Phylogenetic footprinting is a comparative genomics approach for predicting transcription factor binding sites, where a set of orthologous regulatory regions are compared and short...
Background: ChIP-chip data, which indicate binding of transcription factors (TFs) to DNA regions in vivo, are widely used to reconstruct transcriptional regulatory networks. Howev...
Quantification of selective pressures on regulatory sequences is a central question in studying the evolution of gene regulatory networks. Previous methods focus primarily on sing...
Background: This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. Experimental procedures for this are slow and costly, and ...
Irina I. Abnizova, Rene te Boekhorst, Klaudia Walt...
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...
Vincent Ferretti, Christian Poitras, Dominique Ber...