300 related articles for article (PubMed ID: 37486787)
1. Identification of mammalian transcription factors that bind to inaccessible chromatin.
Pop RT; Pisante A; Nagy D; Martin PCN; Mikheeva LA; Hayat A; Ficz G; Zabet NR
Nucleic Acids Res; 2023 Sep; 51(16):8480-8495. PubMed ID: 37486787
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.
Martin PCN; Zabet NR
Comput Struct Biotechnol J; 2020; 18():3590-3605. PubMed ID: 33304457
[TBL] [Abstract][Full Text] [Related]
4. Cooperative binding of transcription factors in the human genome.
Nie Y; Shu C; Sun X
Genomics; 2020 Sep; 112(5):3427-3434. PubMed ID: 32574834
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. "Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes.
Zhao Y; Vartak SV; Conte A; Wang X; Garcia DA; Stevens E; Kyoung Jung S; Kieffer-Kwon KR; Vian L; Stodola T; Moris F; Chopp L; Preite S; Schwartzberg PL; Kulinski JM; Olivera A; Harly C; Bhandoola A; Heuston EF; Bodine DM; Urrutia R; Upadhyaya A; Weirauch MT; Hager G; Casellas R
Mol Cell; 2022 Sep; 82(18):3398-3411.e11. PubMed ID: 35863348
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans.
Tahara S; Tsuchiya T; Matsumoto H; Ozaki H
BMC Genomics; 2023 Oct; 24(1):597. PubMed ID: 37805453
[TBL] [Abstract][Full Text] [Related]
9. 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.
Ibn-Salem J; Andrade-Navarro MA
BMC Genomics; 2019 Oct; 20(1):777. PubMed ID: 31653198
[TBL] [Abstract][Full Text] [Related]
10. Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors.
Ma X; Ezer D; Adryan B; Stevens TJ
Genome Biol; 2018 Oct; 19(1):174. PubMed ID: 30359306
[TBL] [Abstract][Full Text] [Related]
11. The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells.
Mann-Nüttel R; Ali S; Petzsch P; Köhrer K; Alferink J; Scheu S
BMC Genom Data; 2021 Sep; 22(1):37. PubMed ID: 34544361
[TBL] [Abstract][Full Text] [Related]
12. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.
Tsai ZT; Shiu SH; Tsai HK
PLoS Comput Biol; 2015 Aug; 11(8):e1004418. PubMed ID: 26291518
[TBL] [Abstract][Full Text] [Related]
13. 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]
14. Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.
Luo K; Zhong J; Safi A; Hong LK; Tewari AK; Song L; Reddy TE; Ma L; Crawford GE; Hartemink AJ
Genome Res; 2022 Jun; 32(6):1183-1198. PubMed ID: 35609992
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Mitotic chromosome binding predicts transcription factor properties in interphase.
Raccaud M; Friman ET; Alber AB; Agarwal H; Deluz C; Kuhn T; Gebhardt JCM; Suter DM
Nat Commun; 2019 Jan; 10(1):487. PubMed ID: 30700703
[TBL] [Abstract][Full Text] [Related]
17. Genome-wide in silico prediction of gene expression.
McLeay RC; Lesluyes T; Cuellar Partida G; Bailey TL
Bioinformatics; 2012 Nov; 28(21):2789-96. PubMed ID: 22954627
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data.
Zamanighomi M; Lin Z; Wang Y; Jiang R; Wong WH
Nucleic Acids Res; 2017 Jun; 45(10):5666-5677. PubMed ID: 28472398
[TBL] [Abstract][Full Text] [Related]
20. 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]
[Next] [New Search]
