BIBM
2010
IEEE
13 years 2 months ago
2010
IEEE
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...
NAR
2007
13 years 4 months ago
2007
We describe PReMod, a new database of genomewide cis-regulatory module (CRM) predictions for both the human and the mouse genomes. The prediction algorithm, described previously i...
BMCBI
2005
13 years 4 months ago
2005
Background: Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profi...
BMCBI
2005
13 years 4 months ago
2005
Background: The determination of protein surfaces and the detection of binding sites are essential to our understanding of protein-protein interactions. Such binding sites can be ...
TCBB
2008
13 years 4 months ago
2008
The problem of discovering novel motifs of binding sites is important to the understanding of gene regulatory networks. Motifs are generally represented by matrices (PWM or PSSM) o...
BMCBI
2007
13 years 4 months ago
2007
Background: We performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples ...
BMCBI
2007
13 years 4 months ago
2007
Background: An accurate description of protein shape derived from protein structure is necessary to establish an understanding of protein-ligand interactions, which in turn will l...
BMCBI
2007
13 years 4 months ago
2007
Background: The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites ...
BMCBI
2006
13 years 4 months ago
2006
Background: Identifying cis-regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented tran...
BMCBI
2006
13 years 4 months ago
2006
Background: The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential ...