The compilation of multiple metazoan genome sequences and the deluge of large-scale
expression data have combined to motivate the maturation of bioinformatics methods for the …

The identification and characterization of mammalian core promoters and transcription start
sites is a prerequisite to understanding how RNA polymerase II transcription is controlled …

The analysis of regulatory regions in genome sequences is strongly based on the detection
of potential transcription factor binding sites. The preferred models for representation of …

Mammalian promoters can be separated into two classes, conserved TATA box–enriched
promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG …

Transcription factors (TFs) direct gene expression by binding to DNA regulatory regions. To
explore the evolution of gene regulation, we used chromatin immunoprecipitation with high …

Attainment of a brown adipocyte cell phenotype in white adipocytes, with their abundant
mitochondria and increased energy expenditure potential, is a legitimate strategy for …

Normal brain function depends on the interaction between highly specialized neurons that
operate within anatomically and functionally distinct brain regions. Neuronal specification is …

Background The regulatory map of a genome consists of the binding sites for proteins that
determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was …

JASPAR is a popular open-access database for matrix models describing DNA-binding
preferences for transcription factors and other DNA patterns. With its third major release …

Prediction of gene regulatory sequences using phylogenetic footprinting has advanced
considerably but lacks experimental validation. Here, we report whether transcription factor …