Selection of Target Sites for Mobile DNA Integration in the Human Genome. - Charles C. Berry; Sridhar Hannenhalli; Jeremy Leipzig; Frederic D. Bushman (PLoS Comput. Biol., 2006)

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)

Estimating abundances of retroviral insertion sites from DNA fragment length data. - Charles C. Berry; Nicolas A. Gillet; Anat Melamed; Niall A. Gormley; Charles R. M. Bangham; Frederic D. Bushman (Bioinform., 2012)

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)

Global landscape of HIV-human protein complexes. - Stefanie Jäger; Peter Cimermancic; Natali Gulbahce; Jeffrey R. Johnson; Kathryn E. McGovern; Starlynn C. Clarke; Michael Shales; Gaelle Mercenne; Lars Pache; Kathy Li; Hilda Hernandez; Gwendolyn M. Jang; et al. (Nat., 2012)

Comparing DNA integration site clusters with scan statistics. - Charles C. Berry; Karen E. Ocwieja; Nirav Malani; Frederic D. Bushman (Bioinform., 2014)

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)

swga: a primer design toolkit for selective whole genome amplification. - Erik L. Clarke; Sesh A. Sundararaman; Stephanie N. Seifert; Frederic D. Bushman; Beatrice H. Hahn; Dustin Brisson (Bioinform., 2017)

grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories. - Louis J. Taylor; Arwa Abbas; Frederic D. Bushman (Bioinform., 2020)