Over the last decade, a rich variety of massively parallel assays have revolutionized our
understanding of how biological sequences encode quantitative molecular phenotypes …

Coordinated regulation of gene expression relies on transcription factors (TFs) binding to
specific DNA sites. Our large-scale information–theoretical analysis of> 950 TF-binding …

How should one quantify the strength of association between two random variables without
bias for relationships of a specific form? Despite its conceptual simplicity, this notion of …

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 …

Cells use protein-DNA and protein-protein interactions to regulate transcription. A
biophysical understanding of this process has, however, been limited by the lack of methods …

Life depends as much on the flow of information as on the flow of energy. Here we review
the many efforts to make this intuition precise. Starting with the building blocks of information …

Evolution is a quest for innovation. Organisms adapt to changing natural selection by
evolving new phenotypes. Can we read this dynamics in their genomes? Not every mutation …

We employ a biophysical model that accounts for the non-linear relationship between
binding energy and the statistics of selected binding sites. The model includes the chemical …

To the Editor: In his News Feature published in the February issue, Michael Eisenstein
outlines several alternative methods of drug delivery1 and discusses how several targets in …

Protein–protein interaction (PPI) networks are key to nearly all aspects of cellular activity.
Therefore, the identification of PPIs is important for understanding a specific biological …