305 related articles for article (PubMed ID: 23935523)
1. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy.
Cheng Q; Kazemian M; Pham H; Blatti C; Celniker SE; Wolfe SA; Brodsky MH; Sinha S
PLoS Genet; 2013; 9(8):e1003571. PubMed ID: 23935523
[TBL] [Abstract][Full Text] [Related]
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; 4(12):e8155. PubMed ID: 19956545
[TBL] [Abstract][Full Text] [Related]
3. Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.
Kazemian M; Pham H; Wolfe SA; Brodsky MH; Sinha S
Nucleic Acids Res; 2013 Sep; 41(17):8237-52. PubMed ID: 23847101
[TBL] [Abstract][Full Text] [Related]
4. Heterogeneity of transcription factor binding specificity models within and across cell lines.
Sharmin M; Bravo HC; Hannenhalli S
Genome Res; 2016 Aug; 26(8):1110-23. PubMed ID: 27311443
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. 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]
8. A New Mechanism for Mendelian Dominance in Regulatory Genetic Pathways: Competitive Binding by Transcription Factors.
Porter AH; Johnson NA; Tulchinsky AY
Genetics; 2017 Jan; 205(1):101-112. PubMed ID: 27866169
[TBL] [Abstract][Full Text] [Related]
9. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.
Liu S; Zibetti C; Wan J; Wang G; Blackshaw S; Qian J
BMC Bioinformatics; 2017 Jul; 18(1):355. PubMed ID: 28750606
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. TFregulomeR reveals transcription factors' context-specific features and functions.
Lin QXX; Thieffry D; Jha S; Benoukraf T
Nucleic Acids Res; 2020 Jan; 48(2):e10. PubMed ID: 31754708
[TBL] [Abstract][Full Text] [Related]
12. DNA-dependent formation of transcription factor pairs alters their binding specificity.
Jolma A; Yin Y; Nitta KR; Dave K; Popov A; Taipale M; Enge M; Kivioja T; Morgunova E; Taipale J
Nature; 2015 Nov; 527(7578):384-8. PubMed ID: 26550823
[TBL] [Abstract][Full Text] [Related]
13. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.
Li XY; Thomas S; Sabo PJ; Eisen MB; Stamatoyannopoulos JA; Biggin MD
Genome Biol; 2011; 12(4):R34. PubMed ID: 21473766
[TBL] [Abstract][Full Text] [Related]
14. Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets.
Worsley Hunt R; Wasserman WW
Genome Biol; 2014 Jul; 15(7):412. PubMed ID: 25070602
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. 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]
17. COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.
Ha N; Polychronidou M; Lohmann I
PLoS One; 2012; 7(12):e52055. PubMed ID: 23272209
[TBL] [Abstract][Full Text] [Related]
18. Genome-Wide Analysis of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by
Chumsakul O; Anantsri DP; Quirke T; Oshima T; Nakamura K; Ishikawa S; Nakano MM
J Bacteriol; 2017 Jul; 199(13):. PubMed ID: 28439033
[TBL] [Abstract][Full Text] [Related]
19. An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.
Cheng CY; Chu CH; Hsu HW; Hsu FR; Tang CY; Wang WC; Kung HJ; Chang PC
BMC Genomics; 2014; 15 Suppl 1(Suppl 1):S1. PubMed ID: 24564277
[TBL] [Abstract][Full Text] [Related]
20. Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines.
Foley JW; Sidow A
BMC Genomics; 2013 Oct; 14():720. PubMed ID: 24138567
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
