334 related articles for article (PubMed ID: 20098497)
1. 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]
2. Nucleosome organization in the vicinity of transcription factor binding sites in the human genome.
Nie Y; Cheng X; Chen J; Sun X
BMC Genomics; 2014 Jun; 15(1):493. PubMed ID: 24942981
[TBL] [Abstract][Full Text] [Related]
3. Mapping nucleosome positions using DNase-seq.
Zhong J; Luo K; Winter PS; Crawford GE; Iversen ES; Hartemink AJ
Genome Res; 2016 Mar; 26(3):351-64. PubMed ID: 26772197
[TBL] [Abstract][Full Text] [Related]
4. The DNA-encoded nucleosome organization of a eukaryotic genome.
Kaplan N; Moore IK; Fondufe-Mittendorf Y; Gossett AJ; Tillo D; Field Y; LeProust EM; Hughes TR; Lieb JD; Widom J; Segal E
Nature; 2009 Mar; 458(7236):362-6. PubMed ID: 19092803
[TBL] [Abstract][Full Text] [Related]
5. Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.
He X; Chatterjee R; John S; Bravo H; Sathyanarayana BK; Biddie SC; FitzGerald PC; Stamatoyannopoulos JA; Hager GL; Vinson C
BMC Genomics; 2013 Jun; 14():428. PubMed ID: 23805837
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.
Kumar S; Bucher P
BMC Bioinformatics; 2016 Jan; 17 Suppl 1(Suppl 1):4. PubMed ID: 26818008
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. 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]
10. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Wang J; Zhuang J; Iyer S; Lin X; Whitfield TW; Greven MC; Pierce BG; Dong X; Kundaje A; Cheng Y; Rando OJ; Birney E; Myers RM; Noble WS; Snyder M; Weng Z
Genome Res; 2012 Sep; 22(9):1798-812. PubMed ID: 22955990
[TBL] [Abstract][Full Text] [Related]
11. Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.
Afek A; Cohen H; Barber-Zucker S; Gordân R; Lukatsky DB
PLoS Comput Biol; 2015 Aug; 11(8):e1004429. PubMed ID: 26285121
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.
Vierstra J; Wang H; John S; Sandstrom R; Stamatoyannopoulos JA
Nat Methods; 2014 Jan; 11(1):66-72. PubMed ID: 24185839
[TBL] [Abstract][Full Text] [Related]
14. Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy.
Lubliner S; Segal E
Bioinformatics; 2009 Jun; 25(12):i348-55. PubMed ID: 19478009
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae.
Morris RT; O'Connor TR; Wyrick JJ
Bioinformatics; 2010 Jan; 26(2):168-74. PubMed ID: 19959498
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. Fine-Resolution Mapping of TF Binding and Chromatin Interactions.
Gutin J; Sadeh R; Bodenheimer N; Joseph-Strauss D; Klein-Brill A; Alajem A; Ram O; Friedman N
Cell Rep; 2018 Mar; 22(10):2797-2807. PubMed ID: 29514105
[TBL] [Abstract][Full Text] [Related]
19. Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.
Yadav VK; Thakur RK; Eckloff B; Baral A; Singh A; Halder R; Kumar A; Alam MP; Kundu TK; Pandita R; Pandita TK; Wieben ED; Chowdhury S
Nucleic Acids Res; 2014 Sep; 42(15):9602-11. PubMed ID: 25081206
[TBL] [Abstract][Full Text] [Related]
20. p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy.
Lidor Nili E; Field Y; Lubling Y; Widom J; Oren M; Segal E
Genome Res; 2010 Oct; 20(10):1361-8. PubMed ID: 20716666
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
