Decomposition Theorems for Conditional Sign-Solvability and Sign-Solvability of General Systems. - Shawn Cokus; Victor Klee (SIAM J. Matrix Anal. Appl., 2000)

Inferring protein interactions from phylogenetic distance matrices. - Jason Gertz; Georgiy Elfond; Anna Shustrova; Matt Weisinger; Matteo Pellegrini; Shawn Cokus; Bruce Rothschild (Bioinform., 2003)

Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. - Shawn Cokus; Sherri Rose; David R. Haynor; Niels Grønbech-Jensen; Matteo Pellegrini (BMC Bioinform., 2006)

An improved method for identifying functionally linked proteins using phylogenetic profiles. - Shawn Cokus; Sayaka Mizutani; Matteo Pellegrini (BMC Bioinform., 2007)

Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. - Einat Sprinzak; Shawn Cokus; Todd O. Yeates; David Eisenberg 001; Matteo Pellegrini (BMC Syst. Biol., 2009)

BS Seeker: precise mapping for bisulfite sequencing. - Pao-Yang Chen; Shawn Cokus; Matteo Pellegrini (BMC Bioinform., 2010)

Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. - David López; David Casero; Shawn Cokus; Sabeeha S. Merchant; Matteo Pellegrini (BMC Bioinform., 2011)