PubMed

A flexible representation of omic knowledge for thorough analysis of microarray data.

Hasegawa Y, Seki M, Mochizuki Y, Heida N, Hirosawa K, Okamoto N, Sakurai T, Satou M, Akiyama K, Iida K, Lee K, Kanaya S, Demura T, Shinozaki K, Konagaya A, Toyoda T.

Plant Methods. 2006 Mar 2;2:5.PMID: 16509996 [PubMed - in process]Related articlesFree article

Omic space: coordinate-based integration and analysis of genomic phenomic interactions.

Toyoda T, Wada A.

Bioinformatics. 2004 Jul 22;20(11):1759-65. Epub 2004 Mar 22.PMID: 15037505 [PubMed - indexed for MEDLINE]Related articlesFree article

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

BMC Bioinformatics. 2007 Apr 19;8:129.PMID: 17445272 [PubMed - indexed for MEDLINE]Related articlesFree article

PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments.

Usadel B, Nagel A, Steinhauser D, Gibon Y, Bläsing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M.

BMC Bioinformatics. 2006 Dec 18;7:535.PMID: 17176458 [PubMed - indexed for MEDLINE]Related articlesFree article

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

Feng C, Araki M, Kunimoto R, Tamon A, Makiguchi H, Niijima S, Tsujimoto G, Okuno Y.

BMC Genomics. 2009 Sep 3;10:411.PMID: 19728865 [PubMed - indexed for MEDLINE]Related articlesFree article

A genome-wide 20 K citrus microarray for gene expression analysis.

Martinez-Godoy MA, Mauri N, Juarez J, Marques MC, Santiago J, Forment J, Gadea J.

BMC Genomics. 2008 Jul 3;9:318.PMID: 18598343 [PubMed - indexed for MEDLINE]Related articlesFree article

M@IA: a modular open-source application for microarray workflow and integrative datamining.

Le Béchec A, Zindy P, Sierocinski T, Petritis D, Bihouée A, Le Meur N, Léger J, Théret N.

In Silico Biol. 2008;8(1):63-9.PMID: 18430991 [PubMed - indexed for MEDLINE]Related articles

Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis.

Fernandez P, Di Rienzo J, Fernandez L, Hopp HE, Paniego N, Heinz RA.

BMC Plant Biol. 2008 Jan 26;8:11.PMID: 18221554 [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

EzArray: a web-based highly automated Affymetrix expression array data management and analysis system.

Zhu Y, Zhu Y, Xu W.

BMC Bioinformatics. 2008 Jan 24;9:46.PMID: 18218103 [PubMed - indexed for MEDLINE]Related articlesFree article

DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data.

Glez-Peña D, Alvarez R, Díaz F, Fdez-Riverola F.

BMC Bioinformatics. 2009 Jan 29;10:37.PMID: 19178723 [PubMed - indexed for MEDLINE]Related articlesFree article

MaXlab: a novel application for the cross comparison and integration of biological signatures from microarray studies.

Khalid S, Khan M, Gorle CB, Fraser K, Wang P, Liu X, Li S.

In Silico Biol. 2008;8(3-4):363-76.PMID: 19032168 [PubMed - indexed for MEDLINE]Related articles

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

Li P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, Owen S, Withers D, Oinn T, Pocock MR, Goble CA, Oliver SG, Kell DB.

BMC Bioinformatics. 2008 Aug 7;9:334.PMID: 18687127 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer.

Giancarlo R, Scaturro D, Utro F.

BMC Bioinformatics. 2008 Oct 29;9:462.PMID: 18959783 [PubMed - indexed for MEDLINE]Related articlesFree article

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.

Yi M, Mudunuri U, Che A, Stephens RM.

BMC Bioinformatics. 2009 Jun 29;10:200.PMID: 19563622 [PubMed - indexed for MEDLINE]Related articlesFree article

Independent component analysis of Alzheimer's DNA microarray gene expression data.

Kong W, Mou X, Liu Q, Chen Z, Vanderburg CR, Rogers JT, Huang X.

Mol Neurodegener. 2009 Jan 28;4(1):5.PMID: 19173745 [PubMed - as supplied by publisher]Related articlesFree article

Biclustering of microarray data with MOSPO based on crowding distance.

Liu J, Li Z, Hu X, Chen Y.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S9.PMID: 19426457 [PubMed - indexed for MEDLINE]Related articlesFree article

Mining gene expression data by interpreting principal components.

Roden JC, King BW, Trout D, Mortazavi A, Wold BJ, Hart CE.

BMC Bioinformatics. 2006 Apr 7;7:194.PMID: 16600052 [PubMed - indexed for MEDLINE]Related articlesFree article

Knowledge-guided multi-scale independent component analysis for biomarker identification.

Chen L, Xuan J, Wang C, Shih IeM, Wang Y, Zhang Z, Hoffman E, Clarke R.

BMC Bioinformatics. 2008 Oct 6;9:416.PMID: 18837990 [PubMed - indexed for MEDLINE]Related articlesFree article

Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics.

Phan JH, Quo CF, Wang MD.

Prog Brain Res. 2006;158:83-108. Review.PMID: 17027692 [PubMed - indexed for MEDLINE]Related articles