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Items: 1 to 20 of 132


Finding subtypes of transcription factor motif pairs with distinct regulatory roles.

Bais AS, Kaminski N, Benos PV.

Nucleic Acids Res. 2011 Jun;39(11):e76. doi: 10.1093/nar/gkr205. Epub 2011 Apr 12.


Identification of context-dependent motifs by contrasting ChIP binding data.

Mason MJ, Plath K, Zhou Q.

Bioinformatics. 2010 Nov 15;26(22):2826-32. doi: 10.1093/bioinformatics/btq546. Epub 2010 Sep 23.


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. doi: 10.1371/journal.pone.0052055. Epub 2012 Dec 18.


Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices.

Oh YM, Kim JK, Choi S, Yoo JY.

Nucleic Acids Res. 2012 Mar;40(5):e38. doi: 10.1093/nar/gkr1252. Epub 2011 Dec 19.


An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs.

Garcia-Alcalde F, Blanco A, Shepherd AJ.

BMC Bioinformatics. 2010 Nov 8;11:551. doi: 10.1186/1471-2105-11-551.


Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.

Ng FS, Schütte J, Ruau D, Diamanti E, Hannah R, Kinston SJ, Göttgens B.

Nucleic Acids Res. 2014 Dec 16;42(22):13513-24. doi: 10.1093/nar/gku1254. Epub 2014 Nov 26.


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.


A widespread role of the motif environment in transcription factor binding across diverse protein families.

Dror I, Golan T, Levy C, Rohs R, Mandel-Gutfreund Y.

Genome Res. 2015 Sep;25(9):1268-80. doi: 10.1101/gr.184671.114. Epub 2015 Jul 9.


PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.


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.


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.


An equilibrium partitioning model connecting gene expression and cis-motif content.

Mellor J, DeLisi C.

Bioinformatics. 2006 Jul 15;22(14):e368-74.


Discovery of sequence motifs related to coexpression of genes using evolutionary computation.

Fogel GB, Weekes DG, Varga G, Dow ER, Harlow HB, Onyia JE, Su C.

Nucleic Acids Res. 2004 Jul 20;32(13):3826-35. Print 2004.


Evolutionary computation for discovery of composite transcription factor binding sites.

Fogel GB, Porto VW, Varga G, Dow ER, Craven AM, Powers DM, Harlow HB, Su EW, Onyia JE, Su C.

Nucleic Acids Res. 2008 Dec;36(21):e142. doi: 10.1093/nar/gkn738. Epub 2008 Oct 15.


Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns.

Chan TM, Leung KS, Lee KH, Wong MH, Lau TC, Tsui SK.

Nucleic Acids Res. 2012 Oct;40(19):9392-403. doi: 10.1093/nar/gks749. Epub 2012 Aug 16.


Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

Müller-Molina AJ, Schöler HR, Araúzo-Bravo MJ.

PLoS One. 2012;7(11):e49086. doi: 10.1371/journal.pone.0049086. Epub 2012 Nov 28.


Comparative analysis of regulatory motif discovery tools for transcription factor binding sites.

Wei W, Yu XD.

Genomics Proteomics Bioinformatics. 2007 May;5(2):131-42.


Discovering protein-DNA binding sequence patterns using association rule mining.

Leung KS, Wong KC, Chan TM, Wong MH, Lee KH, Lau CK, Tsui SK.

Nucleic Acids Res. 2010 Oct;38(19):6324-37. doi: 10.1093/nar/gkq500. Epub 2010 Jun 6.


Discovering approximate-associated sequence patterns for protein-DNA interactions.

Chan TM, Wong KC, Lee KH, Wong MH, Lau CK, Tsui SK, Leung KS.

Bioinformatics. 2011 Feb 15;27(4):471-8. doi: 10.1093/bioinformatics/btq682. Epub 2010 Dec 30.

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