ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations. - Boris E. Shakhnovich; John M. Harvey; Steve Comeau; David Lorenz; Charles DeLisi; Eugene I. Shakhnovich (BMC Bioinform., 2003)

Improving the Precision of the Structure-Function Relationship by Considering Phylogenetic Context. - Boris E. Shakhnovich (PLoS Comput. Biol., 2005)

Correction: Improving the Precision of the Structure-Function Relationship by Considering Phylogenetic Context. - Boris E. Shakhnovich (PLoS Comput. Biol., 2005)

Relative contributions of structural designability and functional diversity in molecular evolution of duplicates. - Boris E. Shakhnovich (ISMB (Supplement of Bioinformatics), 2006)

Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites. - Timothy E. Reddy; Charles DeLisi; Boris E. Shakhnovich (PLoS Comput. Biol., 2007)

A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds. - Konstantin B. Zeldovich; Peiqiu Chen; Boris E. Shakhnovich; Eugene I. Shakhnovich (PLoS Comput. Biol., 2007)