Regulation of gene expression is central to many biological processes. Although
reconstruction of regulatory circuits from genomic data alone is therefore desirable, this …

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 …

The unique DNA-binding properties of distinct NF-κB dimers influence the selective
regulation of NF-κB target genes. To more thoroughly investigate these dimer-specific …

Motivation Accurate knowledge of the genome-wide binding of transcription factors in a
particular cell type or under a particular condition is necessary for understanding …

As exome sequencing gives way to genome sequencing, the need to interpret the function of
regulatory DNA becomes increasingly important. To test whether evolutionary conservation …

A major prerequisite for the investigation of tissue-specific processes is the identification of
cis-regulatory elements. No generally applicable technique is available to distinguish them …

Phytohormones regulate many aspects of plant life by activating transcription factors (TFs)
that bind sequence-specific response elements (REs) in regulatory regions of target genes …

To analyze gene regulatory networks, the sequence-dependent DNA/RNA binding affinities
of proteins and noncoding RNAs are crucial. Often, these are deduced from sets of …

Although cell cycle control is an ancient, conserved, and essential process, some core
animal and fungal cell cycle regulators share no more sequence identity than non …

Background The rise of large-scale multi-species genome sequencing projects promises to
shed new light on how genomes encode gene regulatory instructions. To this end, new …