Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate. - Yu Xia 002; Eric A. Franzosa; Mark B. Gerstein (PLoS Comput. Biol., 2009)

Structural Models for Host-Pathogen Protein-Protein Interactions: Assessing Coverage and Bias. - Eric A. Franzosa; Yu Xia 002 (Pacific Symposium on Biocomputing, 2012)

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. - James Kaminski; Molly K. Gibson; Eric A. Franzosa; Nicola Segata; Gautam Dantas; Curtis Huttenhower (PLoS Comput. Biol., 2015)

bioBakery: a meta'omic analysis environment. - Lauren J. McIver; Galeb Abu-Ali; Eric A. Franzosa; Randall Schwager; Xochitl C. Morgan; Levi Waldron; Nicola Segata; Curtis Huttenhower (Bioinform., 2018)

Statistical approaches for differential expression analysis in metatranscriptomics. - Yancong Zhang; Kelsey N. Thompson; Curtis Huttenhower; Eric A. Franzosa (Bioinform., 2021)

A statistical model for describing and simulating microbial community profiles. - Siyuan Ma; Boyu Ren; Himel Mallick; Yo Sup Moon; Emma H. Schwager; Sagun Maharjan; Timothy L. Tickle; Yiren Lu 003; Rachel N. Carmody; Eric A. Franzosa; Lucas Janson; Curtis Huttenhower (PLoS Comput. Biol., 2021)

Multivariable association discovery in population-scale meta-omics studies. - Himel Mallick; Ali Rahnavard; Lauren J. McIver; Siyuan Ma; Yancong Zhang; Long H. Nguyen; Timothy L. Tickle; George Weingart; Boyu Ren; Emma H. Schwager; Suvo Chatterjee; Kelsey N. Thompson; et al. (PLoS Comput. Biol., 2021)

High-sensitivity pattern discovery in large, paired multiomic datasets. - Andrew R. Ghazi; Kathleen Sucipto; Ali Rahnavard; Eric A. Franzosa; Lauren J. McIver; Jason Lloyd-Price; Emma H. Schwager; George Weingart; Yo Sup Moon; Xochitl C. Morgan; Levi Waldron; Curtis Huttenhower (Bioinform., 2022)

Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples. - Moreno Zolfo; Andrea Silverj; Aitor Blanco-Míguez; Paolo Manghi; Omar Rota Stabelli; Vitor Heidrich; Jordan Jensen; Sagun Maharjan; Eric A. Franzosa; Cristina Menni; Alessia Visconti; Federica Pinto; et al. (Zenodo, 2024)