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Items: 1 to 20 of 97

1.

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.

2.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6.

3.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W91-6. Epub 2007 May 3.

4.

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.

Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W460-4.

5.

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).

Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN.

BMC Bioinformatics. 2005 Jul 5;6:168.

6.

A function-centric approach to the biological interpretation of microarray time-series.

Minguez P, Al-Shahrour F, Dopazo J.

Genome Inform. 2006;17(2):57-66.

PMID:
17503379
7.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W341-6. doi: 10.1093/nar/gkn318. Epub 2008 May 31.

8.

GlobalANCOVA: exploration and assessment of gene group effects.

Hummel M, Meister R, Mansmann U.

Bioinformatics. 2008 Jan 1;24(1):78-85. Epub 2007 Nov 17.

PMID:
18024976
9.

DEEP--a tool for differential expression effector prediction.

Degenhardt J, Haubrock M, Dönitz J, Wingender E, Crass T.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W619-24. Epub 2007 Jun 21.

10.

Array2BIO: from microarray expression data to functional annotation of co-regulated genes.

Loots GG, Chain PS, Mabery S, Rasley A, Garcia E, Ovcharenko I.

BMC Bioinformatics. 2006 Jun 16;7:307.

11.

MMG: a probabilistic tool to identify submodules of metabolic pathways.

Sanguinetti G, Noirel J, Wright PC.

Bioinformatics. 2008 Apr 15;24(8):1078-84. doi: 10.1093/bioinformatics/btn066. Epub 2008 Feb 21.

PMID:
18292114
12.

Significance analysis of groups of genes in expression profiling studies.

Chen JJ, Lee T, Delongchamp RR, Chen T, Tsai CA.

Bioinformatics. 2007 Aug 15;23(16):2104-12. Epub 2007 Jun 6.

PMID:
17553853
13.

Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles.

Edelman E, Porrello A, Guinney J, Balakumaran B, Bild A, Febbo PG, Mukherjee S.

Bioinformatics. 2006 Jul 15;22(14):e108-16.

PMID:
16873460
14.

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. doi: 10.1186/1471-2105-9-86.

15.

Reconstructing networks of pathways via significance analysis of their intersections.

Francesconi M, Remondini D, Neretti N, Sedivy JM, Cooper LN, Verondini E, Milanesi L, Castellani G.

BMC Bioinformatics. 2008 Apr 25;9 Suppl 4:S9. doi: 10.1186/1471-2105-9-S4-S9.

16.

MADIBA: a web server toolkit for biological interpretation of Plasmodium and plant gene clusters.

Law PJ, Claudel-Renard C, Joubert F, Louw AI, Berger DK.

BMC Genomics. 2008 Feb 28;9:105. doi: 10.1186/1471-2164-9-105.

17.

Detecting biological associations between genes based on the theory of phase synchronization.

Kim CS, Riikonen P, Salakoski T.

Biosystems. 2008 May;92(2):99-113. doi: 10.1016/j.biosystems.2007.12.006. Epub 2008 Jan 11.

PMID:
18289772
18.

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.

Maere S, Heymans K, Kuiper M.

Bioinformatics. 2005 Aug 15;21(16):3448-9. Epub 2005 Jun 21.

PMID:
15972284
19.

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Bioinformatics. 2008 Apr 21;9:203. doi: 10.1186/1471-2105-9-203.

20.

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