Using the nucleotide substitution rate matrix to detect horizontal gene transfer. - Micah Hamady; Meredith D. Betterton; Rob Knight 001 (BMC Bioinform., 2006)

Fast-Find: A novel computational approach to analyzing combinatorial motifs. - Micah Hamady; Erin Peden; Rob Knight 001; Ravinder Singh (BMC Bioinform., 2006)

UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. - Catherine A. Lozupone; Micah Hamady; Rob Knight 001 (BMC Bioinform., 2006)

Database-Driven Grid Computing and Distributed Web Applications: A Comparison. - Hans De Sterck; Aleks Papo; Chen Zhang 010; Micah Hamady; Rob Knight 001 (Grid Computing for Bioinformatics and Computational Biology, 2007)

CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes. - Micah Hamady; Stephanie A. Wilson; Jesse Zaneveld; Noboru Sueoka; Rob Knight 001 (Bioinform., 2009)