Proteins, such as many transcription factors, that bind to specific DNA sequences are
essential for the proper regulation of gene expression. Identifying the specific sequences …

Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are
currently known for only∼ 1% of eukaryotic TFs. Broadly sampling DNA-binding domain …

DNA binding specificity of transcription factor (TF) has broad impact on cell physiology and
development and in evolution. However, DNA-binding specificity of most known TFs still …

Cys2-His2 zinc finger proteins (ZFPs) are the largest family of transcription factors in higher
metazoans. They also represent the most diverse family with regards to the composition of …

Motivation: Inferring how humans respond to external cues such as drugs, chemicals,
viruses or hormones is an essential question in biomedicine. Very often, however, this …

Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among
eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with …

The ability to predict transcription factors based on sequence information in regulatory
elements is a key step in systems-level investigation of transcriptional regulation. Here, we …

Predicting the affinity profiles of nucleic acid–binding proteins directly from the protein
sequence is a challenging problem. We present a statistical approach for learning the …

ChIP-based genome-wide assays of transcription factor (TF) occupancy have emerged as a
powerful, high-throughput method to understand transcriptional regulation, especially on a …

Motivation: Recognition models for protein-DNA interactions, which allow the prediction of
specificity for a DNA-binding domain based only on its sequence or the alteration of …