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Items: 1 to 20 of 124

1.

An integrative modular approach to systematically predict gene-phenotype associations.

Mehan MR, Nunez-Iglesias J, Dai C, Waterman MS, Zhou XJ.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S62. doi: 10.1186/1471-2105-11-S1-S62.

2.

Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E.

Gene. 2013 Dec 1;531(2):212-9. doi: 10.1016/j.gene.2013.09.011. Epub 2013 Sep 13.

PMID:
24042128
3.

Genome-wide prediction and analysis of function-specific transcription factor binding sites.

Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A.

In Silico Biol. 2004;4(4):395-410.

PMID:
15506990
4.

Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles.

Prieto C, RisueƱo A, Fontanillo C, De las Rivas J.

PLoS One. 2008;3(12):e3911. doi: 10.1371/journal.pone.0003911. Epub 2008 Dec 15.

5.

A graph-based approach to systematically reconstruct human transcriptional regulatory modules.

Yan X, Mehan MR, Huang Y, Waterman MS, Yu PS, Zhou XJ.

Bioinformatics. 2007 Jul 1;23(13):i577-86.

PMID:
17646346
6.

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53.

Wang J, Tian T.

BMC Bioinformatics. 2010 Jan 19;11:36. doi: 10.1186/1471-2105-11-36.

7.
8.

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.

Qian J, Lin J, Luscombe NM, Yu H, Gerstein M.

Bioinformatics. 2003 Oct 12;19(15):1917-26.

PMID:
14555624
9.

Gene expression analysis in clear cell renal cell carcinoma using gene set enrichment analysis for biostatistical management.

Maruschke M, Reuter D, Koczan D, Hakenberg OW, Thiesen HJ.

BJU Int. 2011 Jul;108(2 Pt 2):E29-35. doi: 10.1111/j.1464-410X.2010.09794.x. Epub 2011 Mar 16.

10.

Global screening of potential Candida albicans biofilm-related transcription factors via network comparison.

Wang YC, Lan CY, Hsieh WP, Murillo LA, Agabian N, Chen BS.

BMC Bioinformatics. 2010 Jan 26;11:53. doi: 10.1186/1471-2105-11-53.

11.

From phenotype to gene: detecting disease-specific gene functional modules via a text-based human disease phenotype network construction.

Zhang S, Wu C, Li X, Chen X, Jiang W, Gong BS, Li J, Yan YQ.

FEBS Lett. 2010 Aug 20;584(16):3635-43. doi: 10.1016/j.febslet.2010.07.038. Epub 2010 Jul 24. Erratum in: FEBS Lett. 2013 Feb 14;587(4)386. Zhang, Shi-Hua [corrected to Zhang, Shihua].

12.

Detecting disease associated modules and prioritizing active genes based on high throughput data.

Qiu YQ, Zhang S, Zhang XS, Chen L.

BMC Bioinformatics. 2010 Jan 13;11:26. doi: 10.1186/1471-2105-11-26.

13.

Towards prediction and prioritization of disease genes by the modularity of human phenome-genome assembled network.

Jiang JQ, Dress AW, Chen M.

J Integr Bioinform. 2010 Nov 22;7(2). doi: 10.2390/biecoll-jib-2010-149. Retraction in: J Integr Bioinform. 2011;8(1):154.

PMID:
21098881
14.

Statistical methods in integrative analysis for gene regulatory modules.

Zeng L, Wu J, Xie J.

Stat Appl Genet Mol Biol. 2008;7(1):Article 28. doi: 10.2202/1544-6115.1369. Epub 2008 Oct 10.

PMID:
18976224
15.

Inferring disease and gene set associations with rank coherence in networks.

Hwang T, Zhang W, Xie M, Liu J, Kuang R.

Bioinformatics. 2011 Oct 1;27(19):2692-9. doi: 10.1093/bioinformatics/btr463. Epub 2011 Aug 8.

PMID:
21824970
16.

Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits.

Li H, Chen H, Bao L, Manly KF, Chesler EJ, Lu L, Wang J, Zhou M, Williams RW, Cui Y.

Hum Mol Genet. 2006 Feb 1;15(3):481-92. Epub 2005 Dec 21.

PMID:
16371421
17.

Inferring gene-phenotype associations via global protein complex network propagation.

Yang P, Li X, Wu M, Kwoh CK, Ng SK.

PLoS One. 2011;6(7):e21502. doi: 10.1371/journal.pone.0021502. Epub 2011 Jul 25.

18.

De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.

Niu M, Tabari ES, Su Z.

BMC Genomics. 2014 Dec 2;15:1047. doi: 10.1186/1471-2164-15-1047.

20.

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells.

Zhu M, Deng X, Joshi T, Xu D, Stacey G, Cheng J.

BMC Genomics. 2012 Aug 31;13:437. doi: 10.1186/1471-2164-13-437.

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