455 related articles for article (PubMed ID: 19652015)
1. Distinguishing direct versus indirect transcription factor-DNA interactions.
Gordân R; Hartemink AJ; Bulyk ML
Genome Res; 2009 Nov; 19(11):2090-100. PubMed ID: 19652015
[TBL] [Abstract][Full Text] [Related]
2. High-resolution DNA-binding specificity analysis of yeast transcription factors.
Zhu C; Byers KJ; McCord RP; Shi Z; Berger MF; Newburger DE; Saulrieta K; Smith Z; Shah MV; Radhakrishnan M; Philippakis AA; Hu Y; De Masi F; Pacek M; Rolfs A; Murthy T; Labaer J; Bulyk ML
Genome Res; 2009 Apr; 19(4):556-66. PubMed ID: 19158363
[TBL] [Abstract][Full Text] [Related]
3. Identifying cooperative transcription factors in yeast using multiple data sources.
Lai FJ; Jhu MH; Chiu CC; Huang YM; Wu WS
BMC Syst Biol; 2014; 8 Suppl 5(Suppl 5):S2. PubMed ID: 25559499
[TBL] [Abstract][Full Text] [Related]
4. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.
Liu XS; Brutlag DL; Liu JS
Nat Biotechnol; 2002 Aug; 20(8):835-9. PubMed ID: 12101404
[TBL] [Abstract][Full Text] [Related]
5. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.
Gordân R; Murphy KF; McCord RP; Zhu C; Vedenko A; Bulyk ML
Genome Biol; 2011 Dec; 12(12):R125. PubMed ID: 22189060
[TBL] [Abstract][Full Text] [Related]
6. A nucleosome-guided map of transcription factor binding sites in yeast.
Narlikar L; Gordân R; Hartemink AJ
PLoS Comput Biol; 2007 Nov; 3(11):e215. PubMed ID: 17997593
[TBL] [Abstract][Full Text] [Related]
7. High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.
Agius P; Arvey A; Chang W; Noble WS; Leslie C
PLoS Comput Biol; 2010 Sep; 6(9):. PubMed ID: 20838582
[TBL] [Abstract][Full Text] [Related]
8. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function.
Lickwar CR; Mueller F; Hanlon SE; McNally JG; Lieb JD
Nature; 2012 Apr; 484(7393):251-5. PubMed ID: 22498630
[TBL] [Abstract][Full Text] [Related]
9. Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.
Ozonov EA; van Nimwegen E
PLoS Comput Biol; 2013; 9(8):e1003181. PubMed ID: 23990766
[TBL] [Abstract][Full Text] [Related]
10. Nonspecific transcription-factor-DNA binding influences nucleosome occupancy in yeast.
Afek A; Sela I; Musa-Lempel N; Lukatsky DB
Biophys J; 2011 Nov; 101(10):2465-75. PubMed ID: 22098745
[TBL] [Abstract][Full Text] [Related]
11. Mapping functional transcription factor networks from gene expression data.
Haynes BC; Maier EJ; Kramer MH; Wang PI; Brown H; Brent MR
Genome Res; 2013 Aug; 23(8):1319-28. PubMed ID: 23636944
[TBL] [Abstract][Full Text] [Related]
12. A map of direct TF-DNA interactions in the human genome.
Gheorghe M; Sandve GK; Khan A; Chèneby J; Ballester B; Mathelier A
Nucleic Acids Res; 2019 Feb; 47(4):e21. PubMed ID: 30517703
[TBL] [Abstract][Full Text] [Related]
13. Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays.
Levo M; Avnit-Sagi T; Lotan-Pompan M; Kalma Y; Weinberger A; Yakhini Z; Segal E
Mol Cell; 2017 Feb; 65(4):604-617.e6. PubMed ID: 28212748
[TBL] [Abstract][Full Text] [Related]
14. Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.
Goh WS; Orlov Y; Li J; Clarke ND
PLoS Comput Biol; 2010 Jan; 6(1):e1000649. PubMed ID: 20098497
[TBL] [Abstract][Full Text] [Related]
15. De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae.
Chen MJ; Chou LC; Hsieh TT; Lee DD; Liu KW; Yu CY; Oyang YJ; Tsai HK; Chen CY
Bioinformatics; 2012 Mar; 28(5):701-8. PubMed ID: 22238267
[TBL] [Abstract][Full Text] [Related]
16. A Bayesian hidden Markov model for motif discovery through joint modeling of genomic sequence and ChIP-chip data.
Gelfond JA; Gupta M; Ibrahim JG
Biometrics; 2009 Dec; 65(4):1087-95. PubMed ID: 19210737
[TBL] [Abstract][Full Text] [Related]
17. High-resolution mapping of transcription factor binding sites on native chromatin.
Kasinathan S; Orsi GA; Zentner GE; Ahmad K; Henikoff S
Nat Methods; 2014 Feb; 11(2):203-9. PubMed ID: 24336359
[TBL] [Abstract][Full Text] [Related]
18. A chromatin-mediated mechanism for specification of conditional transcription factor targets.
Buck MJ; Lieb JD
Nat Genet; 2006 Dec; 38(12):1446-51. PubMed ID: 17099712
[TBL] [Abstract][Full Text] [Related]
19. Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data.
Panchy NL; Lloyd JP; Shiu SH
BMC Genomics; 2020 Feb; 21(1):159. PubMed ID: 32054475
[TBL] [Abstract][Full Text] [Related]
20. 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; 4(12):e8155. PubMed ID: 19956545
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
