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Items: 1 to 20 of 103

1.

An atlas of combinatorial transcriptional regulation in mouse and man.

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y.

Cell. 2010 Mar 5;140(5):744-52. doi: 10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr 16;141(2):369. Kamburov, Atanas [added]; Kaur, Mandeep [added]; MacPherson, Cameron Ross [added]; Radovanovic, Aleksandar [added]; Schwartz, Ariel [added].

2.

Circuitry and dynamics of human transcription factor regulatory networks.

Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA.

Cell. 2012 Sep 14;150(6):1274-86. doi: 10.1016/j.cell.2012.04.040. Epub 2012 Sep 5.

3.

Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors.

Österlund T, Bordel S, Nielsen J.

Integr Biol (Camb). 2015 May;7(5):560-8. doi: 10.1039/c4ib00247d. Epub 2015 Apr 9.

PMID:
25855217
4.

Inter- and intra-combinatorial regulation by transcription factors and microRNAs.

Zhou Y, Ferguson J, Chang JT, Kluger Y.

BMC Genomics. 2007 Oct 30;8:396.

5.

Conservation of trans-acting circuitry during mammalian regulatory evolution.

Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA.

Nature. 2014 Nov 20;515(7527):365-70. doi: 10.1038/nature13972.

6.

Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution.

Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP.

BMC Genomics. 2008 Aug 27;9:399. doi: 10.1186/1471-2164-9-399.

7.

Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium.

Pratt CH, Vadigepalli R, Chakravarthula P, Gonye GE, Philp NJ, Grunwald GB.

Mol Vis. 2008 Aug 4;14:1414-28.

9.

Widespread contribution of transposable elements to the innovation of gene regulatory networks.

Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T.

Genome Res. 2014 Dec;24(12):1963-76. doi: 10.1101/gr.168872.113. Epub 2014 Oct 15.

10.
11.

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information.

Liu Q, Tan Y, Huang T, Ding G, Tu Z, Liu L, Li Y, Dai H, Xie L.

BMC Bioinformatics. 2010 Dec 14;11 Suppl 11:S5. doi: 10.1186/1471-2105-11-S11-S5.

12.

Global and local architecture of the mammalian microRNA-transcription factor regulatory network.

Shalgi R, Lieber D, Oren M, Pilpel Y.

PLoS Comput Biol. 2007 Jul;3(7):e131.

13.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M.

Genome Res. 2012 Jul;22(7):1334-49. doi: 10.1101/gr.127191.111. Epub 2012 Mar 28.

14.

Transforming growth factor-beta inhibits pulmonary surfactant protein B gene transcription through SMAD3 interactions with NKX2.1 and HNF-3 transcription factors.

Li C, Zhu NL, Tan RC, Ballard PL, Derynck R, Minoo P.

J Biol Chem. 2002 Oct 11;277(41):38399-408. Epub 2002 Aug 2.

15.

Identification of context-specific gene regulatory networks with GEMULA--gene expression modeling using LAsso.

Geeven G, van Kesteren RE, Smit AB, de Gunst MC.

Bioinformatics. 2012 Jan 15;28(2):214-21. doi: 10.1093/bioinformatics/btr641. Epub 2011 Nov 21.

PMID:
22106333
16.

Characterization of regulatory features of housekeeping and tissue-specific regulators within tissue regulatory networks.

Li P, Hua X, Zhang Z, Li J, Wang J.

BMC Syst Biol. 2013 Oct 31;7:112. doi: 10.1186/1752-0509-7-112.

17.

Coordinated networks of microRNAs and transcription factors with evolutionary perspectives.

Iwama H.

Adv Exp Med Biol. 2013;774:169-87. doi: 10.1007/978-94-007-5590-1_10. Review.

PMID:
23377974
18.

Asymmetric evolution of human transcription factor regulatory networks.

Zhou Z, Zhou J, Su Z, Gu X.

Mol Biol Evol. 2014 Aug;31(8):2149-55. doi: 10.1093/molbev/msu163. Epub 2014 May 19.

PMID:
24847042
19.

Transcription factor interactions in genomic nuclear receptor function.

George CL, Lightman SL, Biddie SC.

Epigenomics. 2011 Aug;3(4):471-85. doi: 10.2217/epi.11.66. Review.

PMID:
22126206
20.

Transcription factors GATA4 and HNF4A control distinct aspects of intestinal homeostasis in conjunction with transcription factor CDX2.

San Roman AK, Aronson BE, Krasinski SD, Shivdasani RA, Verzi MP.

J Biol Chem. 2015 Jan 16;290(3):1850-60. doi: 10.1074/jbc.M114.620211. Epub 2014 Dec 8.

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