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Results: 1 to 20 of 44

1.

Physical Module Networks: an integrative approach for reconstructing transcription regulation.

Novershtern N, Regev A, Friedman N.

Bioinformatics. 2011 Jul 1;27(13):i177-85. doi: 10.1093/bioinformatics/btr222.

PMID:
21685068
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Discovering biological progression underlying microarray samples.

Qiu P, Gentles AJ, Plevritis SK.

PLoS Comput Biol. 2011 Apr;7(4):e1001123. doi: 10.1371/journal.pcbi.1001123. Epub 2011 Apr 14.

PMID:
21533210
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization.

Kao KJ, Chang KM, Hsu HC, Huang AT.

BMC Cancer. 2011 Apr 18;11:143. doi: 10.1186/1471-2407-11-143.

PMID:
21501481
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Large-scale learning of combinatorial transcriptional dynamics from gene expression.

Asif HM, Sanguinetti G.

Bioinformatics. 2011 May 1;27(9):1277-83. doi: 10.1093/bioinformatics/btr113. Epub 2011 Mar 2.

PMID:
21367870
[PubMed - indexed for MEDLINE]
Free Article
5.

Drug-induced regulation of target expression.

Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000925. doi: 10.1371/journal.pcbi.1000925.

PMID:
20838579
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.

Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A.

Bioinformatics. 2010 Oct 1;26(19):2438-44. doi: 10.1093/bioinformatics/btq466. Epub 2010 Aug 13.

PMID:
20709693
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The Gene Ontology in 2010: extensions and refinements.

Gene Ontology Consortium.

Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. Epub 2009 Nov 17.

PMID:
19920128
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.

Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D105-10. doi: 10.1093/nar/gkp950. Epub 2009 Nov 11.

PMID:
19906716
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

GATE: software for the analysis and visualization of high-dimensional time series expression data.

MacArthur BD, Lachmann A, Lemischka IR, Ma'ayan A.

Bioinformatics. 2010 Jan 1;26(1):143-4. doi: 10.1093/bioinformatics/btp628. Epub 2009 Nov 5.

PMID:
19892805
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

KEGG for representation and analysis of molecular networks involving diseases and drugs.

Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M.

Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60. doi: 10.1093/nar/gkp896. Epub 2009 Oct 30.

PMID:
19880382
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

PMID:
19261174
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

KEA: kinase enrichment analysis.

Lachmann A, Ma'ayan A.

Bioinformatics. 2009 Mar 1;25(5):684-6. doi: 10.1093/bioinformatics/btp026. Epub 2009 Jan 28.

PMID:
19176546
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks.

Ma'ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R.

BMC Syst Biol. 2009 Jan 20;3:10. doi: 10.1186/1752-0509-3-10.

PMID:
19154595
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Defining developmental potency and cell lineage trajectories by expression profiling of differentiating mouse embryonic stem cells.

Aiba K, Nedorezov T, Piao Y, Nishiyama A, Matoba R, Sharova LV, Sharov AA, Yamanaka S, Niwa H, Ko MS.

DNA Res. 2009 Feb;16(1):73-80. doi: 10.1093/dnares/dsn035. Epub 2008 Dec 26.

PMID:
19112179
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

RNA-Seq: a revolutionary tool for transcriptomics.

Wang Z, Gerstein M, Snyder M.

Nat Rev Genet. 2009 Jan;10(1):57-63. doi: 10.1038/nrg2484. Review.

PMID:
19015660
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Human Protein Reference Database--2009 update.

Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72. doi: 10.1093/nar/gkn892. Epub 2008 Nov 6.

PMID:
18988627
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Model-based analysis of ChIP-Seq (MACS).

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS.

Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17.

PMID:
18798982
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A ribosomal S-6 kinase-mediated signal to C/EBP-beta is critical for the development of liver fibrosis.

Buck M, Chojkier M.

PLoS One. 2007 Dec 26;2(12):e1372.

PMID:
18159255
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

DrugBank: a knowledgebase for drugs, drug actions and drug targets.

Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D901-6. Epub 2007 Nov 29.

PMID:
18048412
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Novel homeodomain-interacting protein kinase family member, HIPK4, phosphorylates human p53 at serine 9.

Arai S, Matsushita A, Du K, Yagi K, Okazaki Y, Kurokawa R.

FEBS Lett. 2007 Dec 11;581(29):5649-57. Epub 2007 Nov 20.

PMID:
18022393
[PubMed - indexed for MEDLINE]
Free Article

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