174 related articles for article (PubMed ID: 23595148)
1. TherMos: Estimating protein-DNA binding energies from in vivo binding profiles.
Sun W; Hu X; Lim MH; Ng CK; Choo SH; Castro DS; Drechsel D; Guillemot F; Kolatkar PR; Jauch R; Prabhakar S
Nucleic Acids Res; 2013 Jun; 41(11):5555-68. PubMed ID: 23595148
[TBL] [Abstract][Full Text] [Related]
2. MACE: model based analysis of ChIP-exo.
Wang L; Chen J; Wang C; Uusküla-Reimand L; Chen K; Medina-Rivera A; Young EJ; Zimmermann MT; Yan H; Sun Z; Zhang Y; Wu ST; Huang H; Wilson MD; Kocher JP; Li W
Nucleic Acids Res; 2014 Nov; 42(20):e156. PubMed ID: 25249628
[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. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.
Jothi R; Cuddapah S; Barski A; Cui K; Zhao K
Nucleic Acids Res; 2008 Sep; 36(16):5221-31. PubMed ID: 18684996
[TBL] [Abstract][Full Text] [Related]
5. ChIPulate: A comprehensive ChIP-seq simulation pipeline.
Datta V; Hannenhalli S; Siddharthan R
PLoS Comput Biol; 2019 Mar; 15(3):e1006921. PubMed ID: 30897079
[TBL] [Abstract][Full Text] [Related]
6. The Role of Genome Accessibility in Transcription Factor Binding in Bacteria.
Gomes AL; Wang HH
PLoS Comput Biol; 2016 Apr; 12(4):e1004891. PubMed ID: 27104615
[TBL] [Abstract][Full Text] [Related]
7. Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells.
Hutchins AP; Choo SH; Mistri TK; Rahmani M; Woon CT; Ng CK; Jauch R; Robson P
Stem Cells; 2013 Feb; 31(2):269-81. PubMed ID: 23169531
[TBL] [Abstract][Full Text] [Related]
8. Inferring transcription factor complexes from ChIP-seq data.
Whitington T; Frith MC; Johnson J; Bailey TL
Nucleic Acids Res; 2011 Aug; 39(15):e98. PubMed ID: 21602262
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. 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]
11. SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps.
Setty M; Leslie CS
PLoS Comput Biol; 2015 May; 11(5):e1004271. PubMed ID: 26016777
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. DREME: motif discovery in transcription factor ChIP-seq data.
Bailey TL
Bioinformatics; 2011 Jun; 27(12):1653-9. PubMed ID: 21543442
[TBL] [Abstract][Full Text] [Related]
14. MEME-ChIP: motif analysis of large DNA datasets.
Machanick P; Bailey TL
Bioinformatics; 2011 Jun; 27(12):1696-7. PubMed ID: 21486936
[TBL] [Abstract][Full Text] [Related]
15. BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data.
Kähärä J; Lähdesmäki H
Bioinformatics; 2015 Sep; 31(17):2852-9. PubMed ID: 25957350
[TBL] [Abstract][Full Text] [Related]
16. Accurate prediction of inducible transcription factor binding intensities in vivo.
Guertin MJ; Martins AL; Siepel A; Lis JT
PLoS Genet; 2012; 8(3):e1002610. PubMed ID: 22479205
[TBL] [Abstract][Full Text] [Related]
17. Inferring direct DNA binding from ChIP-seq.
Bailey TL; Machanick P
Nucleic Acids Res; 2012 Sep; 40(17):e128. PubMed ID: 22610855
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans.
Brdlik CM; Niu W; Snyder M
Methods Enzymol; 2014; 539():89-111. PubMed ID: 24581441
[TBL] [Abstract][Full Text] [Related]
20. PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Zambelli F; Pesole G; Pavesi G
Nucleic Acids Res; 2013 Jul; 41(Web Server issue):W535-43. PubMed ID: 23748563
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]