PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data. - Thomas J. Sharpton; Samantha J. Riesenfeld; Steven W. Kembel; Joshua Ladau; James P. O'Dwyer; Jessica L. Green; Jonathan A. Eisen; Katherine S. Pollard (PLoS Comput. Biol., 2011)

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. - James P. O'Dwyer; Steven W. Kembel; Jessica L. Green (PLoS Comput. Biol., 2012)

Emergent neutrality in consumer-resource dynamics. - Rafael D'Andrea; Theo Gibbs; James P. O'Dwyer (PLoS Comput. Biol., 2020)

Stability criteria for the consumption and exchange of essential resources. - Theo Gibbs; Yifan Zhang; Zachary R. Miller; James P. O'Dwyer (PLoS Comput. Biol., 2022)