316 related articles for article (PubMed ID: 28334916)
1. Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility.
Chen X; Yu B; Carriero N; Silva C; Bonneau R
Nucleic Acids Res; 2017 May; 45(8):4315-4329. PubMed ID: 28334916
[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. Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.
Worsley Hunt R; Mathelier A; Del Peso L; Wasserman WW
BMC Genomics; 2014 Jun; 15(1):472. PubMed ID: 24927817
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Cell-type specificity of ChIP-predicted transcription factor binding sites.
Håndstad T; Rye M; Močnik R; Drabløs F; Sætrom P
BMC Genomics; 2012 Aug; 13():372. PubMed ID: 22863112
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. Sequence and chromatin determinants of cell-type-specific transcription factor binding.
Arvey A; Agius P; Noble WS; Leslie C
Genome Res; 2012 Sep; 22(9):1723-34. PubMed ID: 22955984
[TBL] [Abstract][Full Text] [Related]
8. Anchor: trans-cell type prediction of transcription factor binding sites.
Li H; Quang D; Guan Y
Genome Res; 2019 Feb; 29(2):281-292. PubMed ID: 30567711
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. 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]
11. Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture.
Bouvy-Liivrand M; Hernández de Sande A; Pölönen P; Mehtonen J; Vuorenmaa T; Niskanen H; Sinkkonen L; Kaikkonen MU; Heinäniemi M
Nucleic Acids Res; 2017 Sep; 45(17):9837-9849. PubMed ID: 28973462
[TBL] [Abstract][Full Text] [Related]
12. TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.
Ouyang N; Boyle AP
Genome Res; 2020 Jul; 30(7):1040-1046. PubMed ID: 32660981
[TBL] [Abstract][Full Text] [Related]
13. Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species.
Huang L; Li X; Dong L; Wang B; Pan L
BMC Biol; 2021 Sep; 19(1):189. PubMed ID: 34488759
[TBL] [Abstract][Full Text] [Related]
14. Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.
Kuznetsov VA; Singh O; Jenjaroenpun P
BMC Genomics; 2010 Feb; 11 Suppl 1(Suppl 1):S12. PubMed ID: 20158869
[TBL] [Abstract][Full Text] [Related]
15. MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.
Xuan Lin QX; Sian S; An O; Thieffry D; Jha S; Benoukraf T
Nucleic Acids Res; 2019 Jan; 47(D1):D145-D154. PubMed ID: 30380113
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. Modeling co-occupancy of transcription factors using chromatin features.
Liu L; Zhao W; Zhou X
Nucleic Acids Res; 2016 Mar; 44(5):e49. PubMed ID: 26590261
[TBL] [Abstract][Full Text] [Related]
18. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.
Schmidt F; Gasparoni N; Gasparoni G; Gianmoena K; Cadenas C; Polansky JK; Ebert P; Nordström K; Barann M; Sinha A; Fröhler S; Xiong J; Dehghani Amirabad A; Behjati Ardakani F; Hutter B; Zipprich G; Felder B; Eils J; Brors B; Chen W; Hengstler JG; Hamann A; Lengauer T; Rosenstiel P; Walter J; Schulz MH
Nucleic Acids Res; 2017 Jan; 45(1):54-66. PubMed ID: 27899623
[TBL] [Abstract][Full Text] [Related]
19. Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome.
Karimzadeh M; Hoffman MM
Genome Biol; 2022 Jun; 23(1):126. PubMed ID: 35681170
[TBL] [Abstract][Full Text] [Related]
20. MEDEA: analysis of transcription factor binding motifs in accessible chromatin.
Mariani L; Weinand K; Gisselbrecht SS; Bulyk ML
Genome Res; 2020 May; 30(5):736-748. PubMed ID: 32424069
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
