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BIBM
2010
IEEE
161views Bioinformatics» more  BIBM 2010»
13 years 5 months ago
Cis-regulatory module detection using constraint programming
We propose a method for finding CRMs in a set of co-regulated genes. Each CRM consists of a set of binding sites of transcription factors. We wish to find CRMs involving the same t...
Tias Guns, Hong Sun, Kathleen Marchal, Siegfried N...
BMCBI
2008
133views more  BMCBI 2008»
13 years 7 months ago
CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated
Background: The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false po...
Matthew S. Hestand, Michiel van Galen, Michel P. V...
RECOMB
2003
Springer
14 years 7 months ago
Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts
Background: Transcriptional regulation in eukaryotes often involves multiple transcription factors binding to the same transcription control region, and to understand the regulato...
Derek Y. Chiang, Alan M. Moses, Manolis Kamvysseli...
BMCBI
2005
102views more  BMCBI 2005»
13 years 7 months ago
Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computatio
Background: A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription...
Emmitt R. Jolly, Chen-Shan Chin, Ira Herskowitz, H...
BMCBI
2010
95views more  BMCBI 2010»
13 years 7 months ago
An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data
Background: ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of prot...
Congmao Wang, Jie Xu, Dasheng Zhang, Zoe A. Wilson...