Mark Gerstein

TL;DR: A simple code for DNA recognition by transcription factors does seem to exist, and the recognition rules allow us to predict DNA-protein interactions, to change the binding specificity of an existing transcription factor, and probably even to design in a rational way a new protein which binds to a particular DNA sequence.

TL;DR: This work annotates variants associated with allele-specific binding and expression in 382 individuals by uniformly processing 1,263 functional genomics data sets, developing approaches to reduce the heterogeneity between data sets due to overdispersion and mapping bias.

TL;DR: This work presents a comparison between the transcriptional regulatory network of a well-studied bacterium and the call graph of a canonical OS (Linux) in terms of topology and evolution, and develops a way to measure evolutionary rates comparably between the two networks.

TL;DR: This work has examined the effect of EBNA1 on cellular gene expression by microarray analysis using the B cell BJAB and the epithelial 293 cell lines transfected withEBNA1 and correlated EBNA 1 bound promoters with changes in gene expression.

TL;DR: DNA-recognition rules for Zn fingers are discussed in terms of crystal structures, and it is discussed that to maintain the correct binding geometry, the residues facing the DNA on the helix must be larger near the C-terminus.