Phylogeny based discovery of regulatory elements. - Jason Gertz; Justin C. Fay; Barak A. Cohen (BMC Bioinform., 2006)

A cis-regulatory logic simulator. - Robert D. Zeigler; Jason Gertz; Barak A. Cohen (BMC Bioinform., 2007)

Thermodynamic State Ensemble Models of cis-Regulation. - Marc S. Sherman; Barak A. Cohen (PLoS Comput. Biol., 2012)

A Computational Framework for Analyzing Stochasticity in Gene Expression. - Marc S. Sherman; Barak A. Cohen (PLoS Comput. Biol., 2014)

Transcription factor interactions explain the context-dependent activity of CRX binding sites. - Kaiser J. Loell; Ryan Z. Friedman; Connie A. Myers; Joseph C. Corbo; Barak A. Cohen; Michael A. White (PLoS Comput. Biol., 2024)