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Items: 1 to 20 of 73

1.

De-novo discovery of differentially abundant transcription factor binding sites including their positional preference.

Keilwagen J, Grau J, Paponov IA, Posch S, Strickert M, Grosse I.

PLoS Comput Biol. 2011 Feb 10;7(2):e1001070. doi: 10.1371/journal.pcbi.1001070. Erratum in: PLoS Comput Biol. 2011 Oct;7(10). doi: 10.1371/annotation/a0b541dc-472b-4076-a435-499ce9519335.

2.

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA.

Nat Genet. 2011 Mar;43(3):264-8. doi: 10.1038/ng.759. Epub 2011 Jan 23.

PMID:
21258342
3.

Assessing computational methods of cis-regulatory module prediction.

Su J, Teichmann SA, Down TA.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001020. doi: 10.1371/journal.pcbi.1001020.

4.

Kernel-based identification of regulatory modules.

Schultheiss SJ.

Methods Mol Biol. 2010;674:213-23. doi: 10.1007/978-1-60761-854-6_13.

PMID:
20827594
5.

Activity-dependent expression of Lmx1b regulates specification of serotonergic neurons modulating swimming behavior.

Demarque M, Spitzer NC.

Neuron. 2010 Jul 29;67(2):321-34. doi: 10.1016/j.neuron.2010.06.006.

6.

Genomics of long-range regulatory elements.

Noonan JP, McCallion AS.

Annu Rev Genomics Hum Genet. 2010;11:1-23. doi: 10.1146/annurev-genom-082509-141651. Review.

PMID:
20438361
7.

Widespread transcription at neuronal activity-regulated enhancers.

Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME.

Nature. 2010 May 13;465(7295):182-7. doi: 10.1038/nature09033. Epub 2010 Apr 14.

8.

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.

Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I.

Genome Res. 2010 May;20(5):565-77. doi: 10.1101/gr.104471.109. Epub 2010 Apr 2.

9.

Genome-wide discovery of human heart enhancers.

Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I.

Genome Res. 2010 Mar;20(3):381-92. doi: 10.1101/gr.098657.109. Epub 2010 Jan 14.

10.

Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263.

Frietze S, Lan X, Jin VX, Farnham PJ.

J Biol Chem. 2010 Jan 8;285(2):1393-403. doi: 10.1074/jbc.M109.063032. Epub 2009 Nov 2.

11.

Identifying cis-regulatory sequences by word profile similarity.

Leung G, Eisen MB.

PLoS One. 2009 Sep 4;4(9):e6901. doi: 10.1371/journal.pone.0006901.

12.

KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.

Schultheiss SJ, Busch W, Lohmann JU, Kohlbacher O, Rätsch G.

Bioinformatics. 2009 Aug 15;25(16):2126-33. doi: 10.1093/bioinformatics/btp278. Epub 2009 Apr 23.

13.

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.

14.

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.

15.

A transcription factor affinity-based code for mammalian transcription initiation.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG.

Genome Res. 2009 Apr;19(4):644-56. doi: 10.1101/gr.085449.108. Epub 2009 Jan 13.

16.

Nuclear factor one transcription factors in CNS development.

Mason S, Piper M, Gronostajski RM, Richards LJ.

Mol Neurobiol. 2009 Feb;39(1):10-23. doi: 10.1007/s12035-008-8048-6. Epub 2008 Dec 5.

PMID:
19058033
17.

The role of the ZEB family of transcription factors in development and disease.

Vandewalle C, Van Roy F, Berx G.

Cell Mol Life Sci. 2009 Mar;66(5):773-87. doi: 10.1007/s00018-008-8465-8. Review.

PMID:
19011757
18.

Support vector machines and kernels for computational biology.

Ben-Hur A, Ong CS, Sonnenburg S, Schölkopf B, Rätsch G.

PLoS Comput Biol. 2008 Oct;4(10):e1000173. doi: 10.1371/journal.pcbi.1000173. Epub 2008 Oct 31. Review. No abstract available.

19.

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.

Newburger DE, Bulyk ML.

Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82. doi: 10.1093/nar/gkn660. Epub 2008 Oct 8.

20.

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.

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