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Results: 1 to 20 of 88

1.

Identifying biological themes within lists of genes with EASE.

Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA.

Genome Biol. 2003;4(10):R70. Epub 2003 Sep 11.

PMID:
14519205
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Extracting biological meaning from large gene lists with DAVID.

Huang da W, Sherman BT, Zheng X, Yang J, Imamichi T, Stephens R, Lempicki RA.

Curr Protoc Bioinformatics. 2009 Sep;Chapter 13:Unit 13.11. doi: 10.1002/0471250953.bi1311s27.

PMID:
19728287
[PubMed - indexed for MEDLINE]
3.

MILANO--custom annotation of microarray results using automatic literature searches.

Rubinstein R, Simon I.

BMC Bioinformatics. 2005 Jan 20;6:12.

PMID:
15661078
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

Huang da W, Sherman BT, Lempicki RA.

Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.

PMID:
19131956
[PubMed - indexed for MEDLINE]
5.

Development of gene ontology tool for biological interpretation of genomic and proteomic data.

Feng W, Wang G, Zeeberg BR, Guo K, Fojo AT, Kane DW, Reinhold WC, Lababidi S, Weinstein JN, Wang MD.

AMIA Annu Symp Proc. 2003:839.

PMID:
14728344
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

PubMatrix: a tool for multiplex literature mining.

Becker KG, Hosack DA, Dennis G Jr, Lempicki RA, Bright TJ, Cheadle C, Engel J.

BMC Bioinformatics. 2003 Dec 10;4:61.

PMID:
14667255
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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. doi: 10.1186/1471-2105-10-200.

PMID:
19563622
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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

Huang da W, 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.

PMID:
17576678
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Lists2Networks: integrated analysis of gene/protein lists.

Lachmann A, Ma'ayan A.

BMC Bioinformatics. 2010 Feb 12;11:87. doi: 10.1186/1471-2105-11-87.

PMID:
20152038
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

Huang da W, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Genome Biol. 2007;8(9):R183.

PMID:
17784955
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists.

Cahan P, Ahmad AM, Burke H, Fu S, Lai Y, Florea L, Dharker N, Kobrinski T, Kale P, McCaffrey TA.

Gene. 2005 Oct 24;360(1):78-82. Epub 2005 Sep 2. Review.

PMID:
16140476
[PubMed - indexed for MEDLINE]
12.

GoMiner: a resource for biological interpretation of genomic and proteomic data.

Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN.

Genome Biol. 2003;4(4):R28. Epub 2003 Mar 25.

PMID:
12702209
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

GeneBrowser 2: an application to explore and identify common biological traits in a set of genes.

Arrais JP, Fernandes J, Pereira J, Oliveira JL.

BMC Bioinformatics. 2010 Jul 21;11:389. doi: 10.1186/1471-2105-11-389.

PMID:
20663121
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A systematic approach to infer biological relevance and biases of gene network structures.

Antonov AV, Tetko IV, Mewes HW.

Nucleic Acids Res. 2006 Jan 10;34(1):e6.

PMID:
16407322
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

GeneTrail--advanced gene set enrichment analysis.

Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Müller R, Meese E, Lenhof HP.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W186-92. Epub 2007 May 25.

PMID:
17526521
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Theme discovery from gene lists for identification and viewing of multiple functional groups.

Pehkonen P, Wong G, Törönen P.

BMC Bioinformatics. 2005 Jun 29;6:162.

PMID:
15987504
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology data.

Trivedi P, Edwards JW, Wang J, Gadbury GL, Srinivasasainagendra V, Zakharkin SO, Kim K, Mehta T, Brand JP, Patki A, Page GP, Allison DB.

BMC Bioinformatics. 2005 Apr 6;6:86.

PMID:
15813968
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Gene function analysis in complex data sets using ErmineJ.

Gillis J, Mistry M, Pavlidis P.

Nat Protoc. 2010 Jun;5(6):1148-59. doi: 10.1038/nprot.2010.78. Epub 2010 Jun 3.

PMID:
20539290
[PubMed - indexed for MEDLINE]
19.

GOAL: a software tool for assessing biological significance of genes groups.

Tchagang AB, Gawronski A, Bérubé H, Phan S, Famili F, Pan Y.

BMC Bioinformatics. 2010 May 6;11:229. doi: 10.1186/1471-2105-11-229.

PMID:
20459620
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB.

Chatziioannou A, Moulos P, Kolisis FN.

BMC Bioinformatics. 2009 Oct 27;10:354. doi: 10.1186/1471-2105-10-354.

PMID:
19860866
[PubMed - indexed for MEDLINE]
Free PMC Article

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