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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. doi: 10.1093/nar/gkt250. Epub 2013 Apr 16.


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. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.


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 9;6(9). pii: e1000916. doi: 10.1371/journal.pcbi.1000916.


Inferring direct DNA binding from ChIP-seq.

Bailey TL, Machanick P.

Nucleic Acids Res. 2012 Sep 1;40(17):e128. Epub 2012 May 18.


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 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.


Accurate prediction of inducible transcription factor binding intensities in vivo.

Guertin MJ, Martins AL, Siepel A, Lis JT.

PLoS Genet. 2012;8(3):e1002610. doi: 10.1371/journal.pgen.1002610. Epub 2012 Mar 29.


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 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.


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 13;15:472. doi: 10.1186/1471-2164-15-472.


Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.


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 10;42(20):e156. doi: 10.1093/nar/gku846. Epub 2014 Sep 23.


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. doi: 10.1002/stem.1279.


ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data.

Wu S, Wang J, Zhao W, Pounds S, Cheng C.

Theor Biol Med Model. 2010 Jun 3;7:18. doi: 10.1186/1742-4682-7-18.


Inferring transcription factor complexes from ChIP-seq data.

Whitington T, Frith MC, Johnson J, Bailey TL.

Nucleic Acids Res. 2011 Aug;39(15):e98. doi: 10.1093/nar/gkr341. Epub 2011 May 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. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.


Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.


MEME-ChIP: motif analysis of large DNA datasets.

Machanick P, Bailey TL.

Bioinformatics. 2011 Jun 15;27(12):1696-7. doi: 10.1093/bioinformatics/btr189. Epub 2011 Apr 12.


DREME: motif discovery in transcription factor ChIP-seq data.

Bailey TL.

Bioinformatics. 2011 Jun 15;27(12):1653-9. doi: 10.1093/bioinformatics/btr261. Epub 2011 May 4.


The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.

Kornacker K, Rye MB, Håndstad T, Drabløs F.

BMC Bioinformatics. 2012 Jul 24;13:176. doi: 10.1186/1471-2105-13-176.


Integrative analysis of ChIP-chip and ChIP-seq dataset.

Zhu LJ.

Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8_8.

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