Long non-coding RNAs (lncRNAs) are associated to a plethora of cellular functions, most of
which require the interaction with one or more RNA-binding proteins (RBPs); similarly, RBPs …

Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …

Protein–ligand interactions are increasingly profiled at high throughput using affinity
selection and massively parallel sequencing. However, these assays do not provide the …

Transcription factors (TFs) that bind common DNA motifs in vitro occupy distinct sets of
promoters in vivo, raising the question of how binding specificity is achieved. TFs are …

Predicting protein–DNA binding specificity is a challenging yet essential task for
understanding gene regulation. Protein–DNA complexes usually exhibit binding to a …

Although the proteins that read the gene regulatory code, transcription factors (TFs), have
been largely identified, it is not well known which sequences TFs can recognize. We have …

Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …

Members of transcription factor families typically have similar DNA binding specificities yet
execute unique functions in vivo. Transcription factors often bind DNA as multiprotein …

Genomic analyses often involve scanning for potential transcription factor (TF) binding sites
using models of the sequence specificity of DNA binding proteins. Many approaches have …

The genetic code—the binding specificity of all transfer-RNAs—defines how protein primary
structure is determined by DNA sequence. DNA also dictates when and where proteins are …