Transcription factors are key cellular components that control gene expression: their activities
determine how cells function and respond to the environment. Currently, there is great …

The regulatory interactions between transcription factors and their target genes can be
conceptualised as a directed graph. At a global level, these regulatory networks display a scale-…

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein
Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different …

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 …

In the nucleus of eukaryotic cells, nascent transcripts are associated with heterogeneous
nuclear ribonucleoprotein (hnRNP) particles that are nucleated by hnRNP C. Despite their …

Network analysis has been applied widely, providing a unifying language to describe
disparate systems ranging from social interactions to power grids. It has recently been used in …

Transcriptional control in large genomes often requires looping interactions between distal
DNA elements, such as enhancers and target promoters. Current chromosome conformation …

… 3A–C, 27 examples) and the side-on approach uses the N ε and N η 1 atoms (Fig. 3D, two
… Lysine performs an analogous interaction to the end-on conformation by placing the N ξ …

… set is called gold standard negatives and is denoted by N. … sets P′ and N′, subsets of P
and N with defined features. … families as described previously (Luscombe and Thornton 2002). …

Background: The recent flood of data from genome sequences and functional genomics has
given rise to new field, bioinformatics, which combines elements of biology and computer …