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Items: 1 to 20 of 39

1.

Animal transcription networks as highly connected, quantitative continua.

Biggin MD.

Dev Cell. 2011 Oct 18;21(4):611-26. doi: 10.1016/j.devcel.2011.09.008. Review.

2.

Broad profiling of DNA-binding transcription factor activities improves regulatory network construction in adult mouse tissues.

Sun YM, Zhang Y, Zeng LQ, Wu JP, Wei L, Ren AH, Shao W, Qiao JY, Zhao YC, Zhang L, Mitchelson KR, Cheng J.

J Proteome Res. 2008 Oct;7(10):4455-64. doi: 10.1021/pr800417e. Epub 2008 Aug 30.

PMID:
18759473
3.

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1. doi: 10.1186/1471-2105-10-S4-S1.

4.

Genomic cis-regulatory networks in the early Ciona intestinalis embryo.

Kubo A, Suzuki N, Yuan X, Nakai K, Satoh N, Imai KS, Satou Y.

Development. 2010 May;137(10):1613-23. doi: 10.1242/dev.046789. Epub 2010 Apr 14.

6.

Transcription factor site dependencies in human, mouse and rat genomes.

Tomovic A, Stadler M, Oakeley EJ.

BMC Bioinformatics. 2009 Oct 16;10:339. doi: 10.1186/1471-2105-10-339.

7.

Global analysis of gene transcription regulation in prokaryotes.

Zhou D, Yang R.

Cell Mol Life Sci. 2006 Oct;63(19-20):2260-90. Review.

PMID:
16927028
8.

cis-Regulatory networks during development: a view of Drosophila.

Bonn S, Furlong EE.

Curr Opin Genet Dev. 2008 Dec;18(6):513-20. doi: 10.1016/j.gde.2008.09.005. Epub 2008 Oct 16. Review.

PMID:
18929653
9.

Inference of active transcriptional networks by integration of gene expression kinetics modeling and multisource data.

Vu TT, Vohradsky J.

Genomics. 2009 May;93(5):426-33. doi: 10.1016/j.ygeno.2009.01.006. Epub 2009 Feb 5.

10.

Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches.

Teixeira MC, Dias PJ, Monteiro PT, Sala A, Oliveira AL, Freitas AT, Sá-Correia I.

Mol Biosyst. 2010 Dec;6(12):2471-81. doi: 10.1039/c004881j. Epub 2010 Oct 11.

PMID:
20938527
11.

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.

Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ.

J Mol Biol. 2001 May 25;309(1):99-120.

PMID:
11491305
12.

Transcriptional regulatory networks in Saccharomyces cerevisiae.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA.

Science. 2002 Oct 25;298(5594):799-804.

13.

Challenges for modeling global gene regulatory networks during development: insights from Drosophila.

Wilczynski B, Furlong EE.

Dev Biol. 2010 Apr 15;340(2):161-9. doi: 10.1016/j.ydbio.2009.10.032. Epub 2009 Oct 27. Review.

14.

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.

15.

Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge.

Vega VB, Woo XY, Hamidi H, Yeo HC, Yeo ZX, Bourque G, Clarke ND.

Ann N Y Acad Sci. 2009 Mar;1158:215-23. doi: 10.1111/j.1749-6632.2008.03759.x.

PMID:
19348643
16.

Quantifying the effect of sequence variation on regulatory interactions.

Manke T, Heinig M, Vingron M.

Hum Mutat. 2010 Apr;31(4):477-83. doi: 10.1002/humu.21209.

PMID:
20127973
17.

Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae.

Datta D, Zhao H.

Bioinformatics. 2008 Feb 15;24(4):545-52. Epub 2007 Nov 7.

PMID:
17989095
18.

Dissecting the transcription networks of a cell using computational genomics.

Li H, Wang W.

Curr Opin Genet Dev. 2003 Dec;13(6):611-6. Review.

PMID:
14638323
19.

Dynamic and complex transcription factor binding during an inducible response in yeast.

Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M.

Genes Dev. 2009 Jun 1;23(11):1351-63. doi: 10.1101/gad.1781909.

20.

Gene regulation by transcription factors and microRNAs.

Hobert O.

Science. 2008 Mar 28;319(5871):1785-6. doi: 10.1126/science.1151651.

PMID:
18369135

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