PubMed

PhyloScan: identification of transcription factor binding sites using cross-species evidence.

Carmack CS, McCue LA, Newberg LA, Lawrence CE.

Algorithms Mol Biol. 2007 Jan 23;2:1.PMID: 17244358 [PubMed]Related articlesFree article

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.PMID: 16477324 [PubMed - indexed for MEDLINE]Related articlesFree article

Assessing phylogenetic motif models for predicting transcription factor binding sites.

Hawkins J, Grant C, Noble WS, Bailey TL.

Bioinformatics. 2009 Jun 15;25(12):i339-47.PMID: 19478008 [PubMed - indexed for MEDLINE]Related articlesFree article

OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.

Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM.

BMC Bioinformatics. 2009 Jul 7;10:208.PMID: 19583839 [PubMed - indexed for MEDLINE]Related articlesFree article

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.

Hestand MS, van Galen M, Villerius MP, van Ommen GJ, den Dunnen JT, 't Hoen PA.

BMC Bioinformatics. 2008 Nov 26;9:495.PMID: 19036135 [PubMed - indexed for MEDLINE]Related articlesFree article

Extracting transcription factor binding sites from unaligned gene sequences with statistical models.

Lu CC, Yuan WH, Chen TM.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S7.PMID: 19091030 [PubMed - indexed for MEDLINE]Related articlesFree article

Factors influencing the identification of transcription factor binding sites by cross-species comparison.

McCue LA, Thompson W, Carmack CS, Lawrence CE.

Genome Res. 2002 Oct;12(10):1523-32.PMID: 12368244 [PubMed - indexed for MEDLINE]Related articlesFree article

Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.

Reddy TE, DeLisi C, Shakhnovich BE.

PLoS Comput Biol. 2007 May;3(5):e90. Epub 2007 Apr 10.PMID: 17500587 [PubMed - indexed for MEDLINE]Related articlesFree article

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.

Redhead E, Bailey TL.

BMC Bioinformatics. 2007 Oct 15;8:385.PMID: 17937785 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrating multiple evidence sources to predict transcription factor binding in the human genome.

Ernst J, Plasterer HL, Simon I, Bar-Joseph Z.

Genome Res. 2010 Mar 10. [Epub ahead of print]PMID: 20219943 [PubMed - as supplied by publisher]Related articles

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.

Francke C, Kerkhoven R, Wels M, Siezen RJ.

BMC Genomics. 2008 Mar 27;9:145.PMID: 18371204 [PubMed - indexed for MEDLINE]Related articlesFree article

ReXSpecies--a tool for the analysis of the evolution of gene regulation across species.

Struckmann S, Araúzo-Bravo MJ, Schöler HR, Reinbold RA, Fuellen G.

BMC Evol Biol. 2008 Apr 14;8:111.PMID: 18410675 [PubMed - indexed for MEDLINE]Related articlesFree article

A model of evolution with constant selective pressure for regulatory DNA sites.

Enikeeva FN, Kotelnikova EA, Gelfand MS, Makeev VJ.

BMC Evol Biol. 2007 Jul 27;7:125.PMID: 17662135 [PubMed - indexed for MEDLINE]Related articlesFree article

Context specific transcription factor prediction.

Yang E, Simcha D, Almon RR, Dubois DC, Jusko WJ, Androulakis IP.

Ann Biomed Eng. 2007 Jun;35(6):1053-67. Epub 2007 Mar 22.PMID: 17377845 [PubMed - indexed for MEDLINE]Related articles

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.PMID: 17914226 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploring conservation of transcription factor binding sites with CONREAL.

Berezikov E, Guryev V, Cuppen E.

Methods Mol Biol. 2007;395:437-48.PMID: 17993690 [PubMed - indexed for MEDLINE]Related articles

Better estimation of protein-DNA interaction parameters improve prediction of functional sites.

Nagaraj VH, O'Flanagan RA, Sengupta AM.

BMC Biotechnol. 2008 Dec 23;8:94.PMID: 19105805 [PubMed - indexed for MEDLINE]Related articlesFree article

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.

Pavesi G, Zambelli F, Pesole G.

BMC Bioinformatics. 2007 Feb 7;8:46.PMID: 17286865 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.

Ward LD, Bussemaker HJ.

Bioinformatics. 2008 Jul 1;24(13):i165-71.PMID: 18586710 [PubMed - indexed for MEDLINE]Related articlesFree article

Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva.

Guo X, Silva JC.

BMC Genomics. 2008 Dec 3;9:582.PMID: 19055776 [PubMed - indexed for MEDLINE]Related articlesFree article