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Items: 1 to 20 of 86

1.

Genome-wide prediction of transcription factor binding sites using an integrated model.

Won KJ, Ren B, Wang W.

Genome Biol. 2010 Jan 22;11(1):R7. doi: 10.1186/gb-2010-11-1-r7.

2.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

3.

Combinatorial binding predicts spatio-temporal cis-regulatory activity.

Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE.

Nature. 2009 Nov 5;462(7269):65-70. doi: 10.1038/nature08531.

PMID:
19890324
4.

A systems biology approach to understanding cis-regulatory module function.

Jeziorska DM, Jordan KW, Vance KW.

Semin Cell Dev Biol. 2009 Sep;20(7):856-62. doi: 10.1016/j.semcdb.2009.07.007. Epub 2009 Aug 4. Review.

PMID:
19660565
5.

Organization of developmental enhancers in the Drosophila embryo.

Papatsenko D, Goltsev Y, Levine M.

Nucleic Acids Res. 2009 Sep;37(17):5665-77. doi: 10.1093/nar/gkp619. Epub 2009 Aug 3.

6.

Unlocking the secrets of the genome.

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium..

Nature. 2009 Jun 18;459(7249):927-30. doi: 10.1038/459927a. No abstract available.

7.

Histone modifications at human enhancers reflect global cell-type-specific gene expression.

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B.

Nature. 2009 May 7;459(7243):108-12. doi: 10.1038/nature07829. Epub 2009 Mar 18.

8.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

9.

Local DNA topography correlates with functional noncoding regions of the human genome.

Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH.

Science. 2009 Apr 17;324(5925):389-92. doi: 10.1126/science.1169050. Epub 2009 Mar 12.

10.

Big genomes facilitate the comparative identification of regulatory elements.

Peterson BK, Hare EE, Iyer VN, Storage S, Conner L, Papaj DR, Kurashima R, Jang E, Eisen MB.

PLoS One. 2009;4(3):e4688. doi: 10.1371/journal.pone.0004688. Epub 2009 Mar 4.

11.

Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.

Shi B, Guo X, Wu T, Sheng S, Wang J, Skogerbø G, Zhu X, Chen R.

BMC Genomics. 2009 Feb 25;10:92. doi: 10.1186/1471-2164-10-92.

12.

ChIP-seq accurately predicts tissue-specific activity of enhancers.

Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA.

Nature. 2009 Feb 12;457(7231):854-8. doi: 10.1038/nature07730.

13.

Species-specific transcription in mice carrying human chromosome 21.

Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VL, Fisher EM, Tavaré S, Odom DT.

Science. 2008 Oct 17;322(5900):434-8. doi: 10.1126/science.1160930. Epub 2008 Sep 11.

14.

The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila.

Williams TM, Selegue JE, Werner T, Gompel N, Kopp A, Carroll SB.

Cell. 2008 Aug 22;134(4):610-23. doi: 10.1016/j.cell.2008.06.052.

15.

Intron-mediated regulation of gene expression.

Rose AB.

Curr Top Microbiol Immunol. 2008;326:277-90. Review.

PMID:
18630758
16.

DiRE: identifying distant regulatory elements of co-expressed genes.

Gotea V, Ovcharenko I.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W133-9. doi: 10.1093/nar/gkn300. Epub 2008 May 17.

17.

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

Van Loo P, Aerts S, Thienpont B, De Moor B, Moreau Y, Marynen P.

Genome Biol. 2008 Apr 7;9(4):R66. doi: 10.1186/gb-2008-9-4-r66.

18.

Systematic identification of mammalian regulatory motifs' target genes and functions.

Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.

Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2.

19.

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD.

PLoS Biol. 2008 Feb;6(2):e27. doi: 10.1371/journal.pbio.0060027.

20.

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U.

Nature. 2008 Jan 31;451(7178):535-40. doi: 10.1038/nature06496. Epub 2008 Jan 2.

PMID:
18172436

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