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Items: 1 to 20 of 29

1.

geWorkbench: an open source platform for integrative genomics.

Floratos A, Smith K, Ji Z, Watkinson J, Califano A.

Bioinformatics. 2010 Jul 15;26(14):1779-80. doi: 10.1093/bioinformatics/btq282. Epub 2010 May 28.

2.

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.

Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W210-3. doi: 10.1093/nar/gkq388. Epub 2010 May 16.

3.

Gene expression-based classification of non-small cell lung carcinomas and survival prediction.

Hou J, Aerts J, den Hamer B, van Ijcken W, den Bakker M, Riegman P, van der Leest C, van der Spek P, Foekens JA, Hoogsteden HC, Grosveld F, Philipsen S.

PLoS One. 2010 Apr 22;5(4):e10312. doi: 10.1371/journal.pone.0010312.

4.

Whole genome analysis of p38 SAPK-mediated gene expression upon stress.

Ferreiro I, Joaquin M, Islam A, Gomez-Lopez G, Barragan M, Lombardía L, Domínguez O, Pisano DG, Lopez-Bigas N, Nebreda AR, Posas F.

BMC Genomics. 2010 Mar 1;11:144. doi: 10.1186/1471-2164-11-144.

5.

IntOGen: integration and data mining of multidimensional oncogenomic data.

Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N.

Nat Methods. 2010 Feb;7(2):92-3. doi: 10.1038/nmeth0210-92. No abstract available.

PMID:
20111033
6.

ConceptGen: a gene set enrichment and gene set relation mapping tool.

Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, Kuick R, Jagadish HV, Mirel B, Weymouth T, Athey B, Omenn GS.

Bioinformatics. 2010 Feb 15;26(4):456-63. doi: 10.1093/bioinformatics/btp683. Epub 2009 Dec 9.

7.

An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.).

Mascarell-Creus A, Cañizares J, Vilarrasa-Blasi J, Mora-García S, Blanca J, Gonzalez-Ibeas D, Saladié M, Roig C, Deleu W, Picó-Silvent B, López-Bigas N, Aranda MA, Garcia-Mas J, Nuez F, Puigdomènech P, Caño-Delgado AI.

BMC Genomics. 2009 Oct 12;10:467. doi: 10.1186/1471-2164-10-467.

8.

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization.

Chen J, Bardes EE, Aronow BJ, Jegga AG.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W305-11. doi: 10.1093/nar/gkp427. Epub 2009 May 22.

9.

Jagged1 is the pathological link between Wnt and Notch pathways in colorectal cancer.

Rodilla V, Villanueva A, Obrador-Hevia A, Robert-Moreno A, Fernández-Majada V, Grilli A, López-Bigas N, Bellora N, Albà MM, Torres F, Duñach M, Sanjuan X, Gonzalez S, Gridley T, Capella G, Bigas A, Espinosa L.

Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6315-20. doi: 10.1073/pnas.0813221106. Epub 2009 Mar 26.

10.

BioMart--biological queries made easy.

Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A.

BMC Genomics. 2009 Jan 14;10:22. doi: 10.1186/1471-2164-10-22.

11.

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Huang da W, Sherman BT, Lempicki RA.

Nucleic Acids Res. 2009 Jan;37(1):1-13. doi: 10.1093/nar/gkn923. Epub 2008 Nov 25.

12.

Ensembl 2009.

Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P.

Nucleic Acids Res. 2009 Jan;37(Database issue):D690-7. doi: 10.1093/nar/gkn828. Epub 2008 Nov 25.

13.

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

Lopez-Bigas N, Kisiel TA, Dewaal DC, Holmes KB, Volkert TL, Gupta S, Love J, Murray HL, Young RA, Benevolenskaya EV.

Mol Cell. 2008 Aug 22;31(4):520-30. doi: 10.1016/j.molcel.2008.08.004.

14.

Functional protein divergence in the evolution of Homo sapiens.

Lopez-Bigas N, De S, Teichmann SA.

Genome Biol. 2008;9(2):R33. doi: 10.1186/gb-2008-9-2-r33. Epub 2008 Feb 15.

15.

DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.

Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W169-75. Epub 2007 Jun 18.

16.

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.

17.

GenePattern 2.0.

Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP.

Nat Genet. 2006 May;38(5):500-1. No abstract available.

PMID:
16642009
18.

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP.

Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. Epub 2005 Sep 30.

19.

EXPANDER--an integrative program suite for microarray data analysis.

Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R.

BMC Bioinformatics. 2005 Sep 21;6:232.

20.

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