AVAILABILITY: Supplementary data at http://noble.gs.washington.edu/proj/sdp-svm Publication Types: Evaluation Studies PMID: 15130933 [PubMed - indexed for MEDLINE]","75: Bioinformatics. 2004 Nov 1;20(16):2626-35. Epub 2004 May 6.","yes","y","Lanckriet GR, De Bie T, Cristianini N, Jordan MI, Noble WS.","PMID: 15130933 [PubMed - indexed for MEDLINE]"]
["n one would expect from a random substitution model, indicating a cooperative behaviour for these surfaces residues in terms of this single variable. SUPPLEMENTARY INFORMATION: Additional plots for all of the proteins examined in this paper can be found at: http://www.ebi.ac.uk/~shanahan/PCon/index.","76: Bioinformatics. 2004 Sep 22;20(14):2197-204. Epub 2004 Apr 8.","yes","y","Shanahan HP, Thornton JM.","PMID: 15073014 [PubMed - indexed for MEDLINE]"]
["OP and CATH classifications of proteins, based on their FSSP Z-scores. AVAILABILITY: Free at http://www.weizmann.ac.il/physics/complex/compphys/f2cs/ SUPPLEMENTARY INFORMATION: The site contains links to additional figures and tables. Publication Types: Evaluation Studies PMID: 15059833 [PubMed - in","77: Bioinformatics. 2004 Sep 1;20(13):2150-2. Epub 2004 Apr 1.","yes","y","Getz G, Starovolsky A, Domany E.","PMID: 15059833 [PubMed - indexed for MEDLINE]"]
["ree from the John Innes Centre's Bioinformatics Research Group website at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html. SUPPLEMENTARY INFORMATION: A full user-guide for newicktree and installation and usage instructions for mswordtree and available at http://jic-bioinfo","78: Bioinformatics. 2004 Sep 22;20(14):2322-3. Epub 2004 Apr 1.","yes","y","Savva G, Conn J, Dicks J.","PMID: 15059821 [PubMed - indexed for MEDLINE]"]
["ach of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. SUPPLEMENTARY INFORMATION: http://bidd.nus.edu.sg/group/trmp/sm.pdf PMID: 15059817 [PubMed - indexed for MEDLINE]","79: Bioinformatics. 2004 Sep 22;20(14):2236-41. Epub 2004 Apr 1.","yes","y","Zheng CJ, Zhou H, Xie B, Han LY, Yap CW, Chen YZ.","PMID: 15059817 [PubMed - indexed for MEDLINE]"]
["eover, its presence in a restricted number of bacteria suggests a possible use for marking plant pathogenicity. CONTACT: francesca.ciccarelli@embl.de SUPPLEMENTARY INFORMATION: Supplementary data (Figures S1 and S2 and Table S1) and the alignment in clustal format are available at http://www.bork.em","8: Bioinformatics. 2005 Apr 15;21(8):1304-7. Epub 2004 Dec 14.","yes","y","Ciccarelli FD, Bork P.","PMID: 15598830 [PubMed - indexed for MEDLINE]"]
["Win32 platform and is free of charge for academic use. For details, visit the web page http://www.bioinfo-hr.org/inca or contact the author directly. SUPPLEMENTARY INFORMATION: Software is accompanied with a user manual and a short tutorial. PMID: 15059815 [PubMed - indexed for MEDLINE]","80: Bioinformatics. 2004 Sep 22;20(14):2329-30. Epub 2004 Apr 1.","yes","y","map.","PMID: 15059815 [PubMed - indexed for MEDLINE]"]
["alias/ and as a web service using a SOAP interface. The complete tool, including sources and data, is available for local installations upon request. SUPPLEMENTARY INFORMATION: Technical documentation is available at http://cbi.labri.fr/outils/alias/asdoc.pdf PMID: 15059813 [PubMed - indexed for MED","81: Bioinformatics. 2004 Sep 22;20(14):2331-2. Epub 2004 Apr 1.","yes","y","Iragne F, Barre A, Goffard N, De Daruvar A.","PMID: 15059813 [PubMed - indexed for MEDLINE]"]
["chical organization. It furthermore has the advantage over both methods of capturing overlapping modules in the presence of combinatorial regulation. SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/~barkai/modules Publication Types: Evaluation Studies Validation Studies PMID: 15044247 [PubMed -","82: Bioinformatics. 2004 Sep 1;20(13):1993-2003. Epub 2004 Mar 25.","yes","y","Ihmels J, Bergmann S, Barkai N.","PMID: 15044247 [PubMed - indexed for MEDLINE]"]
["i-lognormal mixture assigns observations to subgroups with the lowest uncertainty. AVAILABILITY: Software is available upon request from the authors. SUPPLEMENTARY INFORMATION: http://www-rcf.usc.edu/~kims/SupplementaryInfo.html Publication Types: Evaluation Studies Validation Studies PMID: 15044245","83: Bioinformatics. 2004 Aug 12;20(12):1896-904. Epub 2004 Mar 25.","yes","y","Siegmund KD, Laird PW, Laird-Offringa IA.","PMID: 15044245 [PubMed - indexed for MEDLINE]"]
[" be useful for computing the regulatory ability of the transcriptional regulatory networks in more diverse conditions and in more complex eukaryotes. SUPPLEMENTARY INFORMATION: Matlab code and test data are available at http://www.ee.nthu.edu.tw/~bschen/quantitative/regulatory_network.htm Publicatio","84: Bioinformatics. 2004 Aug 12;20(12):1914-27. Epub 2004 Mar 25.","yes","y","yeast cell cycle.","PMID: 15044243 [PubMed - indexed for MEDLINE]"]
["ologies generated is significantly more likely than the others, Kishino-Hasegawa, Shimodaira-Hasegawa and ELW tests are implemented. Availability and SUPPLEMENTARY INFORMATION: http://www.plantbio.uga.edu/~russell/software.html PMID: 15044241 [PubMed - indexed for MEDLINE]","85: Bioinformatics. 2004 Aug 12;20(12):1977-9. Epub 2004 Mar 25.","yes","y","inference.","PMID: 15044241 [PubMed - indexed for MEDLINE]"]
["ray experiments, with minimal user intervention and time investment. AVAILABILITY: microGENIE is freely available from http://www.cs.vu.nl/microgenie SUPPLEMENTARY INFORMATION: The web site above supplies examples of input and output files. PMID: 15044238 [PubMed - indexed for MEDLINE]","86: Bioinformatics. 2004 Aug 12;20(12):1980-2. Epub 2004 Mar 25.","yes","y","Korotkiy M, Middelburg R, Dekker H, van Harmelen F, Lankelma J.","PMID: 15044238 [PubMed - indexed for MEDLINE]"]
[" a simple scoring function based on the KSDP, outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy. SUPPLEMENTARY INFORMATION: http://www.jdl.ac.cn/user/yfu/pfind/index.html Publication Types: Evaluation Studies Validation Studies PMID: 15044235 [Pub","87: Bioinformatics. 2004 Aug 12;20(12):1948-54. Epub 2004 Mar 25.","yes","y","identification via tandem mass spectrometry.","PMID: 15044235 [PubMed - indexed for MEDLINE]"]
["hly conserved non-protein-coding elements in the human genome thus contains rich family-like structures, which merit in-depth analysis. AVAILABILITY: Supplementary material to this work is available at http://www.soe.ucsc.edu/~jill/dark.html PMID: 15262779 [PubMed - in process]","87: Bioinformatics. 2004 Aug 4;20 Suppl 1:I40-I48.","yes","y","Bejerano G, Haussler D, Blanchette M.","PMID: 15262779 [PubMed - in process]"]
["e proposed for data normalized using methods established in the field of proteomics. AVAILABILITY: Software is available on request from the authors. SUPPLEMENTARY INFORMATION: There is supplementary material available online at http://www.flychip.org.uk/kreil/pub/2dgels/ Publication Types: Evaluati","88: Bioinformatics. 2004 Sep 1;20(13):2026-34. Epub 2004 Mar 25.","yes","y","expression analysis of 2D difference gel electrophoresis results.","PMID: 15044229 [PubMed - indexed for MEDLINE]"]
["methods we propose are capable of deducing and quantifying functional interactions within and across cellular gene, signaling and metabolic networks. SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.dbi.tju.edu/bioinformatics2004.pdf Publication Types: Evaluation Studies ","89: Bioinformatics. 2004 Aug 12;20(12):1877-86. Epub 2004 Mar 22.","yes","y","expression, protein and metabolite data.","PMID: 15037511 [PubMed - indexed for MEDLINE]"]
["d during the measurements. AVAILABILITY: All programs used for this publication are available on request from the authors. CONTACT: beyer@imb-jena.de SUPPLEMENTARY INFORMATION: Supplementary information about the model and its interpretation can be downloaded from http://www.imb-jena.de/tsb/pad. Pub","9: Bioinformatics. 2005 Apr 15;21(8):1610-6. Epub 2004 Dec 14.","yes","y","Beyer A, Wilhelm T.","PMID: 15598828 [PubMed - indexed for MEDLINE]"]
["otal proteome. AVAILABILITY: MITOPRED program is freely accessible at http://mitopred.sdsc.edu. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Training data sets are also available at http://mitopred.sdsc.edu Publication Types: Evaluation Studies Validation Studies ","90: Bioinformatics. 2004 Jul 22;20(11):1785-94. Epub 2004 Mar 22.","yes","y","proteins.","PMID: 15037509 [PubMed - indexed for MEDLINE]"]
["t studies of the subsets, make it more amenable to understand the inherent organization and functionality of metabolic networks at the modular level. SUPPLEMENTARY INFORMATION: http://genome.gbf.de/bioinformatics/ PMID: 15037506 [PubMed - indexed for MEDLINE]","91: Bioinformatics. 2004 Aug 12;20(12):1870-6. Epub 2004 Mar 22.","yes","y","connectivity structure of reaction graph.","PMID: 15037506 [PubMed - indexed for MEDLINE]"]
["ons. AVAILABILITY: R code is freely available from http://www.davidbickel.com and may become available from www.r-project.org or www.bioconductor.org SUPPLEMENTARY INFORMATION: Applications to cancer microarrays, an application in the absence of differential expression, pseudocode, and a guide to cu","92: Bioinformatics. 2004 Mar 22;20(5):682-8. Epub 2004 Jan 22.","yes","y","expression differences and estimating their magnitudes.","PMID: 15033875 [PubMed - indexed for MEDLINE]"]
["of traditional journal publications, allowing access to resources, such as video, sound, software, databases, datasets too large to publish, and even supplementary information and discussion. However, unlike traditional publications, continued availability of these online resources is not guaranteed","93: Bioinformatics. 2004 Mar 22;20(5):668-72. Epub 2004 Jan 22.","yes","y","Wren JD.","PMID: 15033874 [PubMed - indexed for MEDLINE]"]
["uch weaker than tRNA genes. Based on the conservation of studied sRNA genes, we also give clues to estimate the total number of sRNA genes in E.coli. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://www.bioinfo.org.cn/SM/sRNAconservation.htm Publication Types: Evaluation S","94: Bioinformatics. 2004 Mar 22;20(5):599-603. Epub 2004 Jan 22.","yes","y","Zhang Y, Zhang Z, Ling L, Shi B, Chen R.","PMID: 15033865 [PubMed - indexed for MEDLINE]"]
["ay outweigh the benefit of saving on microarray cost. The microarray data from both platforms show that the major assumption of pooling may not hold. SUPPLEMENTARY INFORMATION: Supplementary material referenced in the text is available at http://linus.nci.nih.gov/brb/TechReport.htm. Publication Type","95: Bioinformatics. 2004 Dec 12;20(18):3318-25. Epub 2004 Jul 9.","yes","y","Shih JH, Michalowska AM, Dobbin K, Ye Y, Qiu TH, Green JE.","PMID: 15247103 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Comparative Study","Gene Expression Profiling/methods*","Models, Genetic*","Models, Statistical","Oligonucleotide Array Sequence Analysis/methods*","RNA, Messenger/genetics*","Reproducibility of Results","Sample Size","Sensitivity and Specificity","Variation (Genetics)","Substances:","RNA, Messenger"]
["L stylesheets are provided for easy generation of text, html and graphical reports from CisML-formatted data. AVAILABILITY: http://zlab.bu.edu/CisML/ SUPPLEMENTARY INFORMATION: Example CisML-formatted data and XSL stylesheets for report generation are available along with the sample output. PMID: 15","95: Bioinformatics. 2004 Jul 22;20(11):1815-7. Epub 2004 Mar 4.","yes","y","Haverty PM, Weng Z.","PMID: 15001475 [PubMed - indexed for MEDLINE]"]
[" of three or four states. AVAILABILITY: LSBSP1 and the NN algorithm have been implemented in PrISM.1, which is available from www.columbia.edu/~ay1/. SUPPLEMENTARY INFORMATION: Supplementary data for the SVM method can be downloaded from the Website www.cs.columbia.edu/compbio/backbone. Publication ","96: Bioinformatics. 2004 Jul 10;20(10):1612-21. Epub 2004 Feb 26.","yes","y","Kuang R, Leslie CS, Yang AS.","PMID: 14988121 [PubMed - indexed for MEDLINE]"]
["rom http://www.ncbs.res.in/~faculty/mini/imot/iMOTserver.html. Supplementary Material can be accessed from: http://www.ncbs.res.in/~faculty/mini/imot/supplementary.html. MeSH Terms: Amino Acid Motifs* Databases, Protein Internet Protein Folding Protein-Tyrosine-Phosphatase/classification Sequence An","96: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W602-5.","yes","y","Bhaduri A, Pugalenthi G, Gupta N, Sowdhamini R.","PMID: 15215459 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Motifs*","Databases, Protein","Internet","Protein Folding","Protein-Tyrosine-Phosphatase/classification","Sequence Analysis, Protein","Sequence Homology, Amino Acid","Software*","User-Computer Interface","Substances:","Protein-Tyrosine-Phosphatase","Secondary Source ID:","PDB/2HNQ"]
["general and could be easily adopted by other projects. AVAILABILITY: The R package matchprobes is available under LGPL at http://www.bioconductor.org SUPPLEMENTARY INFORMATION: The package contains documentation in the form of a vignette and manual pages. PMID: 14988118 [PubMed - indexed for MEDLINE","97: Bioinformatics. 2004 Jul 10;20(10):1651-2. Epub 2004 Feb 26.","yes","y","probe elements.","PMID: 14988118 [PubMed - indexed for MEDLINE]"]
["icle if you access the article at http://dx.doi.org/10.1007/s00216-004-2494-4. A link in the frame on the left on that page takes you directly to the supplementary material. MeSH Terms: Comparative Study Culture Media/chemistry Culture Media/pharmacology Escherichia coli K12/chemistry* Escherichia c","98: Anal Bioanal Chem. 2004 Mar;378(6):1601-7.","yes","y","species with living bacterial cells.","PMID: 15214423 [PubMed - indexed for MEDLINE]","MeSH Terms:","Comparative Study","Culture Media/chemistry","Culture Media/pharmacology","Escherichia coli K12/chemistry*","Escherichia coli K12/drug effects","Escherichia coli K12/metabolism","Selenium Compounds/analysis*","Selenium Compounds/chemistry","Selenium Compounds/metabolism","Spectroscopy, Fourier Transform Infrared/methods","Time Factors","Substances:","Culture Media","Selenium Compounds"]
["hree-dimensional protein structures across eukaryotic organisms. AVAILABILITY: SEDB is publicly available at http://glinka.bio.neu.edu/SEDB/SEDB.html SUPPLEMENTARY INFORMATION: On the SEDB Web site. PMID: 14988102 [PubMed - indexed for MEDLINE]","98: Bioinformatics. 2004 Jul 22;20(11):1801-3. Epub 2004 Feb 26.","yes","y","structures.","PMID: 14988102 [PubMed - indexed for MEDLINE]"]
[" various molecular mass distributions (Mathematica). These tools are presented here and briefly compared with other DOSY analysis methods. Electronic Supplementary Material: Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00216-003-2457-1. The ","99: Anal Bioanal Chem. 2004 Mar;378(6):1574-8.","yes","y","of a broad, featureless resonance: an application to methylaluminoxane (MAO).","PMID: 15214419 [PubMed]"]
["d and Drug Administration (FDA). The workshop featured presentations by 22 experts and was attended by 65 individuals. The agenda can be found in the supplementary data at www.toxsci.oupjournals.org. Publication Types: Review PMID: 14976355 [PubMed - indexed for MEDLINE]","99: Toxicol Sci. 2004 May;79(1):4-9. Epub 2004 Feb 19.","yes","y","Willett KL, Roth RA, Walker L.","PMID: 14976355 [PubMed - indexed for MEDLINE]"]
["m is useful mainly to improve local marker ordering in linkage groups obtained in other ways. AVAILABILITY: The source code and supplemental data are http://www.iubio.bio.indiana.edu/soft/molbio/qtl/flipper/ CONTACT: ccrane@purdue.edu. Publication Types: Evaluation Studies Validation Studies MeSH Te","1: Bioinformatics. 2005 Apr 15;21(8):1579-91. Epub 2004 Nov 25.","no","n","A nearest-neighboring-end algorithm for genetic mapping.","Crane CF, Crane YM.","PMID: 15564296 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Chromosome Mapping/methods*","Comparative Study","Computer Simulation","DNA Mutational Analysis/methods*","Gene Deletion","Genetic Markers/genetics*","Genetics, Population*","Humans","Linkage (Genetics)/genetics","Models, Genetic*","Models, Statistical","Research Support, U.S. Gov't, Non-P.H.S.","Software*","Substances:","Genetic Markers"]
["pathways and indicate a large diversity in the functional context of the individual gene family members. AVAILABILITY: The SHOPS tool can be found at http://www.bioinformatics.med.uu.nl/shops supplemental data are available at http://humgen.med.uu.nl/publications/vanbakel/pathway/ Publication Types:","2: Bioinformatics. 2004 Nov 1;20(16):2644-55. Epub 2004 May 14.","y","n","Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper","pathway.","PMID: 15145814 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms","Carrier Proteins/genetics*","Carrier Proteins/metabolism*","Comparative Study","Copper/metabolism*","Evolution, Molecular","Gene Expression Profiling/methods*","Gene Expression Regulation, Fungal/physiology","Internet","Operon/genetics","Research Support, Non-U.S. Gov't","Saccharomyces cerevisiae/genetics*","Saccharomyces cerevisiae/metabolism*","Saccharomyces cerevisiae Proteins/genetics*","Saccharomyces cerevisiae Proteins/metabolism*","Sequence Analysis, Protein/methods","Signal Transduction/physiology*","Software","Structure-Activity Relationship","User-Computer Interface","Variation (Genetics)/genetics","Substances:","ATX1 protein, S cerevisiae","Carrier Proteins","Saccharomyces cerevisiae Proteins","Copper"]

{"sheet":"2005","index":9,"n_rows":241,"n_cols":52,"rows_kept":241,"flags":["formulas_cached_only"]}
["Reference",null,"Live?",null,null,"Journal?"]
[", NetBSD, Solaris and Windows XP. It can be downloaded from http://mesord.sourceforge.net. CONTACT: johan.elf@icm.uu.se; johan.hattne@embl-hamburg.de SUPPLEMENTARY INFORMATION: 'MesoRD User's Guide' and other documents are available at http://mesord.sourceforge.net. PMID: 15817692 [PubMed - indexed ","101: Bioinformatics. 2005 Jun 15;21(12):2923-4. Epub 2005 Apr 7.","no","Stochastic reaction-diffusion simulation with MesoRD.","Hattne J, Fange D, Elf J.","n","PMID: 15817692 [PubMed - indexed for MEDLINE]"]
["guidance that appears as an appendix in Supplementary data to this paper should","111: Bioinformatics. 2005 May 1;21(9):1987-94. Epub 2005 Feb 2. ","no","A Bayesian approach to reconstructing genetic regulatory networks with hidden","factors.","n","PMID: 15691856 [PubMed - indexed for MEDLINE]"]
["bentities and associate them to biological processes without compromising overall prediction accuracy. AVAILABILITY: Bioconductor compliant R package SUPPLEMENTARY INFORMATION: Complete analyses are available at http://compdiag.molgen.mpg.de/supplements/lottaz05. Publication Types: Evaluation Studie","114: Bioinformatics. 2005 May 1;21(9):1971-8. Epub 2005 Jan 27. ","no","Genome Properties: a system for the investigation of prokaryotic genetic content","for microbiology, genome annotation and comparative genomics.","n","PMID: 15677704 [PubMed - indexed for MEDLINE]"]
["ontrary to the assumptions of previous models. AVAILABILITY: Programs are available upon request from the authors in the form of Matlab script files. SUPPLEMENTARY INFORMATION: http://www.cis.upenn.edu/biocomp/manuscripts/bioinformatics_bti245/supp-info.htm l. Publication Types: Evaluation Studies V","117: Bioinformatics. 2005 May 1;21(9):2008-16. Epub 2005 Jan 25. ","no","WebACT--an online companion for the Artemis Comparison Tool.","Abbott JC, Aanensen DM, Rutherford K, Butcher S, Spratt BG.","n","PMID: 15671116 [PubMed - indexed for MEDLINE]"]
["2% precision at 50% recall, sufficient for inclusion in a high-quality database. AVAILABILITY: Source code is available from the author upon request. SUPPLEMENTARY INFORMATION: ftp.uni-koeln.de/institute/biochemie/pub/brenda/info/diseaseSupp.pdf. Publication Types: Evaluation Studies PMID: 15661799 ","119: Bioinformatics. 2005 May 1;21(9):2059-66. Epub 2005 Jan 20. ","no","Applying GIFT, a Gene Interactions Finder in Text, to fly literature.","Domedel-Puig N, Wernisch L.","n","PMID: 15661799 [PubMed - indexed for MEDLINE]"]
["ith a previous study of the yeast mitochondrial proteome is presented. AVAILABILITY: A demonstration prototype, interSearch, is available on request. SUPPLEMENTARY INFORMATION: http://ijsr32.infj.ulster.ac.uk/~e10110731/interSearch. PMID: 15657100 [PubMed - indexed for MEDLINE]","121: Bioinformatics. 2005 May 1;21(9):2099-100. Epub 2005 Jan 18. ","no","A precise and scalable method for querying genes in chromosomal banding regions","based on cytogenetic annotations.","n","PMID: 15657100 [PubMed - indexed for MEDLINE]"]
[" using Java language, and can be executed on the platforms that JVM (Java Virtual Machine) is running. It is available from the authors upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at http://dragon.kaist.ac.kr/gk. Publication Types: Evaluation Studies Validation Studies ","124: Bioinformatics. 2005 May 1;21(9):1927-34. Epub 2005 Jan 12. ","no","A hidden Markov model for analyzing ChIP-chip experiments on genome tiling","arrays and its application to p53 binding sequences.","n","PMID: 15647300 [PubMed - indexed for MEDLINE]"]
["mes are 30-40% faster for M-ZDOCK. AVAILABILITY: M-ZDOCK is freely available to academic users at http://zlab.bu.edu/m-zdock/ CONTACT: zhiping@bu.edu SUPPLEMENTARY INFORMATION: http://zlab.bu.edu/m-zdock. Publication Types: Evaluation Studies PMID: 15613396 [PubMed - indexed for MEDLINE]","131: Bioinformatics. 2005 Apr 15;21(8):1472-8. Epub 2004 Dec 21. ","no","Prediction of mitochondrial proteins using support vector machine and hidden","markov model.","n","PMID: 15613396 [PubMed - indexed for MEDLINE]"]
["eover, its presence in a restricted number of bacteria suggests a possible use for marking plant pathogenicity. CONTACT: francesca.ciccarelli@embl.de SUPPLEMENTARY INFORMATION: Supplementary data (Figures S1 and S2 and Table S1) and the alignment in clustal format are available at http://www.bork.em","137: Bioinformatics. 2005 Apr 15;21(8):1304-7. Epub 2004 Dec 14. ","no","Empirical Bayes screening of many p-values with applications to microarray","studies.","N","PMID: 15598830 [PubMed - indexed for MEDLINE]"]
["bly information. Results are output in spreadsheets containing information that facilitates manual validation. AVAILABILITY: The TERMINUS package and supplementary information can be downloaded from http://www.genome.kbrin.uky.edu/fungi_tel/terminus/ CONTACT: farman@uky.edu. PMID: 15585532 [PubMed -","140: Bioinformatics. 2005 Apr 15;21(8):1695-8. Epub 2004 Dec 7. ","no","Molecular decomposition of complex clinical phenotypes using biologically","structured analysis of microarray data.","N","PMID: 15585532 [PubMed - indexed for MEDLINE]"]
[". These mechanisms are key for clonal expansion and for controlling the long term behavior (e.g. programmed cell death) of these cells. AVAILABILITY: Supplementary data is available at http://public.kgi.edu/wild/index.htm and Matlab source code for variational Bayesian learning of SSMs is available ","166: Bioinformatics. 2005 Feb 1;21(3):349-56. Epub 2004 Sep 7. ","no","Investigating metabolite essentiality through genome-scale analysis of","Escherichia coli production capabilities.","N","PMID: 15353451 [PubMed - indexed for MEDLINE]"]
["of uncharacterized proteins, or relationships among properties. AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl. Publication Types: Evaluation Studies PMID: 1534757","169: Bioinformatics. 2005 Feb 1;21(3):293-306. Epub 2004 Sep 3. ","no","Concept-based annotation of enzyme classes.","Hofmann O, Schomburg D.","N","PMID: 15347579 [PubMed - indexed for MEDLINE]"]
["computed genome comparisons, can be viewed online using ACT and are available for download. AVAILABILITY: Freely accessible at http://www.webact.org. SUPPLEMENTARY INFORMATION: User guide and worked examples are available at http://www.webact.org/WebACT/docs. PMID: 16076890 [PubMed - indexed for MED","52: Bioinformatics. 2005 Sep 15;21(18):3665-6. Epub 2005 Aug 2. ","no","Integrative data analysis for functional prediction: a multi-objective","optimization approach.","N","PMID: 16076890 [PubMed - indexed for MEDLINE]"]
["nd a web interface for submission of texts to GIFT analysis are available at http://gift.cryst.bbk.ac.uk/gift CONTACT: n.domedel_puig@cryst.bbk.ac.uk SUPPLEMENTARY INFORMATION: Additional documentation, such as the dictionaries and the reference sets, are available at the GIFT website. PMID: 1601436","63: Bioinformatics. 2005 Sep 1;21(17):3582-3. Epub 2005 Jul 12. ","no","Detecting clusters of different geometrical shapes in microarray gene expression","data.","N","PMID: 16014369 [PubMed - indexed for MEDLINE]"]
["from other species. AVAILABILITY: The CQS is freely accessible over the Internet at http://moris.csie.ncku.edu.tw/cqs/ CONTACT: clh9@mail.ncku.edu.tw SUPPLEMENTARY INFORMATION: http://moris.csie.ncku.edu.tw/cqs/ Publication Types: Evaluation Studies PMID: 15998663 [PubMed - indexed for MEDLINE]","66: Bioinformatics. 2005 Sep 1;21(17):3469-74. Epub 2005 Jul 5. ","no","M-ZDOCK: a grid-based approach for Cn symmetric multimer docking.","Pierce B, Tong W, Weng Z.","N","PMID: 15998663 [PubMed - indexed for MEDLINE]"]
["53 TFBSs are in the promoter region of known genes or associated with previously characterized p53-responsive genes. CONTACT: xsliu@jimmy.harvard.edu SUPPLEMENTARY INFORMATION: Available at the following URL http://genome.dfci.harvard.edu/~xsliu/HMMTiling/index.html. PMID: 15961467 [PubMed - in proc","78: Bioinformatics. 2005 Jun 1;21 Suppl 1:i274-i282. ","no","The WHy domain mediates the response to desiccation in plants and bacteria.","Ciccarelli FD, Bork P.","N","PMID: 15961467 [PubMed - in process]"]
[" as mitochondrial in S. cerevicae, D. melanogaster, C. elegans, mouse and human proteome respectively. MitPred developed on above hybrid approach and supplementary data are available at http://www.imtech.res.in/raghava/mitpred or http://www.imtech.ac.in/raghava/mitpred. PMID: 16339140 [PubMed - as s","9: J Biol Chem. 2005 Dec 8; [Epub ahead of print] ","no","TERMINUS--Telomeric End-Read Mining IN Unassembled Sequences.","Li W, Rehmeyer CJ, Staben C, Farman ML.","N","PMID: 16339140 [PubMed - as supplied by publisher]"]
[" strictly constrained by the mitotic phase of the cell cycle and suggesting additional roles during G- and S-phase progression. This article contains Supplementary Material available at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/2005/95/spada.ht ml. (c) 2005 Wiley-Liss, Inc. MeS","25: J Cell Biochem. 2005 Aug 1;95(5):885-901.","no","Histone H4 post-translational modifications in chordate mitotic and","endoreduplicative cell cycles.","y","PMID: 15937898 [PubMed - indexed for MEDLINE]","MeSH Terms:","Acetylation","Animals","Chromatin/metabolism*","G1 Phase/physiology*","Gene Expression Regulation","Hela Cells","Histones/genetics","Histones/metabolism*","Humans","Immunoblotting","Immunoprecipitation","Mice","Mitosis*","NIH 3T3 Cells","Protein Processing, Post-Translational","Research Support, Non-U.S. Gov't","S Phase/physiology*","Urochordata","Substances:","Chromatin","Histones"]
["MT3B. The implications of these findings for the regulation of de novo methyltransferases and genomic imprinting are discussed. This article contains Supplementary Material available at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/2005/95/chen.htm l. (c) 2005 Wiley-Liss, Inc. MeSH","33: J Cell Biochem. 2005 Aug 1;95(5):902-17.","no","Physical and functional interactions between the human DNMT3L protein and","members of the de novo methyltransferase family.","y","PMID: 15861382 [PubMed - indexed for MEDLINE]","MeSH Terms:","Cells, Cultured","DNA (Cytosine-5-)-Methyltransferase/genetics","DNA (Cytosine-5-)-Methyltransferase/metabolism*","DNA Methylation*","Genomic Imprinting","Glutathione Transferase/genetics","Glutathione Transferase/metabolism","Humans","Immunoprecipitation","Isoenzymes","Kidney/cytology","Kidney/metabolism","Protein Binding","Research Support, N.I.H., Extramural","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Saccharomyces cerevisiae","Two-Hybrid System Techniques","Substances:","Isoenzymes","DNMT3L protein, human","DNA (Cytosine-5-)-Methyltransferase","Glutathione Transferase","Grant Support:","GM50575/GM/NIGMS","GM64378-01/GM/NIGMS"]
["ss in understanding neural tube closure mechanisms and how these studies can inform our search for the genes that underlie human neural tube defects. Supplementary material for this article can be found on the American Journal of Medical Genetics (Part C) website (http://www.mrw.interscience.wiley.c","35: Am J Med Genet C Semin Med Genet. 2005 May 15;135(1):59-68.","no","Neural tube closure and neural tube defects: studies in animal models reveal","known knowns and known unknowns.","y","PMID: 15806594 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Disease Models, Animal*","Embryonic Development*","Humans","Nerve Tissue Proteins/physiology","Neural Tube Defects/embryology","Neural Tube Defects/pathology*","Research Support, Non-U.S. Gov't","Substances:","Nerve Tissue Proteins"]
["in the critical region. Refined mapping studies need to be performed to further narrow the region and additional candidate genes need to be examined. Supplementary material for this article can be found on the Birth Defects Research (Part A) website (http://www.mrw.interscience.wiley.com/suppmat/154","44: Birth Defects Res A Clin Mol Teratol. 2005 Mar;73(3):154-61.","no","Toward positional cloning of the curly tail gene.","Brouns MR, Peeters MC, Geurts JM, Merckx DM, Engelen JJ, Hekking JW,","y","PMID: 15678492 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cloning, Molecular","Cytogenetic Analysis","DNA, Complementary","DNA-Binding Proteins/genetics*","DNA-Binding Proteins/metabolism","Linkage (Genetics)","Mice","Mice, Inbred BALB C","Microsatellite Repeats","Research Support, Non-U.S. Gov't","Sequence Analysis, DNA","Transcription Factors/genetics*","Transcription Factors/metabolism","Substances:","DNA, Complementary","DNA-Binding Proteins","Transcription Factors","grainy head-like 3, mouse"]
[" the CAFASP-DP evaluation results are available at http://cafasp4.bioinformatics.buffalo.edu/dp/update.html CONTACT: hkaur@bioinformatics.buffalo.edu SUPPLEMENTARY INFORMATION: Available at http://cafasp4.bioinformatics.buffalo.edu/dp/update.html. Publication Types: Evaluation Studies PMID: 15840708","96: Bioinformatics. 2005 Jun 15;21(12):2917-20. Epub 2005 Apr 19. ","No","Meta-DP: domain prediction meta-server.","Saini HK, Fischer D.","n","PMID: 15840708 [PubMed - indexed for MEDLINE]"]
["source code and the executable program are available either from http://sienabiografix.com or http://sadic.sourceforge.net CONTACT: niccolai@unisi.it SUPPLEMENTARY INFORMATION: http://www.Sienabiogzefix.com/publication. Publication Types: Evaluation Studies PMID: 15827080 [PubMed - indexed for MEDLI","98: Bioinformatics. 2005 Jun 15;21(12):2856-60. Epub 2005 Apr 12. ","No","Three-dimensional computation of atom depth in complex molecular structures.","Varrazzo D, Bernini A, Spiga O, Ciutti A, Chiellini S, Venditti V, Bracci L,","n","PMID: 15827080 [PubMed - indexed for MEDLINE]"]
["CONCLUSION: There continues to be marked","177: Bioinformatics. 2005 Dec 23; [Epub ahead of print] ","No real Link","Ill-health retirement: national rates and updated guidance for occupational","Poole CJ, Bass CM, Sorrell JE, Thompson ME, Harrison JR, Archer AD; Association","n"]
["icense) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html. PMID: 16377612 [PubMed -","1: Bioinformatics. 2005 Dec 23; [Epub ahead of print]","yes","GenomeDiagram: a Python package for the visualisation of large-scale genomic","data.","n","PMID: 16377612 [PubMed - as supplied by publisher]"]
["s data in dot plot-like matrix views. AVAILABILITY: software is freely available at www.win.tue.nl/dnavis; the source code is available upon request. SUPPLEMENTARY INFORMATION: Figures are at the publisher's site, other information and examples are at www.win.tue.nl/dnavis. PMID: 16332715 [PubMed - ","10: Bioinformatics. 2005 Dec 6; [Epub ahead of print]","yes","DNAVis: interactive visualization of comparative genome annotations.","Fiers MW, van de Wetering H, Peeters TH, van Wijk JJ, Nap JP.","n","PMID: 16332715 [PubMed - as supplied by publisher]"]
["f how genes function in symbiotic processes in both Rhizobia and their host plants. AVAILABILITY: http://nodmutdb.vbi.vt.edu CONTACT: cmao@vbi.vt.edu SUPPLEMENTARY INFORMATION: Database schema and data curation model are available at http://nodmutdb.vbi.vt.edu. PMID: 15817696 [PubMed - indexed for M","100: Bioinformatics. 2005 Jun 15;21(12):2927-9. Epub 2005 Apr 7.","yes","NodMutDB: a database for genes and mutants involved in symbiosis.","Mao C, Qiu J, Wang C, Charles TC, Sobral BW.","n","PMID: 15817696 [PubMed - indexed for MEDLINE]"]
["e-profile alignment algorithms where the normalization of alignment scores has traditionally been a challenging task. CONTACT: aleksandar@eidogen.com SUPPLEMENTARY INFORMATION: http://www.eidogen-sertanty.com/Documents/convergent_island_stats_sup.pdf. Publication Types: Evaluation Studies PMID: 1581","102: Bioinformatics. 2005 Jun 15;21(12):2827-31. Epub 2005 Apr 7.","yes","Convergent Island Statistics: a fast method for determining local alignment","score significance.","n","PMID: 15817690 [PubMed - indexed for MEDLINE]"]
["ide insight into the extent of differential expression across genes. AVAILABILITY: http://www.bioconductor.org CONTACT: stefanie.scheid@molgen.mpg.de SUPPLEMENTARY INFORMATION: Please visit our software webpage on http://compdiag.molgen.mpg.de/software. PMID: 15817688 [PubMed - indexed for MEDLINE]","103: Bioinformatics. 2005 Jun 15;21(12):2921-2. Epub 2005 Apr 7.","yes","twilight; a Bioconductor package for estimating the local false discovery rate.","Scheid S, Spang R.","n","PMID: 15817688 [PubMed - indexed for MEDLINE]"]
["nts to build pipelines for sequence processing is provided. AVAILABILITY: http://www.lbm.fmvz.usp.br/egene/ CONTACT: alan@ime.usp.br; argruber@usp.br SUPPLEMENTARY INFORMATION: http://www.lbm.fmvz.usp.br/egene/ PMID: 15814554 [PubMed - indexed for MEDLINE]","104: Bioinformatics. 2005 Jun 15;21(12):2812-3. Epub 2005 Apr 6.","yes","EGene: a configurable pipeline generation system for automated sequence","analysis.","n","PMID: 15814554 [PubMed - indexed for MEDLINE]"]
[" be perfectly suited to portray transcriptional regulatory networks. AVAILABILITY: The R code is available on request. CONTACT: cykao@csie.ntu.edu.tw SUPPLEMENTARY INFORMATION: http://www.csie.ntu.edu.tw/~b89x035/yeast/ Publication Types: Evaluation Studies PMID: 15802287 [PubMed - indexed for MEDLI","105: Bioinformatics. 2005 Jun 15;21(12):2883-90. Epub 2005 Mar 31.","yes","A stochastic differential equation model for quantifying transcriptional","regulatory network in Saccharomyces cerevisiae.","n","PMID: 15802287 [PubMed - indexed for MEDLINE]"]
["d increase in speed over existing programs. AVAILABILITY: Source code for gmap and associated programs is available at http://www.gene.com/share/gmap SUPPLEMENTARY INFORMATION: http://www.gene.com/share/gmap. Publication Types: Evaluation Studies PMID: 15728110 [PubMed - indexed for MEDLINE]","106: Bioinformatics. 2005 May 1;21(9):1859-75. Epub 2005 Feb 22.","yes","GMAP: a genomic mapping and alignment program for mRNA and EST sequences.","Wu TD, Watanabe CK.","n","PMID: 15728110 [PubMed - indexed for MEDLINE]"]
["onal classes have been affected. MEGO is available free of charge for academic use and may be downloaded from http://www.dxy.cn/mego/MEGOInstall.EXE. Supplementary information can be found on the authors' web page at http://www.dxy.cn/mego/ and at the BioTechniques' web site at http://www. BioTechni","107: Biotechniques. 2005 Feb;38(2):277-83.","yes","MEGO: gene functional module expression based on gene ontology.","Tu K, Yu H, Zhu M.","n","PMID: 15727134 [PubMed - indexed for MEDLINE]"]
["mponents in the mixture model, we suggest an alternative criterion, ICL-BIC, which is shown to perform better in selecting the correct mixture model. SUPPLEMENTARY INFORMATION: http://odin.mdacc.tmc.edu/~yuanj/highcorgeneanno.html. PMID: 15713737 [PubMed - indexed for MEDLINE]","108: Bioinformatics. 2005 May 1;21(9):2118-22. Epub 2005 Feb 15.","yes","Applications of beta-mixture models in bioinformatics.","Ji Y, Wu C, Liu P, Wang J, Coombes KR.","n","PMID: 15713737 [PubMed - indexed for MEDLINE]"]
["fference in their size. AVAILABILITY: http://www.dion.che.udel.edu/multiscale/Introduction.html. Fortran 90 code available for academic use by email. SUPPLEMENTARY INFORMATION: Details about the binomial tau-leap algorithm, software and a manual are available at the above website. PMID: 15699024 [Pu","109: Bioinformatics. 2005 May 1;21(9):2136-7. Epub 2005 Feb 4.","yes","Time accelerated Monte Carlo simulations of biological networks using the","binomial tau-leap method.","n","PMID: 15699024 [PubMed - indexed for MEDLINE]"]
["variation in rates of early retirement due to ill-health within and between","11: Bioinformatics. 2005 Dec 6; [Epub ahead of print] ","yes","physicians.","of Local Authority Medical Advisers.","n","PMID: 16332714 [PubMed - as supplied by publisher]"]
["organizations that warrants further investigation. The general and specific","110: Bioinformatics. 2005 May 1;21(9):1846-52. Epub 2005 Feb 2. ","yes","Identification of GPI anchor attachment signals by a Kohonen self-organizing","map.","n","PMID: 15691858 [PubMed - indexed for MEDLINE]"]
["help occupational physicians to make equitable recommendations when assessing","112: Bioinformatics. 2005 May 1;21(9):2083-4. Epub 2005 Feb 3. ","yes","SNPsFinder--a web-based application for genome-wide discovery of single","nucleotide polymorphisms in microbial genomes.","n","PMID: 15691853 [PubMed - indexed for MEDLINE]"]
["for CADLIVE. AVAILABILITY: All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ SUPPLEMENTARY INFORMATION: http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ Publication Types: Evaluation Studies PMID: ","113: Bioinformatics. 2005 May 1;21(9):2036-42. Epub 2005 Jan 27. ","yes","A grid layout algorithm for automatic drawing of biochemical networks.","Li W, Kurata H.","n","PMID: 15677705 [PubMed - indexed for MEDLINE]"]
[" the methods described in this paper and R code for the virtual mass spectrometer are available at http://bioinformatics.mdanderson.org/software.html SUPPLEMENTARY INFORMATION: http://bioinformatics.mdanderson.org/supplements.html. Publication Types: Clinical Trial Validation Studies PMID: 15673564 ","115: Bioinformatics. 2005 May 1;21(9):1764-75. Epub 2005 Jan 26. ","yes","Feature extraction and quantification for mass spectrometry in biomedical","applications using the mean spectrum.","n","PMID: 15673564 [PubMed - indexed for MEDLINE]"]
["ith homology to all S.cerevisiae mitochondrially targeted proteins. One hundred twenty eight of these proteins are novel and are of unknown function. SUPPLEMENTARY INFORMATION: Supplementary tables will be available from http://www.sickkids.ca/Robinsonlab/ PMID: 15671119 [PubMed - indexed for MEDLIN","116: Bioinformatics. 2005 May 1;21(9):1825-30. Epub 2005 Jan 25. ","yes","Computational identification of human mitochondrial proteins based on homology","to yeast mitochondrially targeted proteins.","n","PMID: 15671119 [PubMed - indexed for MEDLINE]"]
["enome, and an expression and cloning approach has been coupled with the predictions of the method. Two genes discovered by this method are discussed. SUPPLEMENTARY INFORMATION: All data used and the results obtained in the cross-validation analysis are available at http://www.soi.city.ac.uk/~conklin","118: Bioinformatics. 2005 May 1;21(9):1776-81. Epub 2005 Jan 20. ","yes","Gene finding for the helical cytokines.","Conklin D, Haldeman B, Gao Z.","n","PMID: 15661800 [PubMed - indexed for MEDLINE]"]
["fs are consistent with published data regarding the binding specificity of the proteins. AVAILABILITY: THEME is freely available for download. Online SUPPLEMENTARY INFORMATION: http://jura.wi.mit.edu/fraenkel/THEME. PMID: 16332710 [PubMed - as supplied by publisher]","12: Bioinformatics. 2005 Dec 6; [Epub ahead of print] ","yes","A hypothesis-based approach for identifying the binding specificity of","regulatory proteins from chromatin immunoprecipitation data.","n","PMID: 16332710 [PubMed - as supplied by publisher]"]
["ow that these highly central residues are strongly correlated with the presence of hot spots of binding free energy. CONTACT: ao-mesa@fujirebio.co.jp SUPPLEMENTARY INFORMATION: http://www.fujirebio.co.jp/support/index.php (under construction). PMID: 15659419 [PubMed - indexed for MEDLINE]","120: Bioinformatics. 2005 Apr 15;21(8):1311-5. Epub 2005 Jan 19. ","yes","Topology of small-world networks of protein-protein complex structures.","del Sol A, Fujihashi H, O'Meara P.","n","PMID: 15659419 [PubMed - indexed for MEDLINE]"]
["emic users at http://ophid.utoronto.ca, both in tab-delimited and PSI-MI formats. Commercial users, please contact I.J. CONTACT: juris@ai.utoronto.ca SUPPLEMENTARY INFORMATION: http://ophid.utoronto.ca/supplInfo.pdf. Publication Types: Evaluation Studies PMID: 15657099 [PubMed - indexed for MEDLINE]","122: Bioinformatics. 2005 May 1;21(9):2076-82. Epub 2005 Jan 18. ","yes","Online predicted human interaction database.","Brown KR, Jurisica I.","n","PMID: 15657099 [PubMed - indexed for MEDLINE]"]
["s illustrated by outlining several current applications. AVAILABILITY: The database is accessible via the world wide web at http://salilab.org/pibase SUPPLEMENTARY INFORMATION: http://salilab.org/pibase/suppinfo.html. PMID: 15657096 [PubMed - indexed for MEDLINE]","123: Bioinformatics. 2005 May 1;21(9):1901-7. Epub 2005 Jan 18. ","yes","PIBASE: a comprehensive database of structurally defined protein interfaces.","Davis FP, Sali A.","n","PMID: 15657096 [PubMed - indexed for MEDLINE]"]
["gorithm. AVAILABILITY: The web tool and a reduced version for local installation are freely available at http://igbmc.u-strasbg.fr/GOAnno/GOAnno.html SUPPLEMENTARY INFORMATION: The website supplies a detailed explanation and illustration of the algorithm at http://igbmc.u-strasbg.fr/GOAnno/GOAnnoHel","125: Bioinformatics. 2005 May 1;21(9):2095-6. Epub 2005 Jan 12. ","yes","GOAnno: GO annotation based on multiple alignment.","Chalmel F, Lardenois A, Thompson JD, Muller J, Sahel JA, Leveillard T, Poch O.","n","PMID: 15647299 [PubMed - indexed for MEDLINE]"]
["native first exons. As a result, we detected a number of unreported alternative first exons, some of which are regulated in a tissue-specific manner. SUPPLEMENTARY INFORMATION: http://www.bioinfo.sfc.keio.ac.jp/research/intron. PMID: 15647298 [PubMed - indexed for MEDLINE]","126: Bioinformatics. 2005 May 1;21(9):1758-63. Epub 2005 Jan 12. ","yes","Computational analysis suggests that alternative first exons are involved in","tissue-specific transcription in rice (Oryza sativa).","n","PMID: 15647298 [PubMed - indexed for MEDLINE]"]
["er two popular motif-finding programs, MEME and AlignACE. AVAILABILITY: SOMBRERO is available free of charge from http://bioinf.nuigalway.ie/sombrero SUPPLEMENTARY INFORMATION: http://bioinf.nuigalway.ie/sombrero/additional. Publication Types: Evaluation Studies PMID: 15647296 [PubMed - indexed for ","127: Bioinformatics. 2005 May 1;21(9):1807-14. Epub 2005 Jan 12. ","yes","Transcription factor binding site identification using the self-organizing map.","Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS.","n","PMID: 15647296 [PubMed - indexed for MEDLINE]"]
["ific scores in order to obtain reliable and valid estimates. AVAILABILITY: The Selecton web server is available at: http://selecton.bioinfo.tau.ac.il SUPPLEMENTARY INFORMATION: More information is available at http://selecton.bioinfo.tau.ac.il/overview.html. A set of examples is available at http://","128: Bioinformatics. 2005 May 1;21(9):2101-3. Epub 2005 Jan 12. ","yes","Selecton: a server for detecting evolutionary forces at a single amino-acid","site.","n","PMID: 15647294 [PubMed - indexed for MEDLINE]"]
[" (2) multiple tumor subtypes and (3) survival times. AVAILABILITY: Code to implement SAFE in the statistical package R is available from the authors. SUPPLEMENTARY INFORMATION: http://www.bios.unc.edu/~fwright/SAFE. Publication Types: Evaluation Studies Validation Studies PMID: 15647293 [PubMed - in","129: Bioinformatics. 2005 May 1;21(9):1943-9. Epub 2005 Jan 12. ","yes","Significance analysis of functional categories in gene expression studies: a","structured permutation approach.","n","PMID: 15647293 [PubMed - indexed for MEDLINE]"]
["ical knowledge. AVAILABILITY: Software is freely available for academic use as a Matlab package, called GENLAB: http://genlab.tudelft.nl/genlab.html. SUPPLEMENTARY INFORMATION: Additional data, results and figures can be found at http://genlab.tudelft.nl/larna.html. PMID: 16332709 [PubMed - as suppl","13: Bioinformatics. 2005 Dec 6; [Epub ahead of print] ","yes","Least Absolute Regression Network Analysis of the murine osteoblast","differentiation network.","n","PMID: 16332709 [PubMed - as supplied by publisher]"]
[" interface at http://systemsbiology.northwestern.edu/BNICE (site under construction). CONTACT: vassily@northwestern.edu or broadbelt@northwestern.edu SUPPLEMENTARY INFORMATION: http://systemsbiology.northwestern.edu/BNICE/publications. Publication Types: Evaluation Studies PMID: 15613400 [PubMed - i","130: Bioinformatics. 2005 Apr 15;21(8):1603-9. Epub 2004 Dec 21. ","yes","Exploring the diversity of complex metabolic networks.","Hatzimanikatis V, Li C, Ionita JA, Henry CS, Jankowski MD, Broadbelt LJ.","n","PMID: 15613400 [PubMed - indexed for MEDLINE]"]
["ee MIAME compliance. AVAILABILITY: The application is available from the author at http://www.ansorge-group.embl.de/bloader CONTACT: schwager@embl.de SUPPLEMENTARY INFORMATION: For more details on BLoader visit the above web page. PMID: 15613394 [PubMed - indexed for MEDLINE]","132: Bioinformatics. 2005 Apr 15;21(8):1727-9. Epub 2004 Dec 21. \n","yes","Bloader--a batch loader application for MIAMExpress.","Schwager C, Blake J.","n","PMID: 15613394 [PubMed - indexed for MEDLINE]"]
["d improve metabolomics by multidisciplinary cooperation. AVAILABILITY: http://csbdb.mpimp-golm.mpg.de/gmd.html CONTACT: Steinhauser@mpimp-golm.mpg.de SUPPLEMENTARY INFORMATION: http://csbdb.mpimp-golm.mpg.de/ PMID: 15613389 [PubMed - indexed for MEDLINE]","133: Bioinformatics. 2005 Apr 15;21(8):1635-8. Epub 2004 Dec 21. \n","yes","GMD@CSB.DB: the Golm Metabolome Database.","Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmuller E, Dormann P,","n","PMID: 15613389 [PubMed - indexed for MEDLINE]"]
["atics.leeds.ac.uk/ppi_pred. The dataset of 180 proteins used in this study is also available via the same web site. CONTACT: westhead@bmb.leeds.ac.uk SUPPLEMENTARY INFORMATION: http://www.bioinformatics.leeds.ac.uk/ppi-pred/supp-material. Publication Types: Evaluation Studies PMID: 15613384 [PubMed ","134: Bioinformatics. 2005 Apr 15;21(8):1487-94. Epub 2004 Dec 21. ","yes","Improved prediction of protein-protein binding sites using a support vector","machines approach.","n","PMID: 15613384 [PubMed - indexed for MEDLINE]"]
["s on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values. Availability SUPPLEMENTARY INFORMATION: RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http:","135: Bioinformatics. 2005 Feb 15;21(4):456-63. Epub 2004 Dec 17. ","yes","RAxML-III: a fast program for maximum likelihood-based inference of large","phylogenetic trees.","n","PMID: 15608047 [PubMed - indexed for MEDLINE]"]
["analysis results and R functions for the proposed methods can be found at http://www.biostat.umn.edu/~baolin/research CONTACT: baolin@biostat.umn.edu SUPPLEMENTARY INFORMATION: http://www.biostat.umn.edu/~baolin/research. Publication Types: Evaluation Studies Validation Studies PMID: 15598833 [PubMe","136: Bioinformatics. 2005 Apr 15;21(8):1565-71. Epub 2004 Dec 14. ","yes","Differential gene expression detection using penalized linear regression models:","the improved SAM statistics.","n","PMID: 15598833 [PubMed - indexed for MEDLINE]"]
["d during the measurements. AVAILABILITY: All programs used for this publication are available on request from the authors. CONTACT: beyer@imb-jena.de SUPPLEMENTARY INFORMATION: Supplementary information about the model and its interpretation can be downloaded from http://www.imb-jena.de/tsb/pad. Pub","138: Bioinformatics. 2005 Apr 15;21(8):1610-6. Epub 2004 Dec 14. ","yes","Dynamic simulation of protein complex formation on a genomic scale.","Beyer A, Wilhelm T.","n","PMID: 15598828 [PubMed - indexed for MEDLINE]"]
["sting programs (ADHoRe and LineUp) for chromosomal homology detection and found that in general CloseUp compares favorably. AVAILABILITY: CloseUp and supplementary information are available at http://www.igb.uci.edu/servers/cgss.html CONTACT: pfbaldi@ics.uci.edu. Publication Types: Evaluation Studie","139: Bioinformatics. 2005 Apr 15;21(8):1339-48. Epub 2004 Dec 7. ","yes","Statistical detection of chromosomal homology using shared-gene density alone.","Hampson SE, Gaut BS, Baldi P.","n","PMID: 15585535 [PubMed - indexed for MEDLINE]"]
["rve distances between examples in the projected subspaces. AVAILABILITY: http://homes.dsi.unimi.it/~valenti/SW/clusterv/download/clusterv_1.0.tar.gz. SUPPLEMENTARY INFORMATION: http://homes.dsi.unimi.it/~valenti/SW/clusterv. PMID: 16332708 [PubMed - as supplied by publisher]","14: Bioinformatics. 2005 Dec 6; [Epub ahead of print] ","yes","Clusterv: a tool for assessing the reliability of clusters discovered in DNA","microarray data.","n","PMID: 16332708 [PubMed - as supplied by publisher]"]
["classification. AVAILABILITY: The HykGene software is freely available at http://www.cs.dartmouth.edu/~wyh/software.htm CONTACT: wyh@cs.dartmouth.edu SUPPLEMENTARY INFORMATION: Supplementary material is available from http://www.cs.dartmouth.edu/~wyh/hykgene/supplement/index.htm. Publication Types: ","141: Bioinformatics. 2005 Apr 15;21(8):1530-7. Epub 2004 Dec 7. ","yes","HykGene: a hybrid approach for selecting marker genes for phenotype","classification using microarray gene expression data.","n","PMID: 15585531 [PubMed - indexed for MEDLINE]"]
["e use of a variety of score matrices for different subclasses of glycans due to their complexity is also discussed. CONTACT: mami@kuicr.kyoto-u.ac.jp SUPPLEMENTARY INFORMATION: The glycan score matrix can be downloaded from http://kanehisa.kuicr.kyoto-u.ac.jp/Paper/kcam/glycanMatrix0.1.txt. Publicat","142: Bioinformatics. 2005 Apr 15;21(8):1457-63. Epub 2004 Dec 7. ","yes","A score matrix to reveal the hidden links in glycans.","Aoki KF, Mamitsuka H, Akutsu T, Kanehisa M.","n","PMID: 15585530 [PubMed - indexed for MEDLINE]"]
["downloaded from http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN. It underlies the GPL version 2. CONTACT: m.futschik@biologie.hu-berlin.de SUPPLEMENTARY INFORMATION: Further information about the methods used in the OLIN software package can be found at http://itb.biologie.hu-berlin.de/~f","143: Bioinformatics. 2005 Apr 15;21(8):1724-6. Epub 2004 Dec 7. ","yes","OLIN: optimized normalization, visualization and quality testing of two-channel","microarray data.","n","PMID: 15585527 [PubMed - indexed for MEDLINE]"]
["Gene Ontology database. AVAILABILITY: VennMaster is platform-independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/ven","144: Bioinformatics. 2005 Apr 15;21(8):1592-5. Epub 2004 Nov 30. ","yes","Generalized Venn diagrams: a new method of visualizing complex genetic set","relations.","n","PMID: 15572472 [PubMed - indexed for MEDLINE]"]
["est possible mechanisms of action of the core elements in the promoters with multiple transcription start sites. CONTACT: ioschikhes-1@medctr.osu.edu SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bmi.osu.edu/~ilya/synergy/Gershenzon_SuppMat-R.pdf. Publication Types: Eva","145: Bioinformatics. 2005 Apr 15;21(8):1295-300. Epub 2004 Nov 30. ","yes","Synergy of human Pol II core promoter elements revealed by statistical sequence","analysis.","n","PMID: 15572469 [PubMed - indexed for MEDLINE]"]
["data set on acute lymphocytic leukemia. AVAILABILITY: The R-package MACAT can be obtained from http://www.compdiag.molgen.mpg.de/software/macat.shtml SUPPLEMENTARY INFORMATION: http://www.compdiag.molgen.mpg.de/software/macat.shtml. Publication Types: Evaluation Studies PMID: 15572464 [PubMed - inde","146: Bioinformatics. 2005 May 1;21(9):2112-3. Epub 2004 Nov 30. ","yes","MACAT--microarray chromosome analysis tool.","Toedling J, Schmeier S, Heinig M, Georgi B, Roepcke S.","n","PMID: 15572464 [PubMed - indexed for MEDLINE]"]
["ILABILITY: The software is publicly available under the GNU general public licence from http://www.cs.may.ie/distributed CONTACT: tom.naughton@may.ie SUPPLEMENTARY INFORMATION: Full documentation and a user manual is available from http://www.cs.may.ie/distributed. Publication Types: Evaluation Stud","147: Bioinformatics. 2005 Apr 15;21(8):1705-6. Epub 2004 Nov 25. ","yes","DSEARCH: sensitive database searching using distributed computing.","Keane TM, Naughton TJ.","n","PMID: 15564297 [PubMed - indexed for MEDLINE]"]
["f signal pathway databases. AVAILABILITY: The pipeline software components are freely available on request to the authors. CONTACT: dstates@umich.edu SUPPLEMENTARY INFORMATION: http://stateslab.bioinformatics.med.umich.edu/software.html. PMID: 15564295 [PubMed - indexed for MEDLINE]","148: Bioinformatics. 2005 Apr 15;21(8):1653-8. Epub 2004 Nov 25. ","yes","Wnt pathway curation using automated natural language processing: combining","statistical methods with partial and full parse for knowledge extraction.","n","PMID: 15564295 [PubMed - indexed for MEDLINE]"]
[" were written in PERL and are freely available at http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html CONTACT: nelsonrt@iastate.edu SUPPLEMENTARY INFORMATION: Figures and dataset can be obtained from: http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html. Publicatio","149: Bioinformatics. 2005 Mar 1;21(5):691-3. Epub 2004 Nov 5. ","yes","ESTminer: a suite of programs for gene and allele identification.","Nelson RT, Grant D, Shoemaker RC.","n","PMID: 15531616 [PubMed - indexed for MEDLINE]"]
[" on proteins of known structure. AVAILABILITY: Paircoil2 is freely available as a web application and for download at http://paircoil2.csail.mit.edu. SUPPLEMENTARY INFORMATION: Available at the journal's web site and at the Paircoil2 web site. PMID: 16317077 [PubMed - as supplied by publisher]","15: Bioinformatics. 2005 Nov 29; [Epub ahead of print] ","yes","Paircoil2: improved prediction of coiled coils from sequence.","McDonnell AV, Jiang T, Keating AE, Berger B.","n","PMID: 16317077 [PubMed - as supplied by publisher]"]
[" provide a coherent framework for functional genomic datamining. AVAILABILITY: Free availability over the Internet. CONTACT: f.c.p.holstege@med.uu.nl SUPPLEMENTARY INFORMATION: http://www.genomics.med.uu.nl/pub/pk/comb_gen_network. Publication Types: Evaluation Studies Validation Studies PMID: 15531","150: Bioinformatics. 2005 Apr 15;21(8):1644-52. Epub 2004 Nov 5. ","yes","Predicting gene function through systematic analysis and quality assessment of","high-throughput data.","n","PMID: 15531615 [PubMed - indexed for MEDLINE]"]
["ring of microarray signals. AVAILABILITY: LabArray is available at http://www.eng.nus.edu.sg/civil/Labarray/labarray.htm CONTACT: cveliuwt@nus.edu.sg SUPPLEMENTARY INFORMATION: Screenshots and instructions for use are available at the above website. Publication Types: Evaluation Studies PMID: 155095","151: Bioinformatics. 2005 Mar 1;21(5):689-90. Epub 2004 Oct 27. ","yes","LabArray: real-time imaging and analytical tool for microarrays.","Ng JK, Liu WT.","n","PMID: 15509598 [PubMed - indexed for MEDLINE]"]
["quence data, with the emphasis on studies of rates and patterns of sequence evolution. AVAILABILITY: http://www.hyphy.org CONTACT: muse@stat.ncsu.edu SUPPLEMENTARY INFORMATION: HyPhydocumentation and tutorials are available at http://www.hyphy.org. PMID: 15509596 [PubMed - indexed for MEDLINE]","152: Bioinformatics. 2005 Mar 1;21(5):676-9. Epub 2004 Oct 27. ","yes","HyPhy: hypothesis testing using phylogenies.","Pond SL, Frost SD, Muse SV.","n","PMID: 15509596 [PubMed - indexed for MEDLINE]"]
["www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. CONTACT: psort-mail@sfu.ca, brinkman@sfu.ca SUPPLEMENTARY INFORMATION: http://www.psort.org/psortb/supplementaryinfo.html. Publication Types: Evaluation Studies PMID: 15501914 [PubMed - indexed ","153: Bioinformatics. 2005 Mar 1;21(5):617-23. Epub 2004 Oct 22. ","yes","PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization","and insights gained from comparative proteome analysis.","n","PMID: 15501914 [PubMed - indexed for MEDLINE]"]
["vel follow-up analysis. AVAILABILITY: The R package arrayMagic is available with BSD license at http://www.bioconductor.org CONTACT: a.buness@dkfz.de SUPPLEMENTARY INFORMATION: The package contains documentation in the form of manual pages and a vignette with a guided tour of a typical workflow. PMI","154: Bioinformatics. 2005 Feb 15;21(4):554-6. Epub 2004 Sep 28. ","yes","arrayMagic: two-colour cDNA microarray quality control and preprocessing.","Buness A, Huber W, Steiner K, Sultmann H, Poustka A.","n","PMID: 15454413 [PubMed - indexed for MEDLINE]"]
["automated assignment program. AVAILABILITY: APART is available from http://sir.lanl.gov/NMR/APART.htm CONTACT: npawley@lanl.gov; rmichalczyk@lanl.gov SUPPLEMENTARY INFORMATION: Manual pages with installation instructions, procedures and screen shots can also be found at http://sir.lanl.gov/NMR/APART","155: Bioinformatics. 2005 Mar 1;21(5):680-2. Epub 2004 Sep 23. ","yes","APART: automated preprocessing for NMR assignments with reduced tedium.","Pawley NH, Gans JD, Michalczyk R.","n","PMID: 15388520 [PubMed - indexed for MEDLINE]"]
["blically available at the GeneNote website, http://genecards.weizmann.ac.il/genenote/ and, GEO accession GSE803. CONTACT: doron.lancet@weizmann.ac.il SUPPLEMENTARY INFORMATION: Four tables available at the above site. Publication Types: Evaluation Studies PMID: 15388519 [PubMed - indexed for MEDLINE","156: Bioinformatics. 2005 Mar 1;21(5):650-9. Epub 2004 Sep 23. ","yes","Genome-wide midrange transcription profiles reveal expression level","relationships in human tissue specification.","n","PMID: 15388519 [PubMed - indexed for MEDLINE]"]
["atabase of Interacting Proteins. The validity of our approach is successfully tested against other available techniques. CONTACT: leone@isiosf.isi.it SUPPLEMENTARY INFORMATION: http://isiosf.isi.it/~pagnani Publication Types: Evaluation Studies Validation Studies PMID: 15377508 [PubMed - indexed for","157: Bioinformatics. 2005 Jan 15;21(2):239-47. Epub 2004 Sep 17. \n","yes","Predicting protein functions with message passing algorithms.","Leone M, Pagnani A.","n","PMID: 15377508 [PubMed - indexed for MEDLINE]"]
["e drawing methods. AVAILABILITY: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html) CONTACT: darren@science.uct.ac.za SUPPLEMENTARY INFORMATION: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded fro","158: Bioinformatics. 2005 Jan 15;21(2):260-2. Epub 2004 Sep 17. ","yes","RDP2: recombination detection and analysis from sequence alignments.","Martin DP, Williamson C, Posada D.","n","PMID: 15377507 [PubMed - indexed for MEDLINE]"]
["scribed below. A PhenomicDB implementation differing in some technical details has been set up for the public at Metalife AG http://www.phenomicDB.de SUPPLEMENTARY INFORMATION: database model, semantic mapping table. PMID: 15374875 [PubMed - indexed for MEDLINE]","159: Bioinformatics. 2005 Feb 1;21(3):418-20. Epub 2004 Sep 16. ","yes","PhenomicDB: a multi-species genotype/phenotype database for comparative","phenomics.","n","PMID: 15374875 [PubMed - indexed for MEDLINE]"]
["slightly exceeded that of the Smith-Waterman algorithm and two Hidden Markov Model-based algorithms. AVAILABILITY: www.inf.u-szeged.hu/~kocsor/CBM05 (supplementary data). PMID: 16317070 [PubMed - as supplied by publisher]","3: Bioinformatics. 2005 Dec 20; [Epub ahead of print] ","yes","Application of compression-based distance measures to protein sequence","classification: a methodological study.","n","PMID: 16317070 [PubMed - as supplied by publisher]"]
["intosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Clann has been written in the C programming language. Source code is available on request. PMID: 15374874 [PubMed - indexed","159: Bioinformatics. 2005 Feb 1;21(3):418-20. Epub 2004 Sep 16. ","yes","Clann: investigating phylogenetic information through supertree analyses.","Creevey CJ, McInerney JO.","n","PMID: 15374874 [PubMed - indexed for MEDLINE]"]
["LITY: The R package is freely available at http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html CONTACT: delmar@inapg.inra.fr SUPPLEMENTARY INFORMATION: http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html. Publication Types: Evaluation Studies PMID: 1","161: Bioinformatics. 2005 Feb 15;21(4):502-8. Epub 2004 Sep 16. ","yes","VarMixt: efficient variance modelling for the differential analysis of","replicated gene expression data.","n","PMID: 15374871 [PubMed - indexed for MEDLINE]"]
["ion on time-lagged co-regulation between genes/gene clusters. AVAILABILITY: The software is available upon request. CONTACT: jiliping@comp.nus.edu.sg SUPPLEMENTARY INFORMATION: Supplementary tables and figures for this paper can be found at c. Publication Ty","162: Bioinformatics. 2005 Feb 15;21(4):509-16. Epub 2004 Sep 16. ","yes","Identifying time-lagged gene clusters using gene expression data.","Ji L, Tan KL.","n","PMID: 15374868 [PubMed - indexed for MEDLINE]"]
["n sequences. AVAILABILITY: The program is freely available for non-profit organizations, upon request to the authors. CONTACT: giorgio.valle@unipd.it SUPPLEMENTARY INFORMATION: The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analys","163: Bioinformatics. 2005 Mar 1;21(5):582-8. Epub 2004 Sep 16. ","yes","RAP: a new computer program for de novo identification of repeated sequences in","whole genomes.","n","PMID: 15374857 [PubMed - indexed for MEDLINE]"]
["s against random patterns. Wet-experimentally discovered motifs reported in the literature were also used to confirm the effectiveness of our method. SUPPLEMENTARY INFORMATION: http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs. Publication Types: Evaluation Studies Validation Studies PMID: 15374856 [P","164: Bioinformatics. 2005 Feb 1;21(3):314-24. Epub 2004 Sep 16. ","yes","Discovery of stable and significant binding motif pairs from PDB complexes and","protein interaction datasets.","n","PMID: 15374856 [PubMed - indexed for MEDLINE]"]
["nsional functional genomics datasets, VizRank can systematically find relevant biological patterns. AVAILABILITY: http://www.ailab.si/supp/bi-vizrank SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-vizrank. PMID: 15358614 [PubMed - indexed for MEDLINE]","165: Bioinformatics. 2005 Feb 1;21(3):413-4. Epub 2004 Sep 9. ","yes","VizRank: finding informative data projections in functional genomics by machine","learning.","n","PMID: 15358614 [PubMed - indexed for MEDLINE]"]
["AILABILITY: A CRC card template, XML representation and XML schema are freely available at http://people.musc.edu/~zhengw/CRCCard/CRC_Card_Index.html SUPPLEMENTARY INFORMATION: Supplemental Figures 1-4. PMID: 15353449 [PubMed - indexed for MEDLINE]","167: Bioinformatics. 2005 Feb 1;21(3):415-7. Epub 2004 Sep 7. ","yes","Capturing biological information with class-responsibility-collaboration cards.","Shegogue D, Zheng WJ.","n","PMID: 15353449 [PubMed - indexed for MEDLINE]"]
[" downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset. SUPPLEMENTARY INFORMATION: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu. PMID: 1535344","168: Bioinformatics. 2005 Feb 1;21(3):402-4. Epub 2004 Sep 7. ","yes","SNAP: workbench management tool for evolutionary population genetic analysis.","Price EW, Carbone I.","n","PMID: 15353448 [PubMed - indexed for MEDLINE]"]
["LITY: All data generated in this study are available for download and browsing at http://pedant.gsf.de/ARIA/index.htm. CONTACT: d.frishman@wzw.tum.de SUPPLEMENTARY INFORMATION: http://pedant.gsf.de/ARIA/index.htm. PMID: 16306393 [PubMed - as supplied by publisher]","17: Bioinformatics. 2005 Nov 1;21(Suppl_3):iii49-iii57. ","yes","Mining sequence annotation databanks for association patterns.","Artamonova II, Frishman G, Gelfand MS, Frishman D.","n","PMID: 16306393 [PubMed - as supplied by publisher]"]
["D scores, NPL scores, P-values and other parameters. AVAILABILITY: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.ht m SUPPLEMENTARY INFORMATION: Supplementary information is available on the website. PMID: 15347576 [PubMed - indexed for MEDLINE]","170: Bioinformatics. 2005 Feb 1;21(3):405-7. Epub 2004 Sep 3. ","yes","easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage","analyses.","n","PMID: 15347576 [PubMed - indexed for MEDLINE]"]
["prove useful for detecting novel overlapping genes--especially short coding ORFs in viruses. AVAILABILITY: Programs may be obtained from the authors. SUPPLEMENTARY INFORMATION: http://biochem.otago.ac.nz/double.html. Publication Types: Evaluation Studies PMID: 15347574 [PubMed - indexed for MEDLINE]","171: Bioinformatics. 2005 Feb 1;21(3):282-92. Epub 2004 Sep 3. ","yes","Detecting overlapping coding sequences with pairwise alignments.","Firth AE, Brown CM.","n","PMID: 15347574 [PubMed - indexed for MEDLINE]"]
["or factorial experiment design and template loading methods to ease the submission process for large experiments. AVAILABILITY: http://barleybase.org SUPPLEMENTARY INFORMATION: BarleyExpress Users Manual. PMID: 15347571 [PubMed - indexed for MEDLINE]","172: Bioinformatics. 2005 Feb 1;21(3):399-401. Epub 2004 Sep 3. ","yes","BarleyExpress: a web-based submission tool for enriched microarray database","annotations.","n","PMID: 15347571 [PubMed - indexed for MEDLINE]"]
["pare and query libraries of frequency matrices for TFBSs. AVAILABILITY: Software is available to use over the Web at http://rulai.cshl.edu/MatCompare SUPPLEMENTARY INFORMATION: Database and clustering statistics, matrix families and representatives are available at http://rulai.cshl.edu/MatCompare/S","173: Bioinformatics. 2005 Feb 1;21(3):307-13. Epub 2004 Aug 19. ","yes","Similarity of position frequency matrices for transcription factor binding","sites.","n","PMID: 15319260 [PubMed - indexed for MEDLINE]"]
[" simulation package Dizzy. It is available for download at http://labs.systemsbiology.net/bolouri/software/Dizzy/ CONTACT: dorrell@systemsbiology.org SUPPLEMENTARY INFORMATION: A conceptual model of the regulatory part of the galactose utilization pathway in yeast, used as an example in the paper, i","174: Bioinformatics. 2005 Jan 15;21(2):208-17. Epub 2004 Aug 19. ","yes","A method for estimating stochastic noise in large genetic regulatory networks.","Orrell D, Ramsey S, de Atauri P, Bolouri H.","n","PMID: 15319259 [PubMed - indexed for MEDLINE]"]
["ta flow and to customize their analyses by combining common data analysis tools to fit their needs. AVAILABILITY: http://www.ailab.si/supp/bi-visprog SUPPLEMENTARY INFORMATION: http://www.ailab.si/supp/bi-visprog. PMID: 15308546 [PubMed - indexed for MEDLINE]","175: Bioinformatics. 2005 Feb 1;21(3):396-8. Epub 2004 Aug 12. ","yes","Microarray data mining with visual programming.","Curk T, Demsar J, Xu Q, Leban G, Petrovic U, Bratko I, Shaulsky G, Zupan B.","n","PMID: 15308546 [PubMed - indexed for MEDLINE]"]
["easured over different subsets of patients. A possible biological explanation for these properties is discussed. CONTACT: eytan.domany@weizmann.ac.il SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/downloads/liate/ Publication Types: Evaluation Studies Validation Studie","176: Bioinformatics. 2005 Jan 15;21(2):171-8. Epub 2004 Aug 12. ","yes","Outcome signature genes in breast cancer: is there a unique set?","Ein-Dor L, Kela I, Getz G, Givol D, Domany E.","n","PMID: 15308542 [PubMed - indexed for MEDLINE]"]
["lassification scheme named DALI, which is found to be more accurate, but extremely slow. The software is available upon request from the authors. The supplementary information on ProtClass method can be found at: http://xena1.ddns.comp.nus.edu.sg/ approximately genesis/PClass.htm. PMID: 16305330 [Pu","18: J Comput Biol. 2005 Nov;12(9):1221-41. ","yes","Automatic 3D protein structure classification without structural alignment.","Aung Z, Tan KL.","n","PMID: 16305330 [PubMed - in process]"]
[" algorithm, BDTree provides a higher prediction accuracy in cross-validations. AVAILABILITY: The software is available upon request from the authors. SUPPLEMENTARY INFORMATION: http://cic.cs.wustl.edu/bdtree/. PMID: 16303796 [PubMed - as supplied by publisher]","19: Bioinformatics. 2005 Nov 22; [Epub ahead of print] ","yes","A bi-dimensional regression tree approach to the modeling of gene expression","regulation.","n","PMID: 16303796 [PubMed - as supplied by publisher]"]
["s successful in estimating gene networks that capture many known relationships as well as several unknown relationships which are likely to be novel. Supplementary information is available at http://bonsai.ims.u-tokyo.ac.jp/~tamada/bayesnet/. PMID: 16374908 [PubMed - in process]","2: J Bioinform Comput Biol. 2005 Dec;3(6):1295-313. ","yes","Utilizing evolutionary information and gene expression data for estimating gene","networks with bayesian network models.","n","PMID: 16374908 [PubMed - in process]"]
["he first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera. SUPPLEMENTARY INFORMATION: http://www.unil.ch/comparativegenometrics/collyn_et_al_2005/collyn.htm. PMID: 16303795 [PubMed - as supplied by publisher]","20: Bioinformatics. 2005 Nov 22; [Epub ahead of print] ","yes","Describing ancient horizontal gene transfers at the nucleotide and gene levels","by comparative pathogenicity island genometrics.","n","PMID: 16303795 [PubMed - as supplied by publisher]"]
["iption factor binding sites in non-coding DNA. AVAILABILITY: ACANA software and test sequence data are publicly available at http://BioMedEmpire.org/ SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. CONTACT: li3@niehs.nih.gov. PMID: 16301203 [PubMed - in pro","21: Bioinformatics. 2006 Jan 1;22(1):29-34. Epub 2005 Nov 13. ","yes","PATIKAweb: a Web interface for analyzing biological pathways through advanced","querying and visualization.","n","PMID: 16301203 [PubMed - in process]"]
["g facilities to various pathway exchange formats. AVAILABILITY: The Web site is freely accessible to non-commercial users from http://web.patika.org. SUPPLEMENTARY INFORMATION: Detailed information is available on the tool Web site (http://www.cs.bilkent.edu.tr/~patikaweb), including key features, s","22: Bioinformatics. 2005 Nov 15; [Epub ahead of print] ","yes","Intervention in a family of Boolean networks.","Choudhary A, Datta A, Bittner ML, Dougherty ER.","n","PMID: 16287939 [PubMed - as supplied by publisher]"]
["evise a control strategy that reduces the WNT5A gene's action in affecting biological regulation. AVAILABILITY: The software is available on request. SUPPLEMENTARY INFORMATION: The supplementary Information is available at http://ee.tamu.edu/~edward/tree. PMID: 16286362 [PubMed - as supplied by publ","23: Bioinformatics. 2005 Nov 12; [Epub ahead of print] ","yes","Pathway recognition and augmentation by computational analysis of microarray","expression data.","n","PMID: 16286362 [PubMed - as supplied by publisher]"]
["ith rates of 10-fold or better 10-20% of the time. AVAILABILITY: The software is available for academic research use free of charge by email request. SUPPLEMENTARY INFORMATION: Data used in the paper may be downloaded from http://www.jainlab.org/downloads.html. PMID: 16278238 [PubMed - as supplied b","24: Bioinformatics. 2005 Nov 8; [Epub ahead of print] ","yes","ClaNC: point-and-click software for classifying microarrays to nearest","centroids.","n","PMID: 16278238 [PubMed - as supplied by publisher]"]
["vailable as an R package. AVAILABILITY: ClaNC is freely available from http://students.washington.edu/adabney/clanc CONTACT: adabney@u.washington.edu SUPPLEMENTARY INFORMATION: http://students.washington.edu/adabney/clanc/figure2.pdf. PMID: 16269418 [PubMed - in process]","25: Bioinformatics. 2006 Jan 1;22(1):122-3. Epub 2005 Nov 2. ","yes","An efficient comprehensive search algorithm for tagSNP selection using linkage","disequilibrium criteria.","n","PMID: 16269418 [PubMed - in process]"]
["d FESTA has been developed based on this algorithm. The program is freely available and can be downloaded at http://www.sph.umich.edu/csg/qin/FESTA/. SUPPLEMENTARY INFORMATION: http://www.sph.umich.edu/csg/qin/FESTA/. PMID: 16269414 [PubMed - as supplied by publisher]","26: Bioinformatics. 2005 Nov 3; [Epub ahead of print] ","yes","A genotype calling algorithm for affymetrix SNP arrays.","Rabbee N, Speed TP.","n","PMID: 16269414 [PubMed - as supplied by publisher]"]
["tware is implemented in R and is available from Bioconductor or from the first author at nrabbee@post.harvard.edu. CONTACT: nrabbee@stat.berkeley.edu SUPPLEMENTARY INFORMATION: http://www.stat.berkeley.edu/users/nrabbee/693.pdf. PMID: 16267090 [PubMed - in process]","27: Bioinformatics. 2006 Jan 1;22(1):7-12. Epub 2005 Nov 2. ","yes","Sequence-based heuristics for faster annotation of non-coding RNA families.","Weinberg Z, Ruzzo WL.","n","PMID: 16267090 [PubMed - in process]"]
["f ncRNA families. AVAILABILITY: The source code is available under GNU Public License at the supplementary web site. CONTACT: zasha@cs.washington.edu SUPPLEMENTARY INFORMATION: http://bio.cs.washington.edu/supplements/zasha-HeurHmm-2004/ (Technical details, results, C++ code). PMID: 16267089 [PubMed","28: Bioinformatics. 2006 Jan 1;22(1):35-9. Epub 2005 Nov 2. ","yes","Improved spliced alignment from an information theoretic approach.","Zhang M, Gish W.","n","PMID: 16267089 [PubMed - in process]"]
["http://blast.wustl.edu/exalin. The software (scripts, source code and binaries) is copyrighted but free for all to use. CONTACT: gish@blast.wustl.edu SUPPLEMENTARY INFORMATION: http://blast.wustl.edu/exalin/exalin-supplement.pdf. PMID: 16267086 [PubMed - in process]","29: Bioinformatics. 2006 Jan 1;22(1):13-20. Epub 2005 Nov 2. ","yes","BioContrasts: extracting and exploiting protein-protein contrastive relations","from biomedical literature.","n","PMID: 16267086 [PubMed - in process]"]
["ways. AVAILABILITY: BioContrasts can be accessed at http://biocontrasts.i2r.a-star.edu.sg. It is also mirrored at http://biocontrasts.biopathway.org. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. PMID: 16368768 [PubMed - as supplied by publisher]","3: Bioinformatics. 2005 Dec 20; [Epub ahead of print] ","yes","BioThesaurus: a web-based thesaurus of protein and gene names.","Liu H, Hu ZZ, Zhang J, Wu C.","n","PMID: 16368768 [PubMed - as supplied by publisher]"]
[" same names. AVAILABILITY: BioThesaurus is accessible for online searching at http://pir.georgetown.edu/iprolink/biothesaurus Contact: hfliu@umbc.edu SUPPLEMENTARY INFORMATION: Supplementary data are accessible at http://pir.georgetown.edu/iprolink/biothesaurus/supplement/ PMID: 16267085 [PubMed - i","30: Bioinformatics. 2006 Jan 1;22(1):103-5. Epub 2005 Nov 2. ","yes","SSEP-Domain: protein domain prediction by alignment of secondary structure","elements and profiles.","n","PMID: 16267085 [PubMed - in process]"]
["riments. Evaluation of the final version shows further improvement over these results together with a significant speed-up. AVAILABILITY: The server, supplementary information, and the detailed predictions are available at http://www.bio.ifi.lmu.de/SSEP/. PMID: 16267083 [PubMed - as supplied by publ","4: Genome Inform Ser Workshop Genome Inform. 2005;16(1):49-58. ","yes","libSRES: a C library for stochastic ranking evolution strategy for parameter","estimation.","n","PMID: 16267083 [PubMed - as supplied by publisher]"]
["tisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/ CONTACT: xyn@bmb.uga.edu SUPPLEMENTARY INFORMATION: Detailed documentation for libSRES is available at http://csbl.bmb.uga.edu/~jix/science/libSRES/ PMID: 16267082 [PubMed - i","32: Bioinformatics. 2006 Jan 1;22(1):124-6. Epub 2005 Nov 2. ","yes","Intelligent client for integrating bioinformatics services.","Navas-Delgado I, Rojano-Munoz Mdel M, Ramirez S, Perez AJ, Andres Leon E,","n","PMID: 16267082 [PubMed - in process]"]
["s in Spain. AVAILABILITY: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ CONTACT: ots@ac.uma.es SUPPLEMENTARY INFORMATION: http://www.inab.org/Help/Main/index.html. PMID: 16257987 [PubMed - in process]","33: Bioinformatics. 2006 Jan 1;22(1):106-11. Epub 2005 Oct 27. ","yes","A generic motif discovery algorithm for sequential data.","Jensen KL, Styczynski MP, Rigoutsos I, Stephanopoulos GN.","n","PMID: 16257987 [PubMed - in process]"]
["e discovery of conserved protein substructures. AVAILABILITY: Gemoda is freely available at http://web.mit.edu/bamel/gemoda CONTACT: gregstep@mit.edu SUPPLEMENTARY INFORMATION: Available at http://web.mit.edu/bamel/gemoda. PMID: 16257985 [PubMed - in process]","34: Bioinformatics. 2006 Jan 1;22(1):21-8. Epub 2005 Oct 27. ","yes","Robust multi-scale clustering of large DNA microarray datasets with the","consensus algorithm.","n","PMID: 16257985 [PubMed - in process]"]
["m ClusterLustre, and the simulated dataset for testing are available upon request from T.G. and O.W. CONTACT: tg@biocentrum.dtu.dk and owi@imm.dtu.dk SUPPLEMENTARY INFORMATION: http://www.cmb.dtu.dk/ PMID: 16257984 [PubMed - as supplied by publisher]","35: Bioinformatics. 2006 Jan 1;22(1):58-67. Epub 2005 Oct 27. ","yes","Gene selection using support vector machines with non-convex penalty.","Zhang HH, Ahn J, Lin X, Park C.","n","PMID: 16257984 [PubMed - as supplied by publisher]"]
["tasets and has produced very promising results. AVAILABILITY: MATLAB codes are available upon request from the authors. CONTACT: hzhang@stat.ncsu.edu SUPPLEMENTARY INFORMATION: http://www4.stat.ncsu.edu/~hzhang/research.html. PMID: 16249260 [PubMed - in process]","36: Bioinformatics. 2006 Jan 1;22(1):88-95. Epub 2005 Oct 25. ","yes","Integrating time-course microarray gene expression profiles with cytotoxicity","for identification of biomarkers in primary rat hepatocytes exposed to cadmium.","n","PMID: 16249260 [PubMed - in process]"]
["atlab source code is available upon request and DNA microarray data are available at GEO (http://www.ncbi.nlm.nih.gov/geo). Contact: cwang61@ucla.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. PMID: 16249259 [PubMed - in process]","37: Bioinformatics. 2006 Jan 1;22(1):77-87. Epub 2005 Oct 25. ","yes","PilZ domain is part of the bacterial c-di-GMP binding protein.","Amikam D, Galperin MY.","n","PMID: 16249259 [PubMed - in process]"]
[" system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Contact: galperin@ncbi.nlm.nih.gov SUPPLEMENTARY INFORMATION: http://www.ncbi.nlm.nih.gov/Complete_Genomes/SigCensus/PilZ.html. PMID: 16249258 [PubMed - in process]","38: Bioinformatics. 2006 Jan 1;22(1):3-6. Epub 2005 Oct 25. ","yes","Identifying genes from up-down properties of microarray expression series.","Willbrand K, Radvanyi F, Nadal JP, Thiery JP, Fink TM.","n","PMID: 16249258 [PubMed - in process]"]
["hmark, we blindly identified genes from yeast cell cycles without selecting for periodic or any other anticipated behaviour. CONTACT: tmf20@cam.ac.uk SUPPLEMENTARY INFORMATION: The complete versions of Table 2 and Figure 4, as well as other material, can be found at http://www.lps.ens.fr/~willbran/u","39: Bioinformatics. 2005 Oct 15;21(20):3859-64. ","yes","Identification of conserved structural features at sequentially degenerate","locations in transcription factor binding sites.","n","PMID: 16221984 [PubMed - indexed for MEDLINE]"]
["vement in our ability to find these sites in genomic sequences. Availability: ICSF is freely available to academic users at http://zlab.bu.edu/ICSF . Supplementary information: http://zlab.bu.edu/ICSF . PMID: 16362906 [PubMed - indexed for MEDLINE]","4: Genome Inform Ser Workshop Genome Inform. 2005;16(1):49-58. ","yes","ARTS: alignment of RNA tertiary structures.","Dror O, Nussinov R, Wolfson H.","n","PMID: 16362906 [PubMed - indexed for MEDLINE]"]
["uct an all-against-all comparison of all the RNA structures currently available in the Protein Data Bank. AVAILABILITY: The program, a web-server and supplementary information are available on http://bioinfo3d.cs.tau.ac.il/ARTS CONTACT: oranit@post.tau.ac.il. PMID: 16204124 [PubMed - in process]","40: Bioinformatics. 2005 Sep 1;21 Suppl 2:ii47-ii53. ","yes","Implementing the iHOP concept for navigation of biomedical literature.","Hoffmann R, Valencia A.","n","PMID: 16204124 [PubMed - in process]"]
["s cerevisiae and Escherichia coli. AVAILABILITY: iHOP is freely accessible at http://www.pdg.cnb.uam.es/UniPub/iHOP/ CONTACT: hoffmann@cbio.mskcc.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. PMID: 16204114 [PubMed - in process]","41: Bioinformatics. 2005 Sep 1;21 Suppl 2:ii252-ii258. ","yes","Lineage-specific gene loss following mitochondrial endosymbiosis and its","potential for function prediction in eukaryotes.","n","PMID: 16204114 [PubMed - in process]"]
["ar history of gene loss events, and we use this property to predict functional interactions among proteins in our set. CONTACT: T.Gabaldon@cmbi.ru.nl SUPPLEMENTARY INFORMATION: Sequences and trees for the selected orthologous groups can be accessed at http://www.cmbi.kun.nl/~jagabald/table_groupsb.h","42: Bioinformatics. 2005 Sep 1;21 Suppl 2:ii144-ii150. ","yes","A fully Bayesian model to cluster gene-expression profiles.","Vogl C, Sanchez-Cabo F, Stocker G, Hubbard S, Wolkenhauer O, Trajanoski Z.","n","PMID: 16204094 [PubMed - in process]"]
["n when some values were missing. AVAILABILITY: The code is available at http://genome.tugraz.at/BayesianClustering/ CONTACT: claus.vogl@vu-wien.ac.at SUPPLEMENTARY INFORMATION: The supplementary material is available at http://genome.tugraz.at/BayesianClustering/ PMID: 16204092 [PubMed - in process]","43: Bioinformatics. 2005 Sep 1;21 Suppl 2:ii130-ii136. ","yes","Inference of transcriptional regulatory network by two-stage constrained space","factor analysis.","n","PMID: 16204092 [PubMed - in process]"]
["ulatory networks obtained for Saccharomyces cerevisiae, one under the normal growth condition and the other under the environmental stress condition. SUPPLEMENTARY INFORMATION: http://kiefer.stat.ucla.edu/lap2/download/bti656_supplement.pdf. PMID: 16144806 [PubMed - indexed for MEDLINE]","44: Bioinformatics. 2005 Nov 1;21(21):4033-8. Epub 2005 Sep 6. ","yes","Detection of DNA copy number alterations using penalized least squares","regression.","n","PMID: 16144806 [PubMed - indexed for MEDLINE]"]
["nts while appropriately controlling the false positives. AVAILABILITY: http://bioinformatics.med.yale.edu/DNACopyNumber CONTACT: hongyu.zhao@yale.edu SUPPLEMENTARY INFORMATION: http://bioinformatics.med.yale.edu/DNACopyNumber. PMID: 16131523 [PubMed - indexed for MEDLINE]","45: Bioinformatics. 2005 Oct 15;21(20):3811-7. Epub 2005 Aug 30. ","yes","Detecting single-feature polymorphisms using oligonucleotide arrays and","robustified projection pursuit.","n","PMID: 16131523 [PubMed - indexed for MEDLINE]"]
["e Barley Dominant versus Recessive. AVAILABILITY: The algorithm is available upon request from the corresponding author. CONTACT: xinping.cui@ucr.edu SUPPLEMENTARY INFORMATION: http://faculty.ucr.edu/~xpcui. Publication Types: Evaluation Studies PMID: 16118260 [PubMed - indexed for MEDLINE]","46: Bioinformatics. 2005 Oct 15;21(20):3852-8. Epub 2005 Aug 23. ","yes","ORIOGEN: order restricted inference for ordered gene expression data.","Peddada S, Harris S, Zajd J, Harvey E.","n","PMID: 16118260 [PubMed - indexed for MEDLINE]"]
["iehs.nih.gov/dirbb/oriogen/index.cfm CONTACT: peddada@niehs.nih.gov (for statistical questions) and oriogen@constellagroup.com (for software support) SUPPLEMENTARY INFORMATION: ORIOGEN has a full set of help files. Also, an example input file is provided with the download. PMID: 16109745 [PubMed - i","47: Bioinformatics. 2005 Oct 15;21(20):3933-4. Epub 2005 Aug 18. ","yes","MESHI: a new library of Java classes for molecular modeling.","Kalisman N, Levi A, Maximova T, Reshef D, Zafriri-Lynn S, Gleyzer Y, Keasar C.","n","PMID: 16109745 [PubMed - indexed for MEDLINE]"]
["are freely available at http://www.cs.bgu.ac.il/~meshi; the MESHI API is available at http://www.cs.bgu.ac.il/~meshi/API CONTACT: keasar@cs.bgu.ac.il SUPPLEMENTARY INFORMATION: The Supplementary information includes (1) a detailed description of several key packages and classes, and (2) a brief pres","48: Bioinformatics. 2005 Oct 15;21(20):3931-2. Epub 2005 Aug 16. ","yes","A geometric invariant-based framework for the analysis of protein conformational","space.","n","PMID: 16105898 [PubMed - indexed for MEDLINE]"]
["ailable conformations reveals that the number of preferred local conformations is several orders of magnitude smaller than that suggested previously. SUPPLEMENTARY INFORMATION: www.it.iitb.ac.in/~ashish/bioinfo2005/. PMID: 16096349 [PubMed - indexed for MEDLINE]","49: Bioinformatics. 2005 Sep 15;21(18):3622-8. Epub 2005 Aug 11. ","yes","eQTL Explorer: integrated mining of combined genetic linkage and expression","experiments.","n","PMID: 16096349 [PubMed - indexed for MEDLINE]"]
["nd powerful tool to interrogate these very large and complex datasets. AVAILABILITY: The application is freely available for non-commercial research. SUPPLEMENTARY INFORMATION: Documentation, source code and a demonstration version are available at www.bioinformatics.ic.ac.uk/eqtl/. PMID: 16357031 [","5: Bioinformatics. 2005 Dec 15; [Epub ahead of print] ","yes","ProRule: a new database containing functional and structural information on","PROSITE profiles.","n","PMID: 16357031 [PubMed - as supplied by publisher]"]
["he position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about ","50: Bioinformatics. 2005 Nov 1;21(21):4060-6. Epub 2005 Aug 9. ","yes","Study of coordinative gene expression at the biological process level.","Yu T, Sun W, Yuan S, Li KC.","n","PMID: 16091411 [PubMed - indexed for MEDLINE]"]
["lt to find otherwise. Using another dataset, we report a sharply different network structure featuring cellular responses under environmental stress. SUPPLEMENTARY INFORMATION: http://kiefer.stat.ucla.edu/lap2/download/KL_supplement.pdf. PMID: 16076891 [PubMed - indexed for MEDLINE]","51: Bioinformatics. 2005 Sep 15;21(18):3651-7. Epub 2005 Aug 2. ","yes","Simpleaffy: a BioConductor package for Affymetrix Quality Control and data","analysis.","n","PMID: 16076891 [PubMed - indexed for MEDLINE]"]
["ular algorithms for generating expression summaries and detection calls. AVAILABILITY: Simpleaffy can be downloaded from http://www.bioconductor.org. SUPPLEMENTARY INFORMATION: Additional information can be found on the supplementary website located at http://bioinformatics.picr.man.ac.uk. PMID: 160","53: Bioinformatics. 2005 Sep 15;21(18):3683-5. Epub 2005 Aug 2. ","yes","Chemical-induced atrial thrombosis in NTP rodent studies.","Yoshizawa K, Kissling GE, Johnson JA, Clayton NP, Flagler ND, Nyska A.","n","PMID: 16076888 [PubMed - indexed for MEDLINE]"]
["al activity, such as atrial fibrillation, which could cause stasis of blood within the left atrial appendage, contributing to left atrial thrombosis. Supplementary data referenced in this paper are not printed in this issue of Toxicologic Pathology. They are available as downloadable files at http:/","54: Toxicol Pathol. 2005;33(5):517-32. ","yes","A statistical model for HIV-1 sequence classification using the subtype analyser","(STAR).","n","PMID: 16048847 [PubMed - indexed for MEDLINE]"]
[": STAR is available as compiled (Linux Fedora 3) or source code from http://pgv19.virol.ucl.ac.uk/download/star_linux.tar CONTACT: p.kellam@ucl.ac.uk SUPPLEMENTARY INFORMATION: http://pgv19.virol.ucl.ac.uk/download/star_supplement Publication Types: Evaluation Studies PMID: 16046498 [PubMed - indexe","55: Bioinformatics. 2005 Sep 1;21(17):3535-40. Epub 2005 Jul 26. ","yes","TileMap: create chromosomal map of tiling array hybridizations.","Ji H, Wong WH.","n","PMID: 16046498 [PubMed - indexed for MEDLINE]"]
["iscovery rate for MA and model parameters for HMM. AVAILABILITY: TileMap is freely available at http://biogibbs.stanford.edu/~jihk/TileMap/index.htm. SUPPLEMENTARY INFORMATION: http://biogibbs.stanford.edu/~jihk/TileMap/index.htm (includes coloured versions of all figures). PMID: 16046496 [PubMed - ","56: Bioinformatics. 2005 Sep 15;21(18):3629-36. Epub 2005 Jul 26. ","yes","Erratum in:","Proteomics. 2005 Oct;5(15):4046.","n","PMID: 16046496 [PubMed - indexed for MEDLINE]"]
["are either published directly with the article, resulting in both a voluminous and rather tedious read, or are included on the publisher's website as supplementary information. In either case, these lists are typically only provided as portable document format documents with a custom-made layout, ma","57: Proteomics. 2005 Aug;5(13):3537-45. ","yes","PACdb: PolyA Cleavage Site and 3'-UTR Database.","Brockman JM, Singh P, Liu D, Quinlan S, Salisbury J, Graber JH.","n","PMID: 16041671 [PubMed - indexed for MEDLINE]"]
["ity of 3'-processing events. AVAILABILITY: By web browser or CGI: PACdb: http://harlequin.jax.org/pacdb/; AtPACdb: http://harlequin.jax.org/atpacdb/. SUPPLEMENTARY INFORMATION: Available online at http://harlequin.jax.org/pacdb/supplemental.php. PMID: 16030070 [PubMed - indexed for MEDLINE]","58: Bioinformatics. 2005 Sep 15;21(18):3691-3. Epub 2005 Jul 19. ","yes","MAVisto: a tool for the exploration of network motifs.","Schreiber F, Schwobbermeyer H.","n","PMID: 16030070 [PubMed - indexed for MEDLINE]"]
["rm independent and available free of charge as a Java webstart application at http://mavisto.ipk-gatersleben.de/ CONTACT: schwoebb@ipk-gatersleben.de SUPPLEMENTARY INFORMATION: Can be found at http://mavisto.ipk-gatersleben.de/ PMID: 16020473 [PubMed - indexed for MEDLINE]","59: Bioinformatics. 2005 Sep 1;21(17):3572-4. Epub 2005 Jul 14. ","yes","Differential gene expression detection and sample classification using penalized","linear regression models.","n","PMID: 16020473 [PubMed - indexed for MEDLINE]"]
["near regression models provide a rigorous and unified statistical framework for sample classification and differential gene expression detection. For supplementary information including the computer programs, detailed analysis results, and R functions for the proposed methods, please see http://www.","6: Bioinformatics. 2005 Dec 13; [Epub ahead of print] ","yes","Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus","structure prediction.","n","PMID: 16352654 [PubMed - as supplied by publisher]"]
["e program RNAcast and is available on the Bielefeld Bioinformatics Server. CONTACT: jreeder@TechFak.Uni-Bielefeld.DE, robert@TechFak.Uni-Bielefeld.DE SUPPLEMENTARY INFORMATION: Available at http://bibiserv.techfak.uni-bielefeld.de/rnacast/supplementary.html Publication Types: Evaluation Studies PMID","5: Bioinformatics. 2005 Dec 15; [Epub ahead of print] ","yes","Integration of metabolic networks and gene expression in virtual reality.","Yang Y, Engin L, Wurtele ES, Cruz-Neira C, Dickerson JA.","n","PMID: 16020472 [PubMed - indexed for MEDLINE]"]
["ationships. AVAILABILITY: MetNet3D and some sample datasets are available at http://www.vrac.iastate.edu/research/sites/metnet/Download/Download.htm. SUPPLEMENTARY INFORMATION: Color snapshots and movies are available at http://www.vrac.iastate.edu/research/sites/metnet/Bioinformatics/SupplementaryI","61: Bioinformatics. 2005 Sep 15;21(18):3645-50. Epub 2005 Jul 14. ","yes","easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data.","Hoffmann K, Lindner TH.","n","PMID: 16020466 [PubMed - indexed for MEDLINE]"]
["rameters. AVAILABILITY: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.ht m CONTACT: tom.lindner@mail.uni-wuerzburg.de SUPPLEMENTARY INFORMATION: Supplementary information is available on the website. The current version is v4.01beta. PMID: 16014370 [PubMed - indexed f","62: Bioinformatics. 2005 Sep 1;21(17):3565-7. Epub 2005 Jul 12. ","yes","A parsimonious tree-grow method for haplotype inference.","Li Z, Zhou W, Zhang XS, Chen L.","n","PMID: 16014370 [PubMed - indexed for MEDLINE]"]
["ILITY: The software is available upon request from the authors, or from http://zhangroup.aporc.org/bioinfo/ptg/ CONTACT: chen@elec.osaka-sandai.ac.jp SUPPLEMENTARY INFORMATION: Supporting materials is available from http://zhangroup.aporc.org/bioinfo/ptg/bti572supplementary.pdf Publication Types: Ev","64: Bioinformatics. 2005 Sep 1;21(17):3475-81. Epub 2005 Jul 7. ","yes","Discrimination of yeast genes involved in methionine and phosphate metabolism on","the basis of upstream motifs.","n","PMID: 16002432 [PubMed - indexed for MEDLINE]"]
["nd results, are available on the website on regulatory sequence analysis tools (http://rsat.scmbb.ulb.ac.be/rsat/). CONTACT: jvanheld@scmbb.ulb.ac.be SUPPLEMENTARY INFORMATION: The complete datasets and results are available at http://rsat.scmbb.ulb.ac.be/rsat/data/published_data/Gonze_MET_PHO/ PMID","65: Bioinformatics. 2005 Sep 1;21(17):3490-500. Epub 2005 Jul 5. ","yes","Local modeling of global interactome networks.","Scholtens D, Vidal M, Gentleman R.","n","PMID: 15998664 [PubMed - indexed for MEDLINE]"]
["omplex estimates reported here can be found in the R package apComplex, available at http://www.bioconductor.org CONTACT: dscholtens@northwestern.edu SUPPLEMENTARY INFORMATION: http://daisy.prevmed.northwestern.edu/~denise/pubs/LocalModeling Publication Types: Evaluation Studies PMID: 15998662 [PubM","67: Bioinformatics. 2005 Sep 1;21(17):3548-57. Epub 2005 Jul 5. ","yes","MicroRNA identification based on sequence and structure alignment.","Wang X, Zhang J, Li F, Gu J, He T, Zhang X, Li Y.","n","PMID: 15998662 [PubMed - indexed for MEDLINE]"]
["s method on Anopheles gambiae and detected 59 new miRNA genes. AVAILABILITY: This program is available at http://bioinfo.au.tsinghua.edu.cn/miralign. SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm. PMID: 15994192 [Pub","67: Bioinformatics. 2005 Sep 1;21(17):3548-57. Epub 2005 Jul 5. ","yes","The inference of protein-protein interactions by co-evolutionary analysis is","improved by excluding the information about the phylogenetic relationships.","n","PMID: 15994192 [PubMed - indexed for MEDLINE]"]
["tion of protein-protein interactions reported in this manuscript is available at http://timpani.genome.ad.jp/~proj/ CONTACT: sato@kuicr.kyoto-u.ac.jp SUPPLEMENTARY INFORMATION: The information is also available at the same site as the R script. PMID: 15994190 [PubMed - indexed for MEDLINE]","69: Bioinformatics. 2005 Sep 1;21(17):3482-9. Epub 2005 Jun 30. ","yes","Quality classification of tandem mass spectrometry data.","Salmi J, Moulder R, Filen JJ, Nevalainen OS, Nyman TA, Lahesmaa R, Aittokallio","n","PMID: 15994190 [PubMed - indexed for MEDLINE]"]
["at the prefiltering scheme efficiently separates the two spectra classes. AVAILABILITY: The software tools are available on request from the authors. SUPPLEMENTARY INFORMATION: The Mascot ion score distributions and the C4.5 classification rules can be found at address http://staff.cs.utu.fi/staff/j","7: Bioinformatics. 2005 Dec 13; [Epub ahead of print] ","yes","FACT--a framework for the functional interpretation of high-throughput","experiments.","n","PMID: 16352652 [PubMed - as supplied by publisher]"]
["ghly flexible framework for the explorative analysis of large genomic and proteomic result sets. The program can be used online; open source code and supplementary information are available at http://www.factweb.de. PMID: 15985174 [PubMed - in process]","70: BMC Bioinformatics. 2005 Jun 28;6:161. ","yes","DIAL: a web-based server for the automatic identification of structural domains","in proteins.","n","PMID: 15985174 [PubMed - in process]"]
["ain solutions that can also describe domain swapping events. The server can be accessed from http://www.ncbs.res.in/~faculty/mini/DIAL/home.html. The Supplementary data can be accessed from http://www.ncbs.res.in/~faculty/mini/DIAL/supplement.html. PMID: 15980441 [PubMed - indexed for MEDLINE]","71: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W130-2. ","yes","Inter-laboratory validation of PCR-based detection of Mycobacterium tuberculosis","in formalin-fixed, paraffin-embedded tissues.","n","PMID: 15980441 [PubMed - indexed for MEDLINE]"]
["ation with the histology and provide recommendations for applying PCR-based methodology for the detection of mycobacterial DNA in surgical specimens. Supplementary data are available online at http://www.charite.de/ch/patho (rubric Forschung\"). Pre-tested specimens are now available for the externa\"","72: Virchows Arch. 2005 Sep;447(3):573-85. Epub 2005 Jun 21. ","yes","Automatic detection of subsystem/pathway variants in genome analysis.","Ye Y, Osterman A, Overbeek R, Godzik A.","n","PMID: 15968546 [PubMed - indexed for MEDLINE]"]
["vergence of species, are briefly discussed in the context of these universally conserved and essential metabolic subsystems. CONTACT: yye@burnham.org SUPPLEMENTARY INFORMATION: The details of the variant detection results are available at http://ffas.burnham.org/svar/supp.html. PMID: 15961494 [PubMe","73: Bioinformatics. 2005 Jun 1;21 Suppl 1:i478-i486. ","yes","Experimental design for three-color and four-color gene expression microarrays.","Woo Y, Krueger W, Kaur A, Churchill G.","n","PMID: 15961494 [PubMed - in process]"]
["ial expression more efficiently than two-color loop designs. AVAILABILITY: http://www.jax.org/staff/churchill/labsite/software CONTACT: garyc@jax.org SUPPLEMENTARY INFORMATION: Multicolor cyclic design construction methods and examples along with additional results of the experiment are provided at ","74: Bioinformatics. 2005 Jun 1;21 Suppl 1:i459-i467. ","yes","How old is your fold?","Winstanley HF, Abeln S, Deane CM.","n","PMID: 15961491 [PubMed - in process]"]
["terparts. AVAILABILITY: Example trees and additional material are available at http://www.stats.ox.ac.uk/~abeln/foldage CONTACT: deane@stats.ox.ac.uk SUPPLEMENTARY INFORMATION: http://www.stats.ox.ac.uk/~abeln/foldage. PMID: 15961490 [PubMed - in process]","75: Bioinformatics. 2005 Jun 1;21 Suppl 1:i449-i458. ","yes","Families of membranous proteins can be characterized by the amino acid","composition of their transmembrane domains.","n","PMID: 15961490 [PubMed - in process]"]
["ty and approximately 90% specificity among unrelated polytopic functional families with the same number of TM domains. CONTACT: michall@cc.huji.ac.il SUPPLEMENTARY INFORMATION: Available at www.protonet.cs.huji.ac.il/TM/ PMID: 15961481 [PubMed - in process]","76: Bioinformatics. 2005 Jun 1;21 Suppl 1:i378-i386. ","yes","RASE: recognition of alternatively spliced exons in C.elegans.","Ratsch G, Sonnenburg S, Scholkopf B.","n","PMID: 15961481 [PubMed - in process]"]
["edictions and additional experimental results are available at http://www.fml.tuebingen.mpg.de/~raetsch/RASE CONTACT: Gunnar.Raetsch@tuebingen.mpg.de SUPPLEMENTARY INFORMATION: http://www.fml.tuebingen.mpg.de/raetsch/RASE. PMID: 15961480 [PubMed - in process]","77: Bioinformatics. 2005 Jun 1;21 Suppl 1:i369-i377. ","yes","Modeling the organization of the WUSCHEL expression domain in the shoot apical","meristem.","n","PMID: 15961480 [PubMed - in process]"]
["ge processing algorithms can be found at http://www.computableplant.org, together with additional results and simulation movies. CONTACT: emj@uci.edu SUPPLEMENTARY INFORMATION: http://www.computableplant.org/ and alternatively for a direct link to the page, http://computableplant.ics.uci.edu/bti1036","79: Bioinformatics. 2005 Jun 1;21 Suppl 1:i232-i240. ","yes","Survival prediction of diffuse large-B-cell lymphoma based on both clinical and","gene expression information.","n","PMID: 15961462 [PubMed - in process]"]
["hieved by using either clinical data or molecular predictors alone. AVAILABILITY: R programs are available at http://www4.stat.ncsu.edu/~li/survipi/. SUPPLEMENTARY INFORMATION: http://www4.stat.ncsu.edu/~li/survipi/bioinfo-supp.pdf. PMID: 16339281 [PubMed - as supplied by publisher]","8: Bioinformatics. 2005 Dec 8; [Epub ahead of print] ","yes","CaSPredictor: a new computer-based tool for caspase substrate prediction.","Garay-Malpartida HM, Occhiucci JM, Alves J, Belizario JE.","n","PMID: 16339281 [PubMed - as supplied by publisher]"]
["ins in a dataset containing 9986 protein entries. AVAILABILITY: Requests for software should be made to Dr Jose E. Belizario CONTACT: jebeliza@usp.br SUPPLEMENTARY INFORMATION: Supplementary information is available for academic users at site http://icb.usp.br/~farmaco/Jose/CaSpredictorfiles. PMID: ","6: Bioinformatics. 2005 Dec 13; [Epub ahead of print] ","yes","Clustering short time series gene expression data.","Ernst J, Nau GJ, Bar-Joseph Z.","n","PMID: 15961454 [PubMed - in process]"]
[" obtaining a Java implementation with a graphical user interface (GUI) is available from http://www.cs.cmu.edu/~jernst/st/ CONTACT: jernst@cs.cmu.edu SUPPLEMENTARY INFORMATION: Available at http://www.cs.cmu.edu/~jernst/st/ PMID: 15961453 [PubMed - in process]","81: Bioinformatics. 2005 Jun 1;21 Suppl 1:i159-i168. ","yes","Detecting coevolving amino acid sites using Bayesian mutational mapping.","Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R.","n","PMID: 15961453 [PubMed - in process]"]
["s discriminating test, yielding a marked increase in the number of reported positives at both contact and non-contact sites. CONTACT: matt@dimmic.net SUPPLEMENTARY INFORMATION: http://www.dimmic.net/supplement/ PMID: 15961449 [PubMed - in process]","82: Bioinformatics. 2005 Jun 1;21 Suppl 1:i126-i135. ","yes","Satellog: a database for the identification and prioritization of satellite","repeats in disease association studies.","n","PMID: 15961449 [PubMed - in process]"]
["oritization of repeats. Here we present Satellog, a database that catalogs all pure 1-16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism. RESULTS: A total of 5,546 such repeats","83: BMC Bioinformatics. 2005 Jun 10;6(1):145. ","yes","Statistics of protein library construction.","Firth AE, Patrick WM.","n","PMID: 15949044 [PubMed - in process]"]
["ation, synthetic shuffling, DHR, ADO and SISDC. AVAILABILITY: Web interface and C++ source code available at http://guinevere.otago.ac.nz/stats.html. SUPPLEMENTARY INFORMATION: Complete mathematical notes, model assumptions and justification, users' guide and worked examples at above website. PMID: ","84: Bioinformatics. 2005 Aug 1;21(15):3314-5. Epub 2005 Jun 2. ","yes","MeSHer: identifying biological concepts in microarray assays based on PubMed","references and MeSH terms.","n","PMID: 15932904 [PubMed - indexed for MEDLINE]"]
["t this approach can aid in the interpretation of the resulting 'significant' gene set. AVAILABILITY: The software is available at http://www.tm4.org. SUPPLEMENTARY INFORMATION: Results from the analysis of significant genes from the published Ang II study. PMID: 15919728 [PubMed - indexed for MEDLIN","85: Bioinformatics. 2005 Aug 1;21(15):3324-6. Epub 2005 May 26. ","yes","Functional annotation from predicted protein interaction networks.","McDermott J, Bumgarner R, Samudrala R.","n","PMID: 15919728 [PubMed - indexed for MEDLINE]"]
["able at http://bioverse.compbio.washington.edu and datasets used for analysis at http://data.compbio.washington.edu/misc/downloads/nannotation_data/. SUPPLEMENTARY INFORMATION: A supplemental appendix gives additional details not in the main text. (http://data.compbio.washington.edu/misc/downloads/n","86: Bioinformatics. 2005 Aug 1;21(15):3217-26. Epub 2005 May 26. ","yes","A latent variable model for chemogenomic profiling.","Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP.","n","PMID: 15919725 [PubMed - indexed for MEDLINE]"]
["useful for summarizing the relationship among treatments and genes affected by those treatments in a compendium of microarray profiles. AVAILABILITY: Supplementary information and computer code at http://genomics.lbl.gov/llda. Publication Types: Evaluation Studies PMID: 15919724 [PubMed - indexed fo","87: Bioinformatics. 2005 Aug 1;21(15):3286-93. Epub 2005 May 26. ","yes","Resmap: automated representation of macromolecular interfaces as two-dimensional","networks.","n","PMID: 15919724 [PubMed - indexed for MEDLINE]"]
["VAILABILITY: Various alternative and supplemental networks (not given in the text) as well as source code extensions, are available from the authors. SUPPLEMENTARY INFORMATION: http://bioinformatics.oxfordjournals.org. Publication Types: Evaluation Studies PMID: 15914545 [PubMed - indexed for MEDLIN","88: Bioinformatics. 2005 Aug 1;21(15):3273-8. Epub 2005 May 24. ","yes","Comparative interactomics analysis of protein family interaction networks using","PSIMAP (protein structural interactome map).","n","PMID: 15914545 [PubMed - indexed for MEDLINE]"]
["Protein Data Bank files and represents subunit/domain interfaces as two-dimensional networks. AVAILABILITY: http://www.kumc.edu/biochemistry/resmap/. SUPPLEMENTARY INFORMATION: Default definitions and directions for graphically managing networks are available at the same website. PMID: 15914544 [Pub","89: Bioinformatics. 2005 Aug 1;21(15):3327-8. Epub 2005 May 24. ","yes","Efficient recognition of folds in protein 3D structures by the improved PRIDE","algorithm.","n","PMID: 15914544 [PubMed - indexed for MEDLINE]"]
["very small number of expansive protein families led to the evolution of interactomes and seemed to have played a key role in species diversification. SUPPLEMENTARY INFORMATION: http://interactomics.org. Publication Types: Evaluation Studies PMID: 15914543 [PubMed - indexed for MEDLINE]","90: Bioinformatics. 2005 Aug 1;21(15):3234-40. Epub 2005 May 24. ","yes","Computational cluster validation in post-genomic data analysis.","Handl J, Knowles J, Kell DB.","n","PMID: 15914543 [PubMed - indexed for MEDLINE]"]
["hierarchy. AVAILABILITY: The new algorithm is integrated into the PRIDE2 web servers at http://pride.szbk.u-szeged.hu and http://www.icgeb.org/pride. SUPPLEMENTARY INFORMATION: Detailed documentation and performance evaluation is available in the description section of the PRIDE2 web server. PMID: 1","91: Bioinformatics. 2005 Aug 1;21(15):3322-3. Epub 2005 May 24. ","yes","Semi-supervised protein classification using cluster kernels.","Weston J, Leslie C, Ie E, Zhou D, Elisseeff A, Noble WS.","n","PMID: 15914542 [PubMed - indexed for MEDLINE]"]
["alytical clustervalidation. AVAILABILITY: The software used in the experiments is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/. SUPPLEMENTARY INFORMATION: Enlarged colour plots are provided in the Supplementary Material, which is available at http://dbkweb.ch.umist.ac.uk/handl/","93: Bioinformatics. 2005 Aug 1;21(15):3241-7. Epub 2005 May 19. ","yes","Prediction error estimation: a comparison of resampling methods.","Molinaro AM, Simon R, Pfeiffer RM.","n","PMID: 15914541 [PubMed - indexed for MEDLINE]"]
["available at www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot. The Spider matlab package is available at www.kyb.tuebingen.mpg.de/bs/people/spider. SUPPLEMENTARY INFORMATION: www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot. Publication Types: Evaluation Studies PMID: 15905279 [PubMed - indexed ","93: Bioinformatics. 2005 Aug 1;21(15):3241-7. Epub 2005 May 19. ","yes","Differential network expression during drug and stress response.","Cabusora L, Sutton E, Fulmer A, Forst CV.","n","PMID: 15905279 [PubMed - indexed for MEDLINE]"]
["es with strong signal-to-noise ratios. Differences in performance among resampling methods are reduced as the number of specimens available increase. SUPPLEMENTARY INFORMATION: A complete compilation of results and R code for simulations and analyses are available in Molinaro et al. (2005) (http://l","94: Bioinformatics. 2005 Aug 1;21(15):3301-7. Epub 2005 May 19. ","yes","LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple","information sources.","n","PMID: 15905277 [PubMed - indexed for MEDLINE]"]
["pate that this approach will be able to accelerate target identification and drug development for tuberculosis in the future. CONTACT: chris@lanl.gov SUPPLEMENTARY INFORMATION: Supplementary Figures 1 through 6 on drug response networks and differential network analyses on cerulenin, chlorpromazine,","95: Bioinformatics. 2005 Jun 15;21(12):2898-905. Epub 2005 Apr 19. ","yes","Modeling and simulation of cancer immunoprevention vaccine.","Pappalardo F, Lollini PL, Castiglione F, Motta S.","n","PMID: 15840709 [PubMed - indexed for MEDLINE]"]
["n probing molecular mechanisms responsible for functional impacts of nsSNPs. AVAILABILITY: http://www.salilab.org/LS-SNP CONTACT: rachelk@salilab.org SUPPLEMENTARY INFORMATION: http://salilab.org/LS-SNP/supp-info.pdf. Publication Types: Evaluation Studies PMID: 15827081 [PubMed - indexed for MEDLINE","97: Bioinformatics. 2005 Jun 15;21(12):2814-20. Epub 2005 Apr 12. ","yes","Improving missing value estimation in microarray data with gene ontology.","Tuikkala J, Elo L, Nevalainen OS, Aittokallio T.","n","PMID: 15827081 [PubMed - indexed for MEDLINE]"]
["the tumor growth and therefore suggest the selection and timing of experiments for measuring the activity of T cells. CONTACT: francesco@dmi.unict.it SUPPLEMENTARY INFORMATION: http://www.dmi.unict.it/CIG/suppdata_bioinf.html. Publication Types: Evaluation Studies Validation Studies PMID: 15817697 [","99: Bioinformatics. 2005 Jun 15;21(12):2891-7. Epub 2005 Apr 7. ","yes","A simple method to predict protein binding from aligned sequences -- application","to MHC superfamily and beta2-microglobulin.","n","PMID: 15817697 [PubMed - indexed for MEDLINE]"]
["ificant for the eventual interpretation of the microarray experiments. AVAILABILITY: Java and Matlab codes are available on request from the authors. Supplementary material: available online at http://users.utu.fi/jotatu/GOImpute.html. PMID: 16377613 [PubMed - as supplied by publisher]","1: Bioinformatics. 2005 Dec 23; [Epub ahead of print]","yes","The choice of optimal distance measure in genome-wide datasets.","Glazko G, Gordon A, Mushegian A.","n","PMID: 16377613 [PubMed - as supplied by publisher]"]
["r data, which showed heterogeneous and low-level methylation of CpG islands, have obvious implications for methylation studies. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2005 Wiley-Liss, Inc. PMID: 16372313 [PubMed - as ","2: Genes Chromosomes Cancer. 2005 Dec 21; [Epub ahead of print]","yes","Generating Boolean networks with a prescribed attractor structure.","Pal R, Ivanov I, Datta A, Bittner ML, Dougherty ER.","n","PMID: 16372313 [PubMed - as supplied by publisher]"]
["ion or interaction prediction problems. AVAILABILITY: Data and MhcSF multiple alignment are available on the IMGT website (http://imgt.cines.fr), and supplementary material is downloadable at http://imgt.igh.cnrs.fr/MhcSF-B2M.html. PMID: 16352655 [PubMed - as supplied by publisher]","3: Bioinformatics. 2005 Dec 13; [Epub ahead of print]","yes","Blast2GO: a universal tool for annotation, visualization and analysis in","functional genomics research.","n","PMID: 16352655 [PubMed - as supplied by publisher]"]
["ighly correlated genes were enriched for gene ontology categories involved in the DNA damage response and telomere maintenance. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2005 Wiley-Liss, Inc. PMID: 16323170 [PubMed - as ","4: Genes Chromosomes Cancer. 2005 Dec 1; [Epub ahead of print]","yes","An integrative approach to CTL epitope prediction: a combined algorithm","integrating MHC class I binding, TAP transport efficiency, and proteasomal","n","PMID: 16323170 [PubMed - as supplied by publisher]"]
[" in 3q26.3-q27 in EA revealed multiple genetic alterations that had occurred sequentially and/or concurrently during EA development. This article has supplementary material, available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2005 Wiley-Liss, Inc. PMID: 16320248 [PubMed - as","5: Genes Chromosomes Cancer. 2005 Nov 30; [Epub ahead of print]","yes","ExonHunter: a comprehensive approach to gene finding.","Brejova B, Brown DG, Li M, Vinar T.","n","PMID: 16320248 [PubMed - as supplied by publisher]"]
[" distance properties, such as metric and additivity, appear to have much less effect on the performance of distances. AVAILABILITY: R code GADIST and Supplementary material are available at http://research.stowers-institute.org/bioinfo/ CONTACT: gvg@stowers-institute.org. PMID: 16306389 [PubMed - in","6: Bioinformatics. 2005 Nov 1;21 Suppl 3:iii3-iii11.","yes","Inferring protein-protein interactions through high-throughput interaction data","from diverse organisms.","n","PMID: 16306389 [PubMed - in process]"]
["cadherin expression in the SW480 colon cancer cell line indicates that L-plastin plays an important mechanistic role in colorectal cancer metastasis (supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","7: Int J Cancer. 2005 Nov 14; [Epub ahead of print]","yes","Detecting interspecific recombination with a pruned probabilistic divergence","measure.","n","PMID: 16287074 [PubMed - as supplied by publisher]"]
["method for suggesting SNP-SNP interactions that may be validated in future studies, using more traditional statistical methods on different datasets (Supplementary material can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7136/suppmat). Pub","8: Int J Cancer. 2005 Oct 10;118(7):1790-1797 [Epub ahead of print]","yes","Correlation of amino acid preference and mammalian viral genome type.","Rose JR, Turkett WH Jr, Oroian IC, Laegreid WW, Keele J.","n","PMID: 16217767 [PubMed - as supplied by publisher]"]
["ure clinical cancer response prediction feasible. The TaqMan-validated gene expression patterns provide new gene candidates for multidrug resistance. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","9: Int J Cancer. 2005 Oct 10;118(7):1699-1712 [Epub ahead of print]","yes","The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium,","strain EbN1.","n","PMID: 16217747 [PubMed - as supplied by publisher]"]
["tural part of recombinational DNA repair. Additionally, we find that Rad51C plays an important role in regulating this process. This article contains supplementary material, which may be viewed at the Journal of Cellular Biochemistry website at http://www.interscience.wiley.com/jpages/0730-2312/supp","10: J Cell Biochem. 2005 Dec 15;96(6):1095-109.","yes","Accurate anchoring alignment of divergent sequences.","Huang W, Umbach DM, Li L.","y","PMID: 16215984 [PubMed - in process]"]
[" design algorithm; and check the concordance between the attractor states of the designed network and the data states. AVAILABILITY: The software and supplementary material is available at http://gsp.tamu.edu/Publications/BNs/bn.htm MeSH Terms: Algorithms* Computer Simulation Gene Expression Profili","12: Bioinformatics. 2005 Nov 1;21(21):4021-5. Epub 2005 Sep 8.","yes","Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and","example application (plasma apoE levels).","y","PMID: 16150807 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Computer Simulation","Gene Expression Profiling/methods*","Gene Expression Regulation/physiology*","Models, Biological*","Pattern Recognition, Automated/methods","Proteome/metabolism*","Research Support, N.I.H., Extramural","Research Support, U.S. Gov't, Non-P.H.S.","Signal Transduction/physiology*","Trans-Activation (Genetics)/physiology","Transcription Factors/metabolism*","Substances:","Proteome","Transcription Factors","Grant Support:","CA 90301/CA/NCI"]
[" comprehension of the whole annotation and analysis process. AVAILABILITY: Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL: http://www.blast2go.de -> Evaluation. MeSH Terms: Algorithms Computational Biology/methods* Computer Graphics Database Managem","13: Bioinformatics. 2005 Sep 15;21(18):3674-6. Epub 2005 Aug 4.","yes","Detailed methylation analysis of CpG islands on human chromosome region 9p21.","Weeks RJ, Morison IM.","y","PMID: 16081474 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms","Computational Biology/methods*","Computer Graphics","Database Management Systems","Databases, Protein","Gene Expression Profiling/methods*","Genome","Genomics*","Information Storage and Retrieval/methods*","Internet","Oligonucleotide Array Sequence Analysis","Research Support, Non-U.S. Gov't","Sequence Alignment","Sequence Analysis, Protein","Software*","User-Computer Interface"]
["ine-tiling oaCGH analysis provides an unprecedented level of resolution, allowing detailed mapping of recurrent unbalanced chromosomal abnormalities. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience.wiley.com/jpages/1045-22","14: Genes Chromosomes Cancer. 2005 Nov;44(3):305-19.","yes","Comparison of gene expression and DNA copy number changes in a murine model of","lung cancer.","y","PMID: 16075461 [PubMed - indexed for MEDLINE]","MeSH Terms:","Chromosome Breakage*","Chromosomes, Human, Pair 11*","Chromosomes, Human, Pair 17*","Genome, Human","Humans","In Situ Hybridization, Fluorescence","Neuroblastoma/genetics*","Nucleic Acid Hybridization/methods","Oligonucleotide Array Sequence Analysis*","Reverse Transcriptase Polymerase Chain Reaction","Translocation, Genetic*"]
["oin other broken ends or eroded telomeres, producing massive chromosomal instability at the later passages of the cell culture. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2005 Wiley-Liss, Inc. MeSH Terms: Blotting, Wester","15: Genes Chromosomes Cancer. 2005 Dec;44(4):339-50.","yes","Multiple forms of genetic instability within a 2-Mb chromosomal segment of","3q26.3-q27 are associated with development of esophageal adenocarcinoma.","y","PMID: 16052508 [PubMed - indexed for MEDLINE]","MeSH Terms:","Blotting, Western","Cell Culture Techniques","Cell Line","Chromosomal Instability*","Chromosome Painting","Chromosomes, Human, Pair 1","Comparative Study","DNA/genetics","Epithelial Cells/cytology*","Female","Fluorescent Antibody Technique, Direct","Fluorescent Dyes","Humans","In Situ Hybridization, Fluorescence","Indoles","Karyotyping","Mammary Glands, Human/cytology*","Metaphase","Nucleic Acid Hybridization","Research Support, Non-U.S. Gov't","Telomerase/analysis","Telomere/metabolism*","Substances:","Fluorescent Dyes","Indoles","DAPI","DNA","Telomerase"]
["central role in hepatocyte death in fulminant hepatitis through direct and indirect pathways that may have direct therapeutic implications in humans. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me","16: Hepatology. 2005 Aug;42(2):372-80.","yes","The leukocyte protein L-plastin induces proliferation, invasion and loss of","E-cadherin expression in colon cancer cells.","y","PMID: 16025512 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Antigens, CD40/analysis","Antigens, CD40/physiology*","Apoptosis*","CD4-Positive T-Lymphocytes/metabolism","CD40 Ligand/physiology*","Concanavalin A/toxicity","Hepatitis/pathology*","Hepatocytes/pathology*","Immunohistochemistry","Interleukin-12/biosynthesis","Male","Mice","Mice, Inbred C57BL","Research Support, Non-U.S. Gov't","Tumor Necrosis Factor-alpha/biosynthesis","Substances:","Antigens, CD40","Tumor Necrosis Factor-alpha","Concanavalin A","CD40 Ligand","Interleukin-12"]
[" protein with 85% probability is reduced by 20-30% when using the integrated method.The method is available at http://www.cbs.dtu.dk/services/NetCTL. Supplementary material is available at http://www.cbs.dtu.dk/suppl/immunology/CTL.php. MeSH Terms: Algorithms* Data Interpretation, Statistical Epitop","17: Eur J Immunol. 2005 Aug;35(8):2295-303.","yes","Exploring SNP-SNP interactions and colon cancer risk using polymorphism","interaction analysis.","y","PMID: 15997466 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Data Interpretation, Statistical","Epitopes, T-Lymphocyte/immunology*","Epitopes, T-Lymphocyte/metabolism*","Histocompatibility Antigens Class I/immunology","Histocompatibility Antigens Class I/metabolism*","Humans","Hydrolysis","Predictive Value of Tests","Proteasome Endopeptidase Complex/metabolism*","Protein Binding","Research Support, N.I.H., Extramural","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","T-Lymphocytes, Cytotoxic/immunology*","T-Lymphocytes, Cytotoxic/metabolism","Substances:","Epitopes, T-Lymphocyte","Histocompatibility Antigens Class I","transporter associated with antigen processing, human","Proteasome Endopeptidase Complex"]
["d metabolism. Increased abundance of transcripts linked to cellular proliferation in advanced fibrosis is consistent with a predisposition to cancer. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index/html)","18: Hepatology. 2005 Aug;42(2):273-81.","yes","Gene expression profiling of 30 cancer cell lines predicts resistance towards 11","anticancer drugs at clinically achieved concentrations.","y","PMID: 15986378 [PubMed - indexed for MEDLINE]","MeSH Terms:","Actins/analysis*","Adult","Female","Gene Expression Profiling*","Hepatitis C/complications*","Humans","Immunohistochemistry","Liver/metabolism*","Liver Cirrhosis/metabolism*","Male","Middle Aged","Oligonucleotide Array Sequence Analysis","Research Support, N.I.H., Extramural","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Substances:","Actins","Grant Support:","U19 AI 40035/AI/NIAID"]
["e other human HCCs. In conclusion, expression fingerprints may be used for diagnostic purposes and potential new therapeutic intervention strategies. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index/html)","19: Hepatology. 2005 Aug;42(2):353-61.","yes","Cellular localization of human Rad51C and regulation of ubiquitin-mediated","proteolysis of Rad51.","y","PMID: 15965925 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Carcinoma, Hepatocellular/genetics*","Cytoskeletal Proteins/genetics*","Gene Expression Profiling","Genes, ras*","Genotype","Glutamate-Ammonia Ligase/genetics","Humans","Liver Neoplasms/genetics*","Male","Mice","Mice, Inbred C3H","Mutation","Phenotype","Research Support, Non-U.S. Gov't","Signal Transduction","Trans-Activators/genetics*","beta Catenin","Substances:","CTNNB1 protein, human","Catnb protein, mouse","Cytoskeletal Proteins","Trans-Activators","beta Catenin","Glutamate-Ammonia Ligase"]
["e that activity of ERK in the cytoplasm is important for survival during oxidative stress in hepatocytes and that RSK is activated downstream of ERK. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)","20: Hepatology. 2005 Jul;42(1):200-7.","yes","Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution","using fine-tiling oligonucleotide array CGH.","y","PMID: 15962331 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cell Survival/drug effects","Cell Survival/physiology","Cells, Cultured","Cytoplasm","Extracellular Signal-Regulated MAP Kinases/drug effects*","Hepatocytes/drug effects*","Hepatocytes/metabolism","Hydrogen Peroxide/pharmacology*","Male","Models, Animal","Oxidants/pharmacology*","Oxidative Stress","Rats","Rats, Wistar","Reactive Oxygen Species","Ribosomal Protein S6 Kinases, 90-kDa/drug effects*","Ribosomal Protein S6 Kinases, 90-kDa/metabolism","Substances:","Oxidants","Reactive Oxygen Species","Hydrogen Peroxide","Extracellular Signal-Regulated MAP Kinases","Ribosomal Protein S6 Kinases, 90-kDa"]
[" in most individuals, the CD8+ T cell responses generated early in HCV infection decline in peripheral blood and are not replaced with new responses. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)","21: Hepatology. 2005 Jul;42(1):104-12.","yes","Telomere dysfunction drives chromosomal instability in human mammary epithelial","cells.","y","PMID: 15962289 [PubMed - indexed for MEDLINE]","MeSH Terms:","Acute Disease","Adolescent","Adult","CD8-Positive T-Lymphocytes/immunology*","Female","Hepatitis C/immunology*","Humans","Male","Prospective Studies","Research Support, N.I.H., Extramural","Research Support, U.S. Gov't, P.H.S.","Grant Support:","K08 DA11880/DA/NIDA","R01 DK57998/DK/NIDDK","U19 AI40035/AI/NIAID"]
["undescribed posttranscriptional mechanism. A single mutation inactivated a 5' splice site that is obviously essential for pre-S2/S mRNA accumulation. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)","22: Hepatology. 2005 Jul;42(1):93-103.","yes","CD154-CD40 interactions drive hepatocyte apoptosis in murine fulminant","hepatitis.","y","PMID: 15962285 [PubMed - indexed for MEDLINE]","MeSH Terms:","Carrier State/immunology","Clone Cells","Hepatitis B/physiopathology","Hepatitis B/virology*","Hepatitis B Surface Antigens/immunology","Hepatitis B virus/genetics","Hepatitis B virus/immunology","Hepatitis B virus/physiology*","Humans","Mutation","Research Support, Non-U.S. Gov't","Virus Activation*","Virus Latency*","Substances:","Hepatitis B Surface Antigens"]
["interferon alfa-2b in lamivudine treatment was found to neither enhance the potency of blocking HBV production nor the decay rates of infected cells. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)","23: Hepatology. 2005 Jul;42(1):77-85.","yes","Intrahepatic gene expression profiles and alpha-smooth muscle actin patterns in","hepatitis C virus induced fibrosis.","y","PMID: 15962284 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Antiviral Agents/therapeutic use*","Biomechanics","Female","Hepatitis B e Antigens/immunology","Hepatitis B, Chronic/drug therapy","Hepatitis B, Chronic/immunology*","Humans","Interferon Alfa-2a/therapeutic use*","Lamivudine/therapeutic use*","Male","Middle Aged","Models, Biological","Polyethylene Glycols/therapeutic use*","Research Support, Non-U.S. Gov't","Treatment Outcome","Viral Load*","Substances:","Antiviral Agents","Hepatitis B e Antigens","Polyethylene Glycols","peginterferon alfa-2a","Lamivudine","Interferon Alfa-2a"]
["ly better than the existing gene finders ROSETTA, SLAM and TWINSCAN, with more than two-thirds of genes predicted completely correctly. AVAILABILITY: Supplementary material available at http://www.bioinformatics.uwaterloo.ca/supplements/05eh/ CONTACT: bbrejova@uwaterloo.ca. PMID: 15961499 [PubMed - ","24: Bioinformatics. 2005 Jun 1;21 Suppl 1:i57-i65.","yes","Genotype-phenotype relationships in hepatocellular tumors from mice and man.","Stahl S, Ittrich C, Marx-Stoelting P, Kohle C, Altug-Teber O, Riess O, Bonin M,","y","PMID: 15961499 [PubMed - in process]"]
["fied a set of candidate genes, including those regulated by RAS signaling, that may contribute to the process of cancer cell invasion and metastasis. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience.wiley.com/jpages/1045-22","26: Genes Chromosomes Cancer. 2005 Sep;44(1):37-51.","yes","Cytoplasmic retention of peroxide-activated ERK provides survival in primary","cultures of rat hepatocytes.","y","PMID: 15929091 [PubMed - indexed for MEDLINE]","MeSH Terms:","Cell Line, Tumor","DNA, Neoplasm/genetics*","Gene Amplification","Humans","Nucleic Acid Hybridization","Oligonucleotide Array Sequence Analysis*","Pancreatic Neoplasms/genetics*","Point Mutation","Proto-Oncogene Proteins/genetics","RNA, Messenger/genetics*","RNA, Neoplasm/genetics","RNA, Neoplasm/isolation & purification","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Substances:","DNA, Neoplasm","KRAS2 protein, human","Proto-Oncogene Proteins","RNA, Messenger","RNA, Neoplasm"]
["actions from diverse organisms than from a single organism. AVAILABILITY: The program for computing the protein-protein interaction probabilities and supplementary material are available at http://bioinformatics.med.yale.edu/interaction. Publication Types: Evaluation Studies MeSH Terms: Binding Site","28: Bioinformatics. 2005 Aug 1;21(15):3279-85. Epub 2005 May 19.","yes","Comprehensive analyses of CD8+ T cell responses during longitudinal study of","acute human hepatitis C.","y","PMID: 15905281 [PubMed - indexed for MEDLINE]","MeSH Terms:","Binding Sites","Biodiversity","Caenorhabditis elegans Proteins/chemistry","Caenorhabditis elegans Proteins/metabolism*","Computer Simulation","Drosophila Proteins/chemistry","Drosophila Proteins/metabolism*","Models, Biological*","Models, Chemical","Protein Binding","Protein Interaction Mapping/methods*","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Saccharomyces cerevisiae Proteins/chemistry","Saccharomyces cerevisiae Proteins/metabolism*","Sequence Analysis, Protein/methods*","Signal Transduction/physiology*","Species Specificity","Substances:","Caenorhabditis elegans Proteins","Drosophila Proteins","Saccharomyces cerevisiae Proteins"]
["y separate from hematopoietic cells and differentiate into mature, functional hepatocytes in vivo with the capacity for efficient liver repopulation. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)","29: Hepatology. 2005 Jul;42(1):130-9.","yes","Comment in:","Hepatology. 2005 Jul;42(1):21-3.","y","PMID: 15895427 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cell Separation/methods*","Cells, Cultured","Epithelial Cells*","Fetus/cytology","Liver/cytology*","Liver/embryology*","Mice","Research Support, N.I.H., Extramural","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Grant Support:","P30 DK41296/DK/NIDDK","R01 DK17609/DK/NIDDK"]
["ation during the evolution of cirrhosis. These findings have implications for understanding the evolution of cirrhosis and associated carcinogenesis. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me","30: Hepatology. 2005 Jun;41(6):1262-71.","yes","A viral kinetic study using pegylated interferon alfa-2b and/or lamivudine in","patients with chronic hepatitis B/HBeAg negative.","y","PMID: 15880761 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adaptation, Physiological","Animals","Bile Ducts","Biological Markers/metabolism","Cell Cycle","Cell Cycle Proteins/metabolism*","Cell Proliferation","Cyclin-Dependent Kinase Inhibitor p21","Cyclin-Dependent Kinases/antagonists & inhibitors*","Hepatocytes/metabolism*","Hepatocytes/pathology*","Humans","Ki-67 Antigen/metabolism","Ligation","Liver Cirrhosis/pathology*","Liver Cirrhosis/physiopathology","Male","Mice","Mice, Inbred Strains","Mice, Knockout","Mitosis*","Research Support, N.I.H., Extramural","Research Support, U.S. Gov't, P.H.S.","Stress/metabolism*","Substances:","Biological Markers","CDKN1A protein, human","Cdkn1a protein, mouse","Cell Cycle Proteins","Cyclin-Dependent Kinase Inhibitor p21","Ki-67 Antigen","Cyclin-Dependent Kinases","Grant Support:","R01 DK49615/DK/NIDDK"]
["igenesis of intrahepatic cholangiocarcinoma and should contribute to the development of diagnostic and therapeutic strategies for this type of tumor. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)","31: Hepatology. 2005 Jun;41(6):1339-48.","yes","Analysis of genomic DNA alterations and mRNA expression patterns in a panel of","human pancreatic cancer cell lines.","y","PMID: 15880566 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Aged","Bile Duct Neoplasms/genetics","Bile Duct Neoplasms/metabolism*","Bile Ducts, Intrahepatic*","Cholangiocarcinoma/genetics","Cholangiocarcinoma/metabolism*","Cluster Analysis","Dissection","Down-Regulation","Female","Gene Expression*","Gene Expression Profiling","Genome, Human*","Humans","Immunohistochemistry/methods","Lasers","Lymphatic Metastasis/genetics","Male","Middle Aged","Oligonucleotide Array Sequence Analysis/standards","Research Support, Non-U.S. Gov't","Reverse Transcriptase Polymerase Chain Reaction","Staining and Labeling","Up-Regulation"]
["toxic carcinogens because the relatively high levels of cell division in the developing animal facilitate the conversion of DNA damage into mutation. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","32: Int J Cancer. 2005 Nov 1;117(2):182-7.","yes","Purification and characterization of mouse fetal liver epithelial cells with","high in vivo repopulation capacity.","y","PMID: 15880493 [PubMed - indexed for MEDLINE]","MeSH Terms:","Aging","Aminobiphenyl Compounds/toxicity*","Animals","Animals, Newborn","Carcinogens/toxicity*","DNA/genetics","DNA/metabolism","DNA Adducts/metabolism*","Liver/drug effects","Liver/pathology*","Male","Mice","Mice, Inbred Strains","Mutagenicity Tests","Mutagens/toxicity","Mutation*","Substances:","Aminobiphenyl Compounds","Carcinogens","DNA Adducts","Mutagens","DNA","4-biphenylamine"]
["es an immediate burst of ATP that seems to be a general response of human differentiated keratinocytes to the radiation stress. This article contains Supplementary Material available at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/v95.html (c) 2005 Wiley-Liss, Inc. MeSH Terms: Cel","34: J Cell Biochem. 2005 Jun 1;95(3):620-31.","yes","An inhibitor of cyclin-dependent kinase, stress-induced p21Waf-1/Cip-1, mediates","hepatocyte mito-inhibition during the evolution of cirrhosis.","y","PMID: 15832339 [PubMed - indexed for MEDLINE]","MeSH Terms:","Cells, Cultured","Energy Metabolism/genetics","Energy Metabolism/radiation effects*","Gamma Rays*","Humans","Keratinocytes/cytology","Keratinocytes/metabolism*","Mitochondria/enzymology*","Research Support, Non-U.S. Gov't"]
[" in these chimeric animals necessitates a critical review of the observations and conclusions made in experiments with isolated mature\" hepatocytes. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)\"","36: Hepatology. 2005 Apr;41(4):847-56.","yes","Genome-wide analysis of gene expression in human intrahepatic","cholangiocarcinoma.","y","PMID: 15791625 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Blood Proteins/metabolism","Hepatitis B/metabolism","Hepatitis B/pathology","Hepatitis C/metabolism","Hepatitis C/pathology","Humans","Liver/metabolism*","Liver/pathology*","Liver/ultrastructure","Liver Transplantation*","Mice","Mice, SCID","Mice, Transgenic","Microscopy, Electron","Models, Animal*","Research Support, Non-U.S. Gov't","Transplantation Chimera*","Transplantation, Heterologous*","Urinary Plasminogen Activator/genetics","Urinary Plasminogen Activator/metabolism*","Substances:","Blood Proteins","Urinary Plasminogen Activator"]
["le can be used as an estimate of the MCID in HCV, and this value may be used as the basis for power calculations in clinical trials evaluating HRQOL. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html)","37: Hepatology. 2005 Apr;41(4):790-800.","yes","4-Aminobiphenyl induces liver DNA adducts in both neonatal and adult mice but","induces liver mutations only in neonatal mice.","y","PMID: 15791608 [PubMed - indexed for MEDLINE]","MeSH Terms:","Case-Control Studies","Delphi Technique","Health Status*","Hepatitis C/physiopathology*","Hepatitis C/psychology","Hepatitis C/therapy","Hepatitis C/virology","Humans","Neuropsychological Tests","Quality of Life*","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Severity of Illness Index","Viral Load","Grant Support:","AG-02-004/AG/NIA","P20-MD00148-01/MD/NCMHHD"]
["differ between family members and controls. CONCLUSIONS: These six TCII polymorphisms do not strongly influence NTD risk in the Irish population. The Supplementary Material for this article can be found on the Birth Defects Research (Part A) website: http://www.mrw.interscience.wiley.com/suppmat/154","38: Birth Defects Res A Clin Mol Teratol. 2005 Apr;73(4):239-44.","yes","Activation of an energy providing response in human keratinocytes after gamma","irradiation.","y","PMID: 15782407 [PubMed - indexed for MEDLINE]","MeSH Terms:","Alleles","Case-Control Studies","Female","Gene Frequency","Humans","Male","Neural Tube Defects/ethnology*","Neural Tube Defects/genetics*","Polymorphism, Single Nucleotide*","Research Support, N.I.H., Extramural","Research Support, U.S. Gov't, P.H.S.","Risk Factors","Transcobalamins/genetics*","Vitamin B 12/metabolism","Substances:","Transcobalamins","Vitamin B 12"]
["ning array comparative genomic hybridization and microsatellite analysis in elucidating complex genomic rearrangements in primary human tumor tissue. Supplementary material for this article can be found on the Genes, Chromosomes and Cancer website at http://www.interscience.wiley.com/jpages/1045-225","39: Genes Chromosomes Cancer. 2005 Jun;43(2):181-93.","yes","Comment in:","Hepatology. 2005 Apr;41(4):703-6.","y","PMID: 15770670 [PubMed - indexed for MEDLINE]","MeSH Terms:","Astrocytoma/genetics*","Base Sequence","Brain Neoplasms/genetics*","Chromosomes, Human, Pair 22*","DNA Primers","Humans","Microsatellite Repeats/genetics*","Nucleic Acid Hybridization","Polymorphism, Genetic","Research Support, Non-U.S. Gov't","Substances:","DNA Primers"]
["methylation or expression of ZAC mRNA between localized and advanced tumors, our data indicates that loss of ZAC is a relatively early event in HOC. (Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","40: Int J Cancer. 2005 Jul 10;115(5):690-700.","yes","Impact of hepatitis C on health related quality of life: a systematic review and","quantitative assessment.","y","PMID: 15751035 [PubMed - indexed for MEDLINE]","MeSH Terms:","Apoptosis","Cell Cycle Proteins/genetics*","Cell Cycle Proteins/metabolism*","Cell Proliferation","DNA Methylation*","Disease Progression","Female","Gene Expression Profiling*","Gene Silencing*","Genes, Tumor Suppressor","Genomic Imprinting","Humans","In Situ Hybridization","Ovarian Neoplasms/genetics*","Ovarian Neoplasms/pathology*","Polymerase Chain Reaction","Prognosis","RNA, Messenger/biosynthesis","Research Support, Non-U.S. Gov't","Transcription Factors/genetics*","Transcription Factors/metabolism*","Tumor Cells, Cultured","Zinc Fingers","Substances:","Cell Cycle Proteins","PLAGL1 protein, human","RNA, Messenger","Transcription Factors"]
["ic differentiation in vitro and could represent an attractive approach for developing stem cell therapies for treatment of hepatic disease in humans. Supplementary material for this article can be found on the HEPATOLOGY website ( http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html","41: Hepatology. 2005 Apr;41(4):836-46.","yes","Evaluation of transcobalamin II polymorphisms as neural tube defect risk factors","in an Irish population.","y","PMID: 15742390 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cell Differentiation","Cell Movement","Cell Survival","Cells, Cultured","Embryo/cytology*","Green Fluorescent Proteins/metabolism","Growth Substances/physiology*","Hepatocytes/cytology*","Hepatocytes/metabolism","Hepatocytes/transplantation","Liver/metabolism*","Liver Cirrhosis/pathology","Liver Cirrhosis/physiopathology","Liver Cirrhosis/surgery","Mice","Mice, Inbred Strains","Research Support, Non-U.S. Gov't","Stem Cells/cytology*","Stem Cells/metabolism*","Substances:","Growth Substances","Green Fluorescent Proteins"]
["-1; their effects multiplied. In conclusion, combined expression of sFlt-1 and endostatin effectively suppresses HCC growth under in vivo conditions. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley","42: Hepatology. 2005 Apr;41(4):879-86.","yes","Complex chromosome 22 rearrangements in astrocytic tumors identified using","microsatellite and chromosome 22 tile path array analysis.","y","PMID: 15739185 [PubMed - indexed for MEDLINE]","MeSH Terms:","Angiogenesis Inhibitors/genetics*","Animals","Cell Line, Tumor","Endostatins/genetics*","Gene Therapy*","Liver Neoplasms, Experimental/blood supply","Liver Neoplasms, Experimental/pathology","Liver Neoplasms, Experimental/therapy*","Male","Neovascularization, Pathologic/pathology","Rats","Research Support, Non-U.S. Gov't","Solubility","Treatment Outcome","Vascular Endothelial Growth Factor Receptor-1/chemistry","Vascular Endothelial Growth Factor Receptor-1/genetics*","Substances:","Angiogenesis Inhibitors","Endostatins","Vascular Endothelial Growth Factor Receptor-1"]
["ocytes has an impact on several other subcellular compartments and metabolic pathways but is not detrimental to the function of the liver parenchyma. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me","43: Hepatology. 2005 Apr;41(4):868-78.","yes","Epigenetic silencing of the imprinted gene ZAC by DNA methylation is an early","event in the progression of human ovarian cancer.","y","PMID: 15732085 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adenosine Triphosphate/metabolism","Animals","Cells, Cultured","Disease Models, Animal","Endoplasmic Reticulum/ultrastructure*","Gene Expression","Glucose/metabolism","Hepatocytes/ultrastructure*","Liver/metabolism","Liver/ultrastructure","Mice","Mice, Knockout","Mitochondria, Liver/ultrastructure*","Oxidation-Reduction","Oxidative Stress","Peroxisomes/ultrastructure*","Receptors, Cytoplasmic and Nuclear/deficiency","Research Support, Non-U.S. Gov't","Zellweger Syndrome/metabolism","Zellweger Syndrome/pathology*","Substances:","PXR1 protein","Receptors, Cytoplasmic and Nuclear","Glucose","Adenosine Triphosphate"]
["ducibly expressing a protein of interest. As such they represent a useful research tool for example, to dissect oncogene function(s) in colon cancer. Supplementary material for this article be found at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/94/suppmat_welma n.doc. Copyright ","45: J Cell Biochem. 2005 Apr 15;94(6):1148-62.","yes","Direct hepatic fate specification from mouse embryonic stem cells.","Teratani T, Yamamoto H, Aoyagi K, Sasaki H, Asari A, Quinn G, Sasaki H, Terada","y","PMID: 15669025 [PubMed - indexed for MEDLINE]","MeSH Terms:","Blotting, Western","Cell Line, Tumor","Cytomegalovirus/genetics","Doxycycline/pharmacology","Electrophoresis, Polyacrylamide Gel","Gene Expression Regulation, Neoplastic*","Humans","Plasmids","Promoter Regions (Genetics)","Research Support, Non-U.S. Gov't","Subcellular Fractions/metabolism","Transgenes","Substances:","Plasmids","Doxycycline"]
["roteins and with chromatin, spectrin repeat-containing proteins represent strong candidates for important organizational proteins within the nucleus. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html).","46: Bioessays. 2005 Feb;27(2):144-52.","yes","Combined endostatin/sFlt-1 antiangiogenic gene therapy is highly effective in a","rat model of HCC.","y","PMID: 15666356 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cell Membrane/metabolism","Cell Nucleus/metabolism*","Cell Nucleus/physiology*","Chromatin/chemistry","Cytoplasm/metabolism","Evolution, Molecular","Fungal Proteins/chemistry","Humans","Models, Biological","Plant Proteins/chemistry","Protein Binding","Protein Structure, Tertiary","Research Support, Non-U.S. Gov't","Spectrin/chemistry*","Spectrin/physiology*","Substances:","Chromatin","Fungal Proteins","Plant Proteins","Spectrin"]
["that the differential activation of the PKC isoenzymes by DCA may be of critical importance for the functional responses of colonic epithelial cells. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","47: Int J Cancer. 2005 May 10;114(6):887-95.","yes","Absence of peroxisomes in mouse hepatocytes causes mitochondrial and ER","abnormalities.","y","PMID: 15645414 [PubMed - indexed for MEDLINE]","MeSH Terms:","Butyric Acids/pharmacology*","Cell Culture Techniques","Colon/cytology*","Colon/pathology","Colorectal Neoplasms/etiology*","Colorectal Neoplasms/prevention & control*","Cytoskeleton","Deoxycholic Acid/pharmacology*","Detergents/pharmacology*","Enzyme Activation","Epithelium","Humans","Isoenzymes","Protein Kinase C/pharmacokinetics*","Protein Kinase C/pharmacology*","Research Support, Non-U.S. Gov't","Substances:","Butyric Acids","Detergents","Isoenzymes","isobutyric acid","Deoxycholic Acid","Protein Kinase C"]
["esterol hypersecretion, diosgenin probably does not interact directly with Abcg5/Abcg8, but rather increases cholesterol delivery to the heterodimer. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). Me","48: Hepatology. 2005 Jan;41(1):141-50.","yes","Construction and characterization of multiple human colon cancer cell lines for","inducibly regulated gene expression.","y","PMID: 15619238 [PubMed - indexed for MEDLINE]","MeSH Terms:","ATP-Binding Cassette Transporters/metabolism*","Animals","Biliary Tract/drug effects*","Biliary Tract/secretion*","Cholesterol/secretion*","Diosgenin/pharmacology*","Female","Kinetics","Lipoproteins/metabolism*","Male","Mice","Mice, Inbred Strains","Mice, Knockout","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, P.H.S.","Substances:","ABCG5 protein, mouse","ABCG8 protein, mouse","ATP-Binding Cassette Transporters","Lipoproteins","Diosgenin","Cholesterol","Grant Support:","HL060613/HL/NHLBI"]
["rray analysis of new compounds to determine the presence of these expression changes and their usefulness in predicting idiosyncratic hepatotoxicity. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience. Wiley.com/jpages/0270-9139/suppmat/index.htnd). M","49: Hepatology. 2005 Jan;41(1):177-86.","yes","Spectrin repeat proteins in the nucleus.","Young KG, Kothary R.","y","PMID: 15619227 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cells, Cultured","Fluoroquinolones/poisoning*","Gene Expression/drug effects","Glutathione/antagonists & inhibitors","Hepatocytes/drug effects*","Hepatocytes/metabolism","Humans","Liver Diseases/chemically induced","Male","Microarray Analysis*","Mitochondria/drug effects","Naphthyridines/poisoning*","Oxidative Stress","RNA/drug effects","Rats","Rats, Sprague-Dawley","Transcription, Genetic/drug effects","Substances:","Fluoroquinolones","Naphthyridines","trovafloxacin","RNA","Glutathione"]
["rrence and therefore benefit from current antiviral therapy, as well as provide a rationale for the future use of novel immunotherapeutic approaches. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience. wiley.com/jpages/0270-9139/suppmat/index.html). M","50: Hepatology. 2005 Jan;41(1):72-81.","yes","Bile acid deoxycholate induces differential subcellular localisation of the PKC","isoenzymes beta 1, epsilon and delta in colonic epithelial cells in a sodium","y","PMID: 15619226 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Aged","Antibody Formation","Antiviral Agents/therapeutic use","CD4-Positive T-Lymphocytes/immunology","CD8-Positive T-Lymphocytes/immunology","Female","Hepacivirus/immunology*","Hepatitis C/complications*","Hepatitis C/drug therapy","Hepatitis C/prevention & control","Humans","Immunity*","Liver Failure/surgery*","Liver Failure/virology*","Liver Transplantation/immunology*","Male","Middle Aged","Phenotype","Postoperative Period","Prospective Studies","Recurrence","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","T-Lymphocytes/immunology*","Substances:","Antiviral Agents","Grant Support:","R01 DK60590/DK/NIDDK"]
[" decrease in hepatic necrosis following acetaminophen challenge. This suggests a novel role for LBP in modulating acetaminophen-induced liver injury. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/O270-9139/suppmat/index.html). Me","51: Hepatology. 2005 Jan;41(1):187-95.","yes","Diosgenin-induced biliary cholesterol secretion in mice requires Abcg8.","Kosters A, Frijters RJ, Kunne C, Vink E, Schneiders MS, Schaap FG, Nibbering CP,","y","PMID: 15619225 [PubMed - indexed for MEDLINE]","MeSH Terms:","Acetaminophen*/poisoning","Acute-Phase Proteins/genetics","Acute-Phase Proteins/metabolism*","Acute-Phase Proteins/pharmacology","Adenoviridae","Animals","Carrier Proteins/genetics","Carrier Proteins/metabolism*","Carrier Proteins/pharmacology","Cytochrome P-450 Enzyme System/metabolism","Cytokines/metabolism","Endotoxins/blood","Gene Transfer Techniques","Genetic Vectors","Glutathione/metabolism","Liver/drug effects","Liver/metabolism","Liver/pathology","Liver Diseases/chemically induced*","Liver Diseases/prevention & control","Membrane Glycoproteins/genetics","Membrane Glycoproteins/metabolism*","Membrane Glycoproteins/pharmacology","Mice","Mice, Inbred C57BL","Mice, Knockout","Portal System","Rats","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Substances:","Acute-Phase Proteins","Carrier Proteins","Cytokines","Endotoxins","Genetic Vectors","Membrane Glycoproteins","lipopolysaccharide-binding protein","Acetaminophen","Glutathione","Cytochrome P-450 Enzyme System","Grant Support:","DK53296/DK/NIDDK","GM60205/GM/NIGMS"]
["xpressed genes that colocalize in the genome may indicate gene regulatory mechanisms that require further study to evaluate functional coregulation. (Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","52: Int J Cancer. 2005 Apr 20;114(4):590-7.","yes","Microarray analysis in human hepatocytes suggests a mechanism for hepatotoxicity","induced by trovafloxacin.","y","PMID: 15609325 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Blotting, Western","Cell Transformation, Neoplastic","DNA Primers/chemistry","Down-Regulation","Fibroblasts/metabolism","Gene Expression Regulation, Neoplastic*","Genes, erbB-2*","Genome","Glycoproteins/metabolism","Humans","Mice","NIH 3T3 Cells","Neovascularization, Pathologic*","Oligonucleotide Array Sequence Analysis","Receptor, erbB-2/metabolism*","Research Support, Non-U.S. Gov't","Reverse Transcriptase Polymerase Chain Reaction","Signal Transduction","Transfection","Up-Regulation","Substances:","DNA Primers","Glycoproteins","Receptor, erbB-2"]
[" two established recombination detection methods: Recpars and the DSS (difference of sum of squares) method. AVAILABILITY: Software, data and further supplementary material are available at the following website: http://www.bioss.sari.ac.uk/~dirk/Supplements/ Publication Types: Evaluation Studies Me","54: Bioinformatics. 2005 May 1;21(9):1797-806. Epub 2004 Nov 30.","yes","Reconstitution of hepatitis C virus-specific T-cellmediated immunity after liver","transplantation.","y","PMID: 15572473 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Cluster Analysis","DNA Mutational Analysis/methods","Evolution, Molecular","Models, Genetic*","Models, Statistical","Pattern Recognition, Automated/methods*","Phylogeny","Recombination, Genetic/genetics*","Research Support, Non-U.S. Gov't","Sequence Alignment/methods*","Sequence Analysis, DNA/methods*","Variation (Genetics)/genetics*"]
["ults demonstrate that mammalian viral genome types differ in their amino acid preference. AVAILABILITY: The tools used to format and analyze data and supplementary material are available at http://www.cse.sc.edu/~rose/aminoPreference/index.html CONTACT: rose@cse.sc.edu. Publication Types: Evaluation","55: Bioinformatics. 2005 Apr 15;21(8):1349-57. Epub 2004 Nov 30.","yes","Lipopolysaccharide-binding protein modulates acetaminophen-induced liver injury","in mice.","y","PMID: 15572467 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Amino Acid Sequence","Animals","Base Sequence","Chromosome Mapping/methods*","Comparative Study","DNA, Viral/genetics*","Genome, Viral*","Mammals","Models, Genetic","Molecular Sequence Data","Research Support, U.S. Gov't, Non-P.H.S.","Sequence Alignment/methods*","Sequence Analysis, DNA/methods*","Species Specificity","Statistics","Viral Proteins/genetics*","Substances:","DNA, Viral","Viral Proteins"]
["ic interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/. MeSH Terms: Adaptation, Physiolo","56: Arch Microbiol. 2005 Jan;183(1):27-36. Epub 2004 Nov 13.","yes","Identification and validation of novel ERBB2 (HER2, NEU) targets including genes","involved in angiogenesis.","y","PMID: 15551059 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adaptation, Physiological/genetics","Aerobiosis","Anaerobiosis","Azoarcus/genetics","Bacterial Proteins/genetics","Betaproteobacteria/classification","Betaproteobacteria/genetics*","Betaproteobacteria/metabolism*","Biodegradation","Chromosomes, Bacterial/genetics","DNA, Bacterial/chemistry","Evolution, Molecular","Gene Expression Regulation, Bacterial","Gene Transfer, Horizontal","Genes, Bacterial","Genome, Bacterial*","Hydrocarbons, Aromatic/metabolism*","Interspersed Repetitive Sequences","Molecular Sequence Data","Multigene Family","Nitrogen Fixation/genetics","Open Reading Frames","Plasmids/genetics","Research Support, Non-U.S. Gov't","Sequence Analysis, DNA*","Sequence Homology","Substances:","Bacterial Proteins","DNA, Bacterial","Hydrocarbons, Aromatic","Plasmids","Secondary Source ID:","GENBANK/CR555306","GENBANK/CR555307","GENBANK/CR555308"]
["sociated with ConA-treated cells implies that a mechanism independent of furin may perhaps account for the binding of the MMP-2 species to the cells. Supplementary material for this article can be found at http://www.mrw.interscience.wiley.com/suppmat/0730-2312/suppmat/94/suppmat_guo.t if. Copyright","57: J Cell Biochem. 2005 Feb 15;94(3):446-59.","yes","Paradigmatic identification of MMP-2 and MT1-MMP activation systems in cardiac","fibroblasts cultured as a monolayer.","y","PMID: 15534869 [PubMed - indexed for MEDLINE]","MeSH Terms:","Animals","Cells, Cultured","Furin/antagonists & inhibitors","Gelatinase A/metabolism*","Metalloendopeptidases/metabolism*","Myocardium/cytology","Myocardium/enzymology*","Rats","Research Support, Non-U.S. Gov't","Tissue Inhibitor of Metalloproteinase-2/metabolism","Up-Regulation","Substances:","Tissue Inhibitor of Metalloproteinase-2","Furin","Metalloendopeptidases","Gelatinase A","membrane-type matrix metalloproteinase"]
["s were recognized by serum antibodies of melanoma patients but not healthy controls. The role of these antigens in MAR awaits further investigation. (Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","58: Int J Cancer. 2005 Mar 10;114(1):88-93.","yes","SEREX identification of new tumor antigens linked to melanoma-associated","retinopathy.","y","PMID: 15523688 [PubMed - indexed for MEDLINE]","MeSH Terms:","Antigens, Neoplasm/analysis*","Antigens, Neoplasm/genetics","Blotting, Northern","Cell Line, Tumor","DNA, Complementary/analysis","DNA, Neoplasm/analysis","Gene Library","Humans","Melanoma/immunology*","Paraneoplastic Syndromes/immunology*","RNA, Neoplasm/analysis","Research Support, Non-U.S. Gov't","Retinal Diseases/immunology*","Reverse Transcriptase Polymerase Chain Reaction","Rhodopsin/immunology","Serologic Tests/methods*","Skin Neoplasms/immunology*","Substances:","Antigens, Neoplasm","DNA, Complementary","DNA, Neoplasm","RNA, Neoplasm","Rhodopsin"]
["Ps (132C > T in exon V and 196G > A (val66met) in exon XIIIA) of the BDNF gene may not be associated with Japanese MAP abusers. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:","59: Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132(1):70-3.","yes","Association study between brain-derived neurotrophic factor gene polymorphisms","and methamphetamine abusers in Japan.","y","PMID: 15459944 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adult","Alleles","Amphetamine-Related Disorders/etiology","Amphetamine-Related Disorders/genetics*","Brain-Derived Neurotrophic Factor/genetics*","Female","Gene Frequency","Genotype","Humans","Japan","Male","Methamphetamine/poisoning","Middle Aged","Polymorphism, Genetic*","Substances:","Brain-Derived Neurotrophic Factor","Methamphetamine"]
["effects of ethanol, dopamine may be critical for initiating drug use and for reinstating drug use during protracted abstinence. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:","60: Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132(1):29-37.","yes","Relationship between dopaminergic neurotransmission, alcoholism, and Reward","Deficiency syndrome.","y","PMID: 15457501 [PubMed - indexed for MEDLINE]","MeSH Terms:","Alcoholism/physiopathology*","Brain/physiopathology","Dopamine/physiology*","Humans","Models, Biological","Polymorphism, Genetic","Receptors, Dopamine D2/genetics","Receptors, Dopamine D2/physiology*","Research Support, U.S. Gov't, Non-P.H.S.","Research Support, U.S. Gov't, P.H.S.","Reward*","Synaptic Transmission/physiology*","Syndrome","Substances:","Receptors, Dopamine D2","Dopamine","Grant Support:","K05-AA00219/AA/NIAAA","R37-AA07112/AA/NIAAA"]
["e allele reported till date at the MJD/SCA3 locus and may greatly reduce the gap between normal and pathological repeat ranges. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:","61: Am J Med Genet B Neuropsychiatr Genet. 2005 Feb 5;133(1):124-6.","yes","Identification of a novel 45 repeat unstable allele associated with a disease","phenotype at the MJD1/SCA3 locus.","y","PMID: 15457499 [PubMed - indexed for MEDLINE]","MeSH Terms:","Aged","Alleles","Atrophy","Base Sequence","Brain Stem/pathology","Cerebellum/pathology","Family Health","Female","Haplotypes","Humans","India","Machado-Joseph Disease/genetics*","Machado-Joseph Disease/pathology","Magnetic Resonance Imaging","Male","Nerve Tissue Proteins/genetics*","Pedigree","Phenotype","Polymorphism, Single Nucleotide","Research Support, Non-U.S. Gov't","Trinucleotide Repeat Expansion/genetics","Trinucleotide Repeats/genetics*","Substances:","ATXN3 protein, human","Nerve Tissue Proteins"]
[" We found no association between p.V66M or the additionally genotyped variant c.-46C > T and obesity, ADHD or eating disorders. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:","62: Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132(1):96-9.","yes","Mutation screen of the brain derived neurotrophic factor gene (BDNF):","identification of several genetic variants and association studies in patients","y","PMID: 15457498 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adolescent","Attention Deficit Disorder with Hyperactivity/genetics","Body Mass Index","Brain-Derived Neurotrophic Factor/genetics*","Child","Chromatography, High Pressure Liquid/methods","Comparative Study","DNA/chemistry","DNA/genetics","DNA Mutational Analysis","Eating Disorders/genetics","Gene Frequency","Genotype","Humans","Linkage Disequilibrium","Mutation*","Obesity/genetics","Polymorphism, Single Nucleotide","Polymorphism, Single-Stranded Conformational","Research Support, Non-U.S. Gov't","Substances:","Brain-Derived Neurotrophic Factor","DNA"]
["ry finding that needs to be replicated in a larger sample of Caucasian males and relationships sought with clinical phenotypes. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:","63: Am J Med Genet B Neuropsychiatr Genet. 2005 Jan 5;132(1):100-3.","yes","Relationship of MAO-A promoter (u-VNTR) and COMT (V158M) gene polymorphisms to","CSF monoamine metabolites levels in a psychiatric sample of caucasians: A","y","PMID: 15457497 [PubMed - indexed for MEDLINE]","MeSH Terms:","Adolescent","Adult","Aged","Amino Acid Substitution/genetics","Catechol O-Methyltransferase/genetics*","Comparative Study","European Continental Ancestry Group/genetics*","Female","Genotype","Homovanillic Acid/cerebrospinal fluid","Humans","Hydroxyindoleacetic Acid/cerebrospinal fluid","Linkage Disequilibrium","Male","Mental Disorders/cerebrospinal fluid","Mental Disorders/genetics*","Methoxyhydroxyphenylglycol/cerebrospinal fluid","Middle Aged","Minisatellite Repeats/genetics","Monoamine Oxidase/cerebrospinal fluid","Monoamine Oxidase/genetics*","Polymorphism, Genetic*","Promoter Regions (Genetics)/genetics*","Research Support, U.S. Gov't, P.H.S.","Substances:","Homovanillic Acid","Methoxyhydroxyphenylglycol","Hydroxyindoleacetic Acid","Monoamine Oxidase","Catechol O-Methyltransferase","Grant Support:","MH48514/MH/NIMH","MH62185/MH/NIMH"]
[" the diagnosis of prostate cancer. Nevertheless, this risk should not be neglected as it may be of clinical significance under certain circumstances. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","64: Int J Cancer. 2005 Jan 10;113(2):290-7.","yes","Expression of prostate-specific antigen (PSA) and human glandular kallikrein 2","(hK2) in ileum and other extraprostatic tissues.","y","PMID: 15389512 [PubMed - indexed for MEDLINE]","MeSH Terms:","Humans","Ileum/physiology*","Immunohistochemistry","In Situ Hybridization","Male","Prostate-Specific Antigen/analysis*","Prostate-Specific Antigen/biosynthesis*","Prostatic Neoplasms/diagnosis*","Protease Inhibitors/metabolism","Reproducibility of Results","Research Support, Non-U.S. Gov't","Reverse Transcriptase Polymerase Chain Reaction","Tissue Distribution","Tissue Kallikreins/biosynthesis*","Substances:","Protease Inhibitors","Tissue Kallikreins","Prostate-Specific Antigen"]
[" of unknown function, potentially coding for pharmacologically or microbiologically active substances. Supplemental data to this work can be found at http://www.ncbi.nlm.nih.gov/projects/omes/index.html#Ag2. MeSH Terms: Amino Acid Sequence Animals Anopheles gambiae/genetics* Chromosome Mapping Chrom","1: J Exp Biol. 2005 Oct;208(Pt 20):3971-86.","yes",null,"An updated catalogue of salivary gland transcripts in the adult female mosquito,","no","Anopheles gambiae.","PMID: 16215223 [PubMed - indexed for MEDLINE]","MeSH Terms:","Amino Acid Sequence","Animals","Anopheles gambiae/genetics*","Chromosome Mapping","Chromosomes/genetics","Cluster Analysis","Computational Biology","DNA Transposable Elements","Female","Gene Expression Profiling*","Gene Expression Regulation*","Insect Proteins/chemistry","Insect Proteins/genetics*","Molecular Sequence Data","RNA, Messenger/genetics","RNA, Messenger/metabolism","Research Support, N.I.H., Intramural","Research Support, Non-U.S. Gov't","Salivary Glands/metabolism*","Transcription, Genetic/genetics*","Substances:","DNA Transposable Elements","Insect Proteins","RNA, Messenger"]
["m is useful mainly to improve local marker ordering in linkage groups obtained in other ways. AVAILABILITY: The source code and supplemental data are http://www.iubio.bio.indiana.edu/soft/molbio/qtl/flipper/ CONTACT: ccrane@purdue.edu. Publication Types: Evaluation Studies Validation Studies MeSH Te","2: Bioinformatics. 2005 Apr 15;21(8):1579-91. Epub 2004 Nov 25.","no",null,"A nearest-neighboring-end algorithm for genetic mapping.","no","Crane CF, Crane YM.","PMID: 15564296 [PubMed - indexed for MEDLINE]","MeSH Terms:","Algorithms*","Chromosome Mapping/methods*","Comparative Study","Computer Simulation","DNA Mutational Analysis/methods*","Gene Deletion","Genetic Markers/genetics*","Genetics, Population*","Humans","Linkage (Genetics)/genetics","Models, Genetic*","Models, Statistical","Research Support, U.S. Gov't, Non-P.H.S.","Software*","Substances:","Genetic Markers"]

{"sheet":"2006","index":10,"n_rows":28,"n_cols":30,"rows_kept":28,"flags":["formulas_cached_only"]}
["etworks and to infer activity profiles of hidden variables. AVAILABILITY: Supplementary data and Matlab code will be made available at the URL below. SUPPLEMENTARY INFORMATION: http://www.chems.msu.edu/groups/chan/ssm.zip. PMID: 16403793 [PubMed - as supplied by publisher]","no","11: Bioinformatics. 2006 Jan 10; [Epub ahead of print]","Using a state-space model with hidden variables to infer transcription factor","activities.","PMID: 16403793 [PubMed - as supplied by publisher]"]
["itoylation sites. AVAILABILITY: CSS-Palm is implemented in PHP/PERL+MySQL and can be freely accessed at http://bioinformatics.lcd-ustc.org/css_palm/. SUPPLEMENTARY INFORMATION: The supplementary materials, including the details of the algorithm, could be visited from: http://bioinformatics.lcd-ustc.","yes","1: Bioinformatics. 2006 Jan 24; [Epub ahead of print]","CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy","(CSS).","PMID: 16434441 [PubMed - as supplied by publisher]"]
["s can be partly attributed to highly mobile domains. Duplication/deletion has been found in modular proteins such as peptide synthases. Availability: Supplementary material can be found at: http://www.uni-muenster.de/Biologie.Botanik/ebb/projects/cp/ PMID: 16431849 [PubMed - as supplied by publisher","yes","2: Mol Biol Evol. 2006 Jan 23; [Epub ahead of print]","Evolution of Circular Permutations in Multi-Domain Proteins.","Weiner J 3rd, Bornberg-Bauer E.","PMID: 16431849 [PubMed - as supplied by publisher]"]
[" suggest how to find a suitable direction for the extension of a constantly-growing ontology such as GO. AVAILABILITY: http://autogo.biopathway.org/. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. PMID: 16428805 [PubMed - as supplied by publisher]","yes","3: Bioinformatics. 2006 Jan 21; [Epub ahead of print]","Automatic extension of gene ontology with flexible identification of candidate","terms.","PMID: 16428805 [PubMed - as supplied by publisher]"]
["dy that analyzes a large number of microarrays, prepared with RNA from breast tumor samples from each of 295 patients. AVAILABILITY: The software and supplementary material are available at http://public.tgen.org/tgen-cb/support/testbed/. PMID: 16428263 [PubMed - as supplied by publisher]","yes","4: Bioinformatics. 2006 Jan 20; [Epub ahead of print]","Genetic test bed for feature selection.","Choudhary A, Brun M, Hua J, Lowey J, Suh E, Dougherty ER.","PMID: 16428263 [PubMed - as supplied by publisher]"]
["ry still-unknown cryptic genomic alterations that could affect a gene or genes of importance in the disease progression of CML. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2006 Wiley-Liss, Inc. PMID: 16425296 [PubMed - as ","yes","5: Genes Chromosomes Cancer. 2006 Jan 19; [Epub ahead of print]","Genomewide screening of DNA copy number changes in chronic myelogenous leukemia","with the use of high-resolution array-based comparative genomic hybridization.","PMID: 16425296 [PubMed - as supplied by publisher]"]
["ct of annotation bias to significantly improve performance. AVAILABILITY: SUSPECTS is freely available at http://www.genetics.med.ed.ac.uk/suspects/. SUPPLEMENTARY INFORMATION: A quick-start guide in Macromedia Flash format is available at http://www.genetics.med.ed.ac.uk/suspects/help.shtml. Excel ","yes","6: Bioinformatics. 2006 Jan 19; [Epub ahead of print]","SUSPECTS: enabling fast and effective prioritization of positional candidates.","Adie EA, Adams RR, Evans KL, Porteous DJ, Pickard BS.","PMID: 16423925 [PubMed - as supplied by publisher]"]
["e propose that breakage at specific cFS could derive from early epigenetic events at loci involved in radiation carcinogenesis. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. (c) 2006 Wiley-Liss, Inc. PMID: 16419058 [PubMed - as ","yes","7: Genes Chromosomes Cancer. 2006 Jan 17; [Epub ahead of print]","Chromosomal fragile sites FRA3B and FRA16D show correlated expression and","association with failure of apoptosis in lymphocytes from patients with thyroid","PMID: 16419058 [PubMed - as supplied by publisher]"]
["SC genome browser). Availability: TAMAL is a platform independent web-based application available free of charge at http://neoref.ils.unc.edu/tamal/. SUPPLEMENTARY INFORMATION: http://neoref.ils.unc.edu/tamal/. PMID: 16418238 [PubMed - as supplied by publisher]","yes","8: Bioinformatics. 2006 Jan 17; [Epub ahead of print]","TAMAL: an integrated approach to choosing SNPs for genetic studies of human","complex traits.","PMID: 16418238 [PubMed - as supplied by publisher]"]
["ties. Using this method, we make function predictions for multiple proteins, and experimentally confirm predictions for proteins involved in mitosis. SUPPLEMENTARY INFORMATION: Results for the 105 selected GO classes and predictions for 1059 unknown genes are available at: http://function.princeton.","yes","9: Bioinformatics. 2006 Jan 12; [Epub ahead of print]","Hierarchical multi-label prediction of gene function.","Barutcuoglu Z, Schapire RE, Troyanskaya OG.","PMID: 16410319 [PubMed - as supplied by publisher]"]
[" exons. Our results show that GenASAP provides accurate predictions for over one third of the total events, as verified by independent RT-PCR assays. SUPPLEMENTARY INFORMATION: http://www.psi.toronto.edu/GenASAP. PMID: 16403798 [PubMed - as supplied by publisher]","yes","10: Bioinformatics. 2006 Jan 10; [Epub ahead of print]","Inferring global levels of alternative splicing isoforms using a generative","model of microarray data.","PMID: 16403798 [PubMed - as supplied by publisher]"]
["t monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. HvrBase++ is Oracle b","yes","12: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D700-4.","HvrBase++: a phylogenetic database for primate species.","Kohl J, Paulsen I, Laubach T, Radtke A, von Haeseler A.","PMID: 16381963 [PubMed - in process]"]
["iption factor binding sites in non-coding DNA. AVAILABILITY: ACANA software and test sequence data are publicly available at http://BioMedEmpire.org/ SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online. CONTACT: li3@niehs.nih.gov. PMID: 16301203 [PubMed - in pro","yes","13: Bioinformatics. 2006 Jan 1;22(1):29-34. Epub 2005 Nov 13.","Accurate anchoring alignment of divergent sequences.","Huang W, Umbach DM, Li L.","PMID: 16301203 [PubMed - in process]"]
["vailable as an R package. AVAILABILITY: ClaNC is freely available from http://students.washington.edu/adabney/clanc CONTACT: adabney@u.washington.edu SUPPLEMENTARY INFORMATION: http://students.washington.edu/adabney/clanc/figure2.pdf. PMID: 16269418 [PubMed - in process]","yes","14: Bioinformatics. 2006 Jan 1;22(1):122-3. Epub 2005 Nov 2.","ClaNC: point-and-click software for classifying microarrays to nearest","centroids.","PMID: 16269418 [PubMed - in process]"]
["tware is implemented in R and is available from Bioconductor or from the first author at nrabbee@post.harvard.edu. CONTACT: nrabbee@stat.berkeley.edu SUPPLEMENTARY INFORMATION: http://www.stat.berkeley.edu/users/nrabbee/693.pdf. PMID: 16267090 [PubMed - in process]","yes","15: Bioinformatics. 2006 Jan 1;22(1):7-12. Epub 2005 Nov 2.","A genotype calling algorithm for affymetrix SNP arrays.","Rabbee N, Speed TP.","PMID: 16267090 [PubMed - in process]"]
["f ncRNA families. AVAILABILITY: The source code is available under GNU Public License at the supplementary web site. CONTACT: zasha@cs.washington.edu SUPPLEMENTARY INFORMATION: http://bio.cs.washington.edu/supplements/zasha-HeurHmm-2004/ (Technical details, results, C++ code). PMID: 16267089 [PubMed","yes","16: Bioinformatics. 2006 Jan 1;22(1):35-9. Epub 2005 Nov 2.","Sequence-based heuristics for faster annotation of non-coding RNA families.","Weinberg Z, Ruzzo WL.","PMID: 16267089 [PubMed - in process]"]
[" same names. AVAILABILITY: BioThesaurus is accessible for online searching at http://pir.georgetown.edu/iprolink/biothesaurus Contact: hfliu@umbc.edu SUPPLEMENTARY INFORMATION: Supplementary data are accessible at http://pir.georgetown.edu/iprolink/biothesaurus/supplement/ PMID: 16267085 [PubMed - i","yes","18: Bioinformatics. 2006 Jan 1;22(1):103-5. Epub 2005 Nov 2.","BioThesaurus: a web-based thesaurus of protein and gene names.","Liu H, Hu ZZ, Zhang J, Wu C.","PMID: 16267085 [PubMed - in process]"]
["tisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/ CONTACT: xyn@bmb.uga.edu SUPPLEMENTARY INFORMATION: Detailed documentation for libSRES is available at http://csbl.bmb.uga.edu/~jix/science/libSRES/ PMID: 16267082 [PubMed - i","yes","19: Bioinformatics. 2006 Jan 1;22(1):124-6. Epub 2005 Nov 2.","libSRES: a C library for stochastic ranking evolution strategy for parameter","estimation.","PMID: 16267082 [PubMed - in process]"]
["s in Spain. AVAILABILITY: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ CONTACT: ots@ac.uma.es SUPPLEMENTARY INFORMATION: http://www.inab.org/Help/Main/index.html. PMID: 16257987 [PubMed - in process]","yes","20: Bioinformatics. 2006 Jan 1;22(1):106-11. Epub 2005 Oct 27.","Intelligent client for integrating bioinformatics services.","Navas-Delgado I, Rojano-Munoz Mdel M, Ramirez S, Perez AJ, Andres Leon E,","PMID: 16257987 [PubMed - in process]"]
["e discovery of conserved protein substructures. AVAILABILITY: Gemoda is freely available at http://web.mit.edu/bamel/gemoda CONTACT: gregstep@mit.edu SUPPLEMENTARY INFORMATION: Available at http://web.mit.edu/bamel/gemoda. PMID: 16257985 [PubMed - in process]","yes","21: Bioinformatics. 2006 Jan 1;22(1):21-8. Epub 2005 Oct 27.","A generic motif discovery algorithm for sequential data.","Jensen KL, Styczynski MP, Rigoutsos I, Stephanopoulos GN.","PMID: 16257985 [PubMed - in process]"]
["m ClusterLustre, and the simulated dataset for testing are available upon request from T.G. and O.W. CONTACT: tg@biocentrum.dtu.dk and owi@imm.dtu.dk SUPPLEMENTARY INFORMATION: http://www.cmb.dtu.dk/ PMID: 16257984 [PubMed - as supplied by publisher]","yes","22: Bioinformatics. 2006 Jan 1;22(1):58-67. Epub 2005 Oct 27.","Robust multi-scale clustering of large DNA microarray datasets with the","consensus algorithm.","PMID: 16257984 [PubMed - as supplied by publisher]"]
["tasets and has produced very promising results. AVAILABILITY: MATLAB codes are available upon request from the authors. CONTACT: hzhang@stat.ncsu.edu SUPPLEMENTARY INFORMATION: http://www4.stat.ncsu.edu/~hzhang/research.html. PMID: 16249260 [PubMed - in process]","yes","23: Bioinformatics. 2006 Jan 1;22(1):88-95. Epub 2005 Oct 25.","Gene selection using support vector machines with non-convex penalty.","Zhang HH, Ahn J, Lin X, Park C.","PMID: 16249260 [PubMed - in process]"]
["atlab source code is available upon request and DNA microarray data are available at GEO (http://www.ncbi.nlm.nih.gov/geo). Contact: cwang61@ucla.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. PMID: 16249259 [PubMed - in process]","yes","24: Bioinformatics. 2006 Jan 1;22(1):77-87. Epub 2005 Oct 25.","Integrating time-course microarray gene expression profiles with cytotoxicity","for identification of biomarkers in primary rat hepatocytes exposed to cadmium.","PMID: 16249259 [PubMed - in process]"]
[" system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Contact: galperin@ncbi.nlm.nih.gov SUPPLEMENTARY INFORMATION: http://www.ncbi.nlm.nih.gov/Complete_Genomes/SigCensus/PilZ.html. PMID: 16249258 [PubMed - in process]","yes","25: Bioinformatics. 2006 Jan 1;22(1):3-6. Epub 2005 Oct 25.","PilZ domain is part of the bacterial c-di-GMP binding protein.","Amikam D, Galperin MY.","PMID: 16249258 [PubMed - in process]"]
["eats may be associated with endometrial carcinogenesis because of AR's reduced ability to recruit coregulators and other transcriptional components. (supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","yes","26: Int J Cancer. 2006 Mar 1;118(5):1261-8.","Androgen receptor polymorphisms and endometrial cancer risk.","McGrath M, Lee IM, Hankinson SE, Kraft P, Hunter DJ, Buring J, De Vivo I.","PMID: 16161040 [PubMed - in process]"]
["ow 2 Ras isoforms regulate disparate biologic processes, revealing a number of genes whose deregulated expression may influence colon carcinogenesis (supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","yes","27: Int J Cancer. 2006 Mar 1;118(3):616-27.","Microarray analysis of the differential transformation mediated by Kirsten and","Harvey Ras oncogenes in a human colorectal adenocarcinoma cell line.","PMID: 16152623 [PubMed - in process]"]
["tages of disease. Our data suggest that cSHMT, Tbx3 and utrophin can be used as components of multiparameter monitoring of ovarian and breast cancer (supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience.wiley.com/jpages/0020-7","yes","28: Int J Cancer. 2006 Jan 15;118(2):412-21.","Increased expression of cSHMT, Tbx3 and utrophin in plasma of ovarian and breast","cancer patients.","PMID: 16049973 [PubMed - indexed for MEDLINE]","MeSH Terms:","Breast Neoplasms/pathology*","Case-Control Studies","Cytosol/chemistry","Electrophoresis, Gel, Two-Dimensional","Female","Gene Expression Profiling","Glycine Hydroxymethyltransferase/biosynthesis","Glycine Hydroxymethyltransferase/blood*","Humans","Neoplasm Staging/methods","Ovarian Neoplasms/blood*","Research Support, Non-U.S. Gov't","Spectrum Analysis, Mass","T-Box Domain Proteins/biosynthesis","T-Box Domain Proteins/blood*","Tumor Markers, Biological/blood","Utrophin/biosynthesis","Utrophin/blood*","Substances:","T-Box Domain Proteins","Tumor Markers, Biological","Utrophin","Glycine Hydroxymethyltransferase"]
["http://blast.wustl.edu/exalin. The software (scripts, source code and binaries) is copyrighted but free for all to use. CONTACT: gish@blast.wustl.edu SUPPLEMENTARY INFORMATION: http://blast.wustl.edu/exalin/exalin-supplement.pdf. PMID: 16267086 [PubMed - in process]","yes","17: Bioinformatics. 2006 Jan 1;22(1):13-20. Epub 2005 Nov 2.","Improved spliced alignment from an information theoretic approach.","Zhang M, Gish W.","PMID: 16267086 [PubMed - in process]"]

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["#","Live?","Journal?","Reference"]
[1,"y","y","Barbe V, Vallenet D, Fonknechten N, et al. Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucl. Acids Res. %R 10.1093/nar/gkh910. October 28, 2004 2004;32(19):5766-5779."]
[2,"y","y","Bene A, Kurten RC, Chambers TC. Subcellular localization as a limiting factor for utilization of decoy oligonucleotides. Nucl. Acids Res. %R 10.1093/nar/gnh139. October 21, 2004 2004;32(19):e142-."]
[3,"y","y","Cardoso J, Molenaar L, de Menezes RX, et al. Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH. Nucl. Acids Res. %R 10.1093/nar/gnh142. October 28, 2004 2004;32(19):e146-."]
[4,"y","y","Carr PA, Park JS, Lee Y-J, Yu T, Zhang S, Jacobson JM. Protein-mediated error correction for de novo DNA synthesis. Nucl. Acids Res. %R 10.1093/nar/gnh160. November 23, 2004 2004;32(20):e162-."]
[5,"y","y","Champ PC, Maurice S, Vargason JM, Camp T, Ho PS. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucl. Acids Res. %R 10.1093/nar/gkh988. December 14, 2004 2004;32(22):6501-6510."]
[6,"n/a mis-indexed","n/a","Chen Y, Xu D. Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. Nucl. Acids Res. %R 10.1093/nar/gkh978. December 7, 2004 2004;32(21):6414-6424."]
[7,"y","y","D'Anjou H, Chabot C, Chartrand P. Preferential accessibility to specific genomic loci for the repair of double-strand breaks in human cells. Nucl. Acids Res. %R 10.1093/nar/gkh952. November 23, 2004 2004;32(20):6136-6143."]
[8,"y","y","Doe CL, Osman F, Dixon J, Whitby MC. DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51. Nucl. Acids Res. %R 10.1093/nar/gkh853. October 14, 2004 2004;32(18):5570-5581."]
[9,"y","y","Doerks T, von Mering C, Bork P. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucl. Acids Res. %R 10.1093/nar/gkh973. December 1, 2004 2004;32(21):6321-6326."]
[10,"y","y","Galperin MY, Koonin EV. 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucl. Acids Res. %R 10.1093/nar/gkh885. October 12, 2004 2004;32(18):5452-5463."]
[11,"y","y","Glockner G, Lehmann R, Romualdi A, et al. Comparative analysis of the Borrelia garinii genome. Nucl. Acids Res. %R 10.1093/nar/gkh953. November 16, 2004 2004;32(20):6038-6046."]
[12,"y","y","Guglielmi B, van Berkum NL, Klapholz B, et al. A high resolution protein interaction map of the yeast Mediator complex. Nucl. Acids Res. %R 10.1093/nar/gkh878. October 11, 2004 2004;32(18):5379-5391."]
[13,"y","y","Han LY, Cai CZ, Ji ZL, Cao ZW, Cui J, Chen YZ. Predicting functional family of novel enzymes irrespective of sequence similarity: a statistical learning approach. Nucl. Acids Res. %R 10.1093/nar/gkh984. December 7, 2004 2004;32(21):6437-6444."]
[14,"y","y","Hannoush RN, Min K-L, Damha MJ. Diversity-oriented solid-phase synthesis and biological evaluation of oligonucleotide hairpins as HIV-1 RT RNase H inhibitors. Nucl. Acids Res. %R 10.1093/nar/gkh948. November 29, 2004 2004;32(21):6164-6175."]
[15,"y","y","Hartig JS, Kool ET. Small circular DNAs for synthesis of the human telomere repeat: varied sizes, structures and telomere-encoding activities. Nucl. Acids Res. %R 10.1093/nar/gnh149. November 1, 2004 2004;32(19):e152-."]
[16,"y","y","Hashiguchi K, Stuart JA, de Souza-Pinto NC, Bohr VA. The C-terminal {alpha}O helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial {beta}-Ogg1 lacks this domain and does not have glycosylase activity. Nucl. Acids Res. %R 10.1093/nar/gkh863. October 19, 2004 2004;32(18):5596-5608."]
[17,"y","y","Hodas NO, Aalberts DP. Efficient computation of optimal oligo-RNA binding. Nucl. Acids Res. %R 10.1093/nar/gkh1008. December 17, 2004 2004;32(22):6636-6642."]
[18,"y","y","Horisawa K, Tateyama S, Ishizaka M, et al. In vitro selection of Jun-associated proteins using mRNA display. Nucl. Acids Res. %R 10.1093/nar/gnh167. December 2, 2004 2004;32(21):e169-."]
[19,"y","y","Iyer LM, Makarova KS, Koonin EV, Aravind L. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucl. Acids Res. %R 10.1093/nar/gkh828. October 5, 2004 2004;32(17):5260-5279."]
[20,"y","y","Jacobs JL, Dinman JD. Systematic analysis of bicistronic reporter assay data. Nucl. Acids Res. %R 10.1093/nar/gnh157. November 23, 2004 2004;32(20):e160-."]
[21,"y","Y","Janssen CS, Phillips RS, Turner CMR, Barrett MP. Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites. Nucl. Acids Res. %R 10.1093/nar/gkh907. October 26, 2004 2004;32(19):5712-5720."]
[22,"n","y- online","Janzen CJ, Lander F, Dreesen O, Cross GAM. Telomere length regulation and transcriptional silencing in KU80-deficient Trypanosoma brucei. Nucl. Acids Res. %R 10.1093/nar/gkh991. December 15, 2004 2004;32(22):6575-6584."]
[23,"y","y","Jin VX, Leu Y-W, Liyanarachchi S, et al. Identifying estrogen receptor {alpha} target genes using integrated computational genomics and chromatin immunoprecipitation microarray. Nucl. Acids Res. %R 10.1093/nar/gkh1005. December 17, 2004 2004;32(22):6627-6635."]
[24,"y","y","Kroeger KM, Goodman MF, Greenberg MM. A comprehensive comparison of DNA replication past 2-deoxyribose and its tetrahydrofuran analog in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh873. October 11, 2004 2004;32(18):5480-5485."]
[25,"y","y","Le K, Mitsouras K, Roy M, et al. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucl. Acids Res. %R 10.1093/nar/gnh173. December 14, 2004 2004;32(22):e180-."]
[26,"y","y","Le Meur N, Lamirault G, Bihouee A, et al. A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. Nucl. Acids Res. %R 10.1093/nar/gkh870. October 8, 2004 2004;32(18):5349-5358."]
[27,"y","y","Lindenbaum M, Perkins E, Csonka E, et al. A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy. Nucl. Acids Res. %R 10.1093/nar/gnh169. December 7, 2004 2004;32(21):e172-."]
[28,"y","y","Malyarchuk S, Brame KL, Youngblood R, Shi R, Harrison L. Two clustered 8-oxo-7,8-dihydroguanine (8-oxodG) lesions increase the point mutation frequency of 8-oxodG, but do not result in double strand breaks or deletions in Escherichia coli. Nucl. Acids Res. %R 10.1093/nar/gkh911. October 27, 2004 2004;32(19):5721-5731."]
[29,"y","y","Maniura-Weber K, Goffart S, Garstka HL, Montoya J, Wiesner RJ. Transient overexpression of mitochondrial transcription factor A (TFAM) is sufficient to stimulate mitochondrial DNA transcription, but not sufficient to increase mtDNA copy number in cultured cells. Nucl. Acids Res. %R 10.1093/nar/gkh921. November 16, 2004 2004;32(20):6015-6027."]
[30,"y","y","Mao Y, Luo C, Deng W, et al. Reversibly switchable DNA nanocompartment on surfaces. Nucl. Acids Res. %R 10.1093/nar/gnh145. October 26, 2004 2004;32(19):e144-."]
[31,"y","y","Matsubara M, Tanaka T, Terato H, et al. Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylase. Nucl. Acids Res. %R 10.1093/nar/gkh859. October 5, 2004 2004;32(17):5291-5302."]
[32,"y","y","May T, Hauser H, Wirth D. Transcriptional control of SV40 T-antigen expression allows a complete reversion of immortalization. Nucl. Acids Res. %R 10.1093/nar/gkh887. October 14, 2004 2004;32(18):5529-5538."]
[33,"y","y","Navarro A-E, Spinelli N, Moustrou C, Chaix C, Mandrand B, Brisset H. Automated synthesis of new ferrocenyl-modified oligonucleotides: study of their properties in solution. Nucl. Acids Res. %R 10.1093/nar/gkh874. October 5, 2004 2004;32(17):5310-5319."]
[34,"y","y","Ohtani N, Yanagawa H, Tomita M, Itaya M. Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. Nucl. Acids Res. %R 10.1093/nar/gkh917. November 1, 2004 2004;32(19):5809-5819."]
[35,"y","y","Otsuki K, Hayashi Y, Kato M, Yoshida H, Yamaguchi M. Characterization of dRFX2, a novel RFX family protein in Drosophila. Nucl. Acids Res. %R 10.1093/nar/gkh895. October 19, 2004 2004;32(18):5636-5648."]
[36,"y","y","Perez A, Noy A, Lankas F, Luque FJ, Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucl. Acids Res. %R 10.1093/nar/gkh954. November 23, 2004 2004;32(20):6144-6151."]
[37,"y","y","Pincas H, Pingle MR, Huang J, et al. High sensitivity EndoV mutation scanning through real-time ligase proofreading. Nucl. Acids Res. %R 10.1093/nar/gnh150. October 28, 2004 2004;32(19):e148-."]
[38,"y","y","Qin L-X, Kerr KF, Contributing Members of the Toxicogenomics Research C. Empirical evaluation of data transformations and ranking statistics for microarray analysis. Nucl. Acids Res. %R 10.1093/nar/gkh866. October 12, 2004 2004;32(18):5471-5479."]
[39,"y","y","Quere R, Manchon L, Lejeune M, et al. Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression. Nucl. Acids Res. %R 10.1093/nar/gnh161. November 23, 2004 2004;32(20):e163-."]
[40,"y","y","Ruepp A, Zollner A, Maier D, et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucl. Acids Res. %R 10.1093/nar/gkh894. October 14, 2004 2004;32(18):5539-5545."]
[41,"y","y","Rutledge RG. Sigmoidal curve-fitting redefines quantitative real-time PCR with the prospective of developing automated high-throughput applications. Nucl. Acids Res. %R 10.1093/nar/gnh177. December 15, 2004 2004;32(22):e178-."]
[42,"y","y","Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucl. Acids Res. %R 10.1093/nar/gkh951. November 23, 2004 2004;32(20):6129-6135."]
[43,"no -ref but not attached","n","Schatz P, Dietrich D, Schuster M. Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF. Nucl. Acids Res. %R 10.1093/nar/gnh165. December 2, 2004 2004;32(21):e167-."]
[44,"y","y","Schmidt KS, Borkowski S, Kurreck J, et al. Application of locked nucleic acids to improve aptamer in vivo stability and targeting function. Nucl. Acids Res. %R 10.1093/nar/gkh862. October 27, 2004 2004;32(19):5757-5765."]
[45,"y","y","Shen G, Anand MFG, Levicky R. X-ray photoelectron spectroscopy and infrared spectroscopy study of maleimide-activated supports for immobilization of oligodeoxyribonucleotides. Nucl. Acids Res. %R 10.1093/nar/gkh932. November 10, 2004 2004;32(20):5973-5980."]
[46,"y","y","Shukla LI, Adhikary A, Pazdro R, Becker D, Sevilla MD. Formation of 8-oxo-7,8-dihydroguanine-radicals in {gamma}-irradiated DNA by multiple one-electron oxidations. Nucl. Acids Res. %R 10.1093/nar/gkh989. December 15, 2004 2004;32(22):6565-6574."]
[47,"y","y","Sorensen JJ, Nielsen JT, Petersen M. Solution structure of a dsDNA:LNA triplex. Nucl. Acids Res. %R 10.1093/nar/gkh942. November 18, 2004 2004;32(20):6078-6085."]
[48,"y","y","Sun Y, Koo S, White N, et al. Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucl. Acids Res. %R 10.1093/nar/gnh186. December 22, 2004 2004;32(22):e188-."]
[49,"y","y","Takami H, Takaki Y, Chee G-J, et al. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucl. Acids Res. %R 10.1093/nar/gkh970. December 1, 2004 2004;32(21):6292-6303."]
[50,"y","y","Tang S, Tan SL, Ramadoss SK, Kumar AP, Tang M-HE, Bajic VB. Computational method for discovery of estrogen responsive genes. Nucl. Acids Res. %R 10.1093/nar/gkh943. December 1, 2004 2004;32(21):6212-6217."]
[51,"y","y","Thomas H, Senkel S, Erdmann S, et al. Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4{alpha} and HNF1{beta} in a pancreatic {beta}-cell line. Nucl. Acids Res. %R 10.1093/nar/gnh144. November 1, 2004 2004;32(19):e150-."]
[52,"y","y","Tian W, Arakaki AK, Skolnick J. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucl. Acids Res. %R 10.1093/nar/gkh956. December 1, 2004 2004;32(21):6226-6239."]
[53,"y","y","Ting R, Thomas JM, Lermer L, Perrin DM. Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: a putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation. Nucl. Acids Res. %R 10.1093/nar/gkh1007. December 29, 2004 2004;32(22):6660-6672."]
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[2,"y","y","Laurie CC, Chasalow SD, LeDeaux JR, et al. The Genetic Architecture of Response to Long-Term Artificial Selection for Oil Concentration in the Maize Kernel. Genetics %R 10.1534/genetics.104.029686. December 1, 2004 2004;168(4):2141-2155."]
[3,"y","y","Dettman JR, Taylor JW. Mutation and Evolution of Microsatellite Loci in Neurospora. Genetics %R 10.1534/genetics.104.029322. November 1, 2004 2004;168(3):1231-1248."]
[4,"y","y","Kato M, Takashima K, Kakutani T. Epigenetic Control of CACTA Transposon Mobility in Arabidopsis thaliana. Genetics %R 10.1534/genetics.104.029637. October 1, 2004 2004;168(2):961-969."]
[5,"y","n","Munkvold JD, Greene RA, Bermudez-Kandianis CE, et al. Group 3 Chromosome Bin Maps of Wheat and Their Relationship to Rice Chromosome 1. Genetics %R 10.1534/genetics.104.034819. October 1, 2004 2004;168(2):639-650."]
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[7,"n","y","Sandhu D, Gao H, Cianzio S, Bhattacharyya MK. Deletion of a Disease Resistance Nucleotide-Binding-Site Leucine-Rich- Repeat-like Sequence Is Associated With the Loss of the Phytophthora Resistance Gene Rps4 in Soybean. Genetics %R 10.1534/genetics.104.032037. December 1, 2004 2004;168(4):2157-2167."]
[8,"y","n","Peng JH, Zadeh H, Lazo GR, et al. Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis. Genetics %R 10.1534/genetics.104.034793. October 1, 2004 2004;168(2):609-623."]
[9,"n","y","Kiehart DP, Franke JD, Chee MK, et al. Drosophila crinkled, Mutations of Which Disrupt Morphogenesis and Cause Lethality, Encodes Fly Myosin VIIA. Genetics %R 10.1534/genetics.104.026369. November 1, 2004 2004;168(3):1337-1352."]
[10,"n","y","Nikoh N, Duty A, Gibson G. Effects of Population Structure and Sex on Association Between Serotonin Receptors and Drosophila Heart Rate. Genetics %R 10.1534/genetics.104.028712. December 1, 2004 2004;168(4):1963-1974."]
[11,"y","y","Swanson WJ, Wong A, Wolfner MF, Aquadro CF. Evolutionary Expressed Sequence Tag Analysis of Drosophila Female Reproductive Tracts Identifies Genes Subjected to Positive Selection. Genetics %R 10.1534/genetics.104.030478. November 1, 2004 2004;168(3):1457-1465."]
[12,"y","y","Concepcion D, Seburn KL, Wen G, Frankel WN, Hamilton BA. Mutation Rate and Predicted Phenotypic Target Sizes in Ethylnitrosourea-Treated Mice. Genetics %R 10.1534/genetics.104.029843. October 1, 2004 2004;168(2):953-959."]
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[15,"n","y","Adams KL, Percifield R, Wendel JF. Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid. Genetics %R 10.1534/genetics.104.033522. December 1, 2004 2004;168(4):2217-2226."]
[16,"n","y","Chardon F, Virlon B, Moreau L, et al. Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome. Genetics %R 10.1534/genetics.104.032375. December 1, 2004 2004;168(4):2169-2185."]
[17,"y","y","Caetano AR, Johnson RK, Ford JJ, Pomp D. Microarray Profiling for Differential Gene Expression in Ovaries and Ovarian Follicles of Pigs Selected for Increased Ovulation Rate. Genetics %R 10.1534/genetics.104.029595. November 1, 2004 2004;168(3):1529-1537."]
[18,"y","n","Linkiewicz AM, Qi LL, Gill BS, et al. A 2500-Locus Bin Map of Wheat Homoeologous Group 5 Provides Insights on Gene Distribution and Colinearity With Rice. Genetics %R 10.1534/genetics.104.034835. October 1, 2004 2004;168(2):665-676."]
[19,"n","y","Dvorak J, Yang Z-L, You FM, Luo M-C. Deletion Polymorphism in Wheat Chromosome Regions With Contrasting Recombination Rates. Genetics %R 10.1534/genetics.103.024927. November 1, 2004 2004;168(3):1665-1675."]
[20,"n","y","Cinar HN, Chisholm AD. Genetic Analysis of the Caenorhabditis elegans pax-6 Locus: Roles of Paired Domain-Containing and Nonpaired Domain-Containing Isoforms. Genetics %R 10.1534/genetics.104.031724. November 1, 2004 2004;168(3):1307-1322."]
[21,"n","y","Robertson HM. Genes Encoding Vitamin-K Epoxide Reductase Are Present in Drosophila and Trypanosomatid Protists. Genetics %R 10.1534/genetics.104.029744. October 1, 2004 2004;168(2):1077-1080."]
[22,"y","y","Das A, Mohanty S, Stephan W. Inferring the Population Structure and Demography of Drosophila ananassae From Multilocus Data. Genetics %R 10.1534/genetics.104.031567. December 1, 2004 2004;168(4):1975-1985."]
[23,"y","y","Pratt RJ, Lee DW, Aramayo R. DNA Methylation Affects Meiotic trans-sensing, Not Meiotic Silencing, in Neurospora. Genetics %R 10.1534/genetics.104.031526. December 1, 2004 2004;168(4):1925-1935."]
[24,"y","y","Brisson JA, Templeton AR, Duncan I. Population Genetics of the Developmental Gene optomotor-blind (omb) in Drosophila polymorpha: Evidence for a Role in Abdominal Pigmentation Variation. Genetics %R 10.1534/genetics.104.032078. December 1, 2004 2004;168(4):1999-2010."]
[25,"n","y","Anderson JB, Sirjusingh C, Ricker N. Haploidy, Diploidy and Evolution of Antifungal Drug Resistance in Saccharomyces cerevisiae. Genetics %R 10.1534/genetics.104.033266. December 1, 2004 2004;168(4):1915-1923."]
[26,"y","y","Crepieux S, Lebreton C, Servin B, Charmet G. Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs: Recovering QTL Identical-by-Descent Status Information From Marker Data. Genetics %R 10.1534/genetics.104.028993. November 1, 2004 2004;168(3):1737-1749."]
[27,"n","y","Stuurman J, Hoballah ME, Broger L, Moore J, Basten C, Kuhlemeier C. Dissection of Floral Pollination Syndromes in Petunia. Genetics %R 10.1534/genetics.104.031138. November 1, 2004 2004;168(3):1585-1599."]
[28,"y","y","Wayne ML, Pan YJ, Nuzhdin SV, McIntyre LM. Additivity and trans-acting Effects on Gene Expression in Male Drosophila simulans. Genetics %R 10.1534/genetics.104.030973. November 1, 2004 2004;168(3):1413-1420."]
[29,"y","y","Wright SI, Charlesworth B. The HKA Test Revisited: A Maximum-Likelihood-Ratio Test of the Standard Neutral Model. Genetics %R 10.1534/genetics.104.026500. October 1, 2004 2004;168(2):1071-1076."]
[30,"y","n","Miftahudin, Ross K, Ma XF, et al. Analysis of Expressed Sequence Tag Loci on Wheat Chromosome Group 4. Genetics %R 10.1534/genetics.104.034827. October 1, 2004 2004;168(2):651-663."]

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