FastGroup: A program to dereplicate libraries of 16S rDNA sequences. - Victor Seguritan; Forest Rohwer (BMC Bioinform., 2001)

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. - Florent E. Angly; Beltran Rodriguez-Brito; David Bangor; Pat McNairnie; Mya Breitbart; Peter Salamon; Ben Felts; James Nulton; Joseph Mahaffy; Forest Rohwer (BMC Bioinform., 2005)

Finding novel genes in bacterial communities isolated from the environment. - Lutz Krause; Naryttza N. Diaz; Daniela Bartels; Robert A. Edwards; Alfred Pühler; Forest Rohwer; Folker Meyer; Jens Stoye (ISMB (Supplement of Bioinformatics), 2006)

An application of statistics to comparative metagenomics. - Beltran Rodriguez-Brito; Forest Rohwer; Robert A. Edwards (BMC Bioinform., 2006)

FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. - Yanan Yu; Mya Breitbart; Pat McNairnie; Forest Rohwer (BMC Bioinform., 2006)

Mathematical Modeling of Cystic Fibrosis Ecology. - Sara Zarei 002; Forest Rohwer; Peter Salamon (BIOCOMP, 2009)

Building an OptIPlanet collaboratory to support microbial metagenomics. - Larry Smarr; Paul Gilna; Philip M. Papadopoulos; Thomas A. DeFanti; Gregory R. Hidley; John C. Wooley; E. Virginia Armbrust; Forest Rohwer; Eric G. Frost (Future Gener. Comput. Syst., 2009)

Deviations from Ultrametricity in Phage Protein Distances. - Chad Wagner; Anna Salamon; Robert A. Edwards; Forest Rohwer; Peter Salamon (Open Syst. Inf. Dyn., 2009)

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes. - Florent E. Angly; Dana Willner; Alejandra Prieto-Davó; Robert A. Edwards; Robert Schmieder; Rebecca Vega-Thurber; Dionysios A. Antonopoulos; Katie Barott; Matthew T. Cottrell; Christelle Desnues; Elizabeth A. Dinsdale; Mike Furlan; et al. (PLoS Comput. Biol., 2009)

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. - Robert Schmieder; Yan Wei Lim; Forest Rohwer; Robert A. Edwards (BMC Bioinform., 2010)

Mucus Distribution Model in a Lung with Cystic Fibrosis. - Sara Zarei 002; Ali Mirtar; Forest Rohwer; Douglas J. Conrad; Rebecca J. Theilmann; Peter Salamon (Comput. Math. Methods Medicine, 2012)

Entropy in the Tangled Nature Model of Evolution. - Ty N. F. Roach; James Nulton; Paolo Sibani; Forest Rohwer; Peter Salamon (Entropy, 2017)

More Stages Decrease Dissipation in Irreversible Step Processes. - Peter Salamon; Bjarne Andresen; James Nulton; Ty N. F. Roach; Forest Rohwer (Entropy, 2023)