PyNAST: a flexible tool for aligning sequences to a template alignment. - J. Gregory Caporaso; Kyle Bittinger; Frederic D. Bushman; Todd Z. DeSantis; Gary L. Andersen; Rob Knight 001 (Bioinform., 2010)

Associating microbiome composition with environmental covariates using generalized UniFrac distances. - Jun Chen; Kyle Bittinger; Emily S. Charlson; Christian Hoffmann 005; James D. Lewis; Gary D. Wu; Ronald G. Collman; Frederic D. Bushman; Hongzhe Li (Bioinform., 2012)

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. - Brendan J. Kelly; Robert Gross; Kyle Bittinger; Scott A. Sherrill-Mix; James D. Lewis; Ronald G. Collman; Frederic D. Bushman; Hongzhe Li (Bioinform., 2015)