Mark Gerstein

TL;DR: This article showed that a significant fraction of the protein-protein interactions in genome-wide datasets, as well as many of the individual interactions reported in the literature, are inconsistent with the known 3D structures of three recent complexes (RNA polymerase II, Arp2/3 and the proteasome).

TL;DR: The volume of atoms on the protein surface during a molecular-dynamics simulation of a small protein (pancreatic trypsin inhibitor) is analyzed using a particular geometric construction, called Voronoi polyhedra, that divides the total volume of the simulation box amongst the atoms, rendering them relatively larger or smaller depending on how tightly they are packed.

TL;DR: Three pairs of regions exhibit intricate differences in chromosomal locations, chromatin features, factors that bind them, and cell-type specificity, and the machine learning approach enables us to identify features potentially general to all transcription factors, including those not included in the data.

TL;DR: An extensive map of the transcriptional regulatory network in Saccharomyces cerevisiae is created, comprising 7419 interactions connecting 180 transcription factors with their target genes, and it is found that genes targeted by the same TF tend to be co-expressed, with the degree of co-expression increasing if genes share more than one TF.

TL;DR: This system attempts to describe a protein motion as a rigid-body rotation of a small 'core' relative to a larger one, using a set of hinges, and finds that while this model can accommodate most protein motions, it cannot accommodate all; the degree to which a motion can be accommodated provides an aid in classifying it.