Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem. - D. Benjamin Gordon; Stephen L. Mayo (J. Comput. Chem., 1998)

Exact rotamer optimization for protein design. - D. Benjamin Gordon; Geoffrey K. Hom; Stephen L. Mayo; Niles A. Pierce (J. Comput. Chem., 2003)

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. - D. Benjamin Gordon; Lena Nekludova; Scott McCallum; Ernest Fraenkel (Bioinform., 2005)

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. - Kenzie D. MacIsaac; D. Benjamin Gordon; Lena Nekludova; Duncan T. Odom; Joerg Schreiber; David K. Gifford; Richard A. Young; Ernest Fraenkel (Bioinform., 2006)

An improved map of conserved regulatory sites for Saccharomyces cerevisiae. - Kenzie D. MacIsaac; Ting Wang; D. Benjamin Gordon; David K. Gifford; Gary D. Stormo; Ernest Fraenkel (BMC Bioinform., 2006)

Prediction of whole-cell transcriptional response with machine learning. - Mohammed Eslami; Amin Espah Borujeni; Hamed Eramian; Mark Weston; George Zheng; Joshua Urrutia; Carolyn Corbet; Diveena Becker; Paul Maschhoff; Katie Clowers; Alexander Cristofaro; Hamid Doost Hosseini; et al. (Bioinform., 2022)