MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. - Stephen Nayfach; Michael A. Fischbach; Katherine S. Pollard (Bioinform., 2015)

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. - Stephen Nayfach; Patrick H. Bradley; Stacia K. Wyman; Timothy J. Laurent; Alexander G. Williams; Jonathan A. Eisen; Katherine S. Pollard; Thomas J. Sharpton (PLoS Comput. Biol., 2015)

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. - Patrick H. Bradley; Stephen Nayfach; Katherine S. Pollard (PLoS Comput. Biol., 2018)

New insights from uncultivated genomes of the global human gut microbiome. - Stephen Nayfach; Zhou Jason Shi; Rekha Seshadri; Katherine S. Pollard; Nikos Kyrpides (Nat., 2019)

IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses. - Simon Roux; David Páez-Espino; I-Min A. Chen; Krishna Palaniappan; Anna Ratner; Ken Chu; T. B. K. Reddy; Stephen Nayfach; Frederik Schulz; Lee Call; Russell Y. Neches; Tanja Woyke; et al. (Nucleic Acids Res., 2021)

MIDAS2: Metagenomic Intra-species Diversity Analysis System. - Chunyu Zhao; Boris Dimitrov; Miriam Goldman; Stephen Nayfach; Katherine S. Pollard (Bioinform., 2023)

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. - Antonio Pedro Camargo; Stephen Nayfach; I-Min A. Chen; Krishnaveni Palaniappan; Anna Ratner; Ken Chu; Stephan Ritter; T. B. K. Reddy; Supratim Mukherjee; Frederik Schulz; Lee Call; Russell Y. Neches; et al. (Nucleic Acids Res., 2023)