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ProbCD: enrichment analysis accounting for categorization uncertainty.
Vêncio RZ, Shmulevich I.
BMC Bioinformatics. 2007 Oct 12;8:383.PMID: 17935624 [PubMed - indexed for MEDLINE]Related articlesFree article
Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context.
Weniger M, Engelmann JC, Schultz J.
BMC Bioinformatics. 2007 Jun 2;8:179.PMID: 17543125 [PubMed - indexed for MEDLINE]Related articlesFree article
FERN - a Java framework for stochastic simulation and evaluation of reaction networks.
Erhard F, Friedel CC, Zimmer R.
BMC Bioinformatics. 2008 Aug 29;9:356.PMID: 18755046 [PubMed - indexed for MEDLINE]Related articlesFree article
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology.
Chalmel F, Primig M.
BMC Bioinformatics. 2008 Feb 6;9:86.PMID: 18254954 [PubMed - indexed for MEDLINE]Related articlesFree article
GAGE: generally applicable gene set enrichment for pathway analysis.
Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ.
BMC Bioinformatics. 2009 May 27;10:161.PMID: 19473525 [PubMed - indexed for MEDLINE]Related articlesFree article
FACT--a framework for the functional interpretation of high-throughput experiments.
Kokocinski F, Delhomme N, Wrobel G, Hummerich L, Toedt G, Lichter P.
BMC Bioinformatics. 2005 Jun 28;6:161.PMID: 15985174 [PubMed - indexed for MEDLINE]Related articlesFree article
Pomelo II: finding differentially expressed genes.
Morrissey ER, Diaz-Uriarte R.
Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W581-6. Epub 2009 May 12.PMID: 19435879 [PubMed - indexed for MEDLINE]Related articlesFree article
Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes.
Brock GN, Shaffer JR, Blakesley RE, Lotz MJ, Tseng GC.
BMC Bioinformatics. 2008 Jan 10;9:12.PMID: 18186917 [PubMed - indexed for MEDLINE]Related articlesFree article
From genes to functional classes in the study of biological systems.
Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Mínguez P, Montaner D, Dopazo J.
BMC Bioinformatics. 2007 Apr 3;8:114.PMID: 17407596 [PubMed - indexed for MEDLINE]Related articlesFree article
M-BISON: microarray-based integration of data sources using networks.
Daigle BJ Jr, Altman RB.
BMC Bioinformatics. 2008 Apr 25;9:214.PMID: 18439292 [PubMed - indexed for MEDLINE]Related articlesFree article
InterferenceAnalyzer: tools for the analysis and simulation of multi-locus genetic data.
Viswanath L, Housworth EA.
BMC Bioinformatics. 2005 Dec 12;6:297.PMID: 16343334 [PubMed - indexed for MEDLINE]Related articlesFree article
Biological profiling of gene groups utilizing Gene Ontology.
Blüthgen N, Brand K, Cajavec B, Swat M, Herzel H, Beule D.
Genome Inform. 2005;16(1):106-15.PMID: 16362912 [PubMed - indexed for MEDLINE]Related articles
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.
Huan T, Sivachenko AY, Harrison SH, Chen JY.
BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5.PMID: 18793469 [PubMed - indexed for MEDLINE]Related articlesFree article
Extending pathways based on gene lists using InterPro domain signatures.
Hahne F, Mehrle A, Arlt D, Poustka A, Wiemann S, Beissbarth T.
BMC Bioinformatics. 2008 Jan 4;9:3.PMID: 18177498 [PubMed - indexed for MEDLINE]Related articlesFree article
Simcluster: clustering enumeration gene expression data on the simplex space.
Vêncio RZ, Varuzza L, de B Pereira CA, Brentani H, Shmulevich I.
BMC Bioinformatics. 2007 Jul 11;8:246.PMID: 17625017 [PubMed - indexed for MEDLINE]Related articlesFree article
BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.
Turro E, Bochkina N, Hein AM, Richardson S.
BMC Bioinformatics. 2007 Nov 12;8:439.PMID: 17997843 [PubMed - indexed for MEDLINE]Related articlesFree article
Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells.
Selivanov VA, Meshalkina LE, Solovjeva ON, Kuchel PW, Ramos-Montoya A, Kochetov GA, Lee PW, Cascante M.
Bioinformatics. 2005 Sep 1;21(17):3558-64. Epub 2005 Jul 7.PMID: 16002431 [PubMed - indexed for MEDLINE]Related articlesFree article
Extracting falsifiable predictions from sloppy models.
Gutenkunst RN, Casey FP, Waterfall JJ, Myers CR, Sethna JP.
Ann N Y Acad Sci. 2007 Dec;1115:203-11. Epub 2007 Oct 9.PMID: 17925353 [PubMed - indexed for MEDLINE]Related articles
Onto-CC: a web server for identifying Gene Ontology conceptual clusters.
Romero-Zaliz R, Del Val C, Cobb JP, Zwir I.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W352-7. Epub 2008 Jun 10.PMID: 18544607 [PubMed - indexed for MEDLINE]Related articlesFree article
Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.
Kuhn A, Luthi-Carter R, Delorenzi M.
BMC Bioinformatics. 2008 Jan 17;9:26.PMID: 18201381 [PubMed - indexed for MEDLINE]Related articlesFree article
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