Andrew F. Neuwald

The paper develops ChIP-GSM, a Bayesian method to infer cis-regulatory modules from ChIP-seq data, showing improved performance in predicting regulatory element activity.

BICORN integrates transcription factor binding and gene expression data to infer sparse cis-regulatory modules and their regulatory networks.

The paper statistically evaluates DCA's ability to predict residue-residue contacts and assesses its performance across protein superfamilies.