Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin. - Jesse D. Bloom; Matthew J. Glassman (PLoS Comput. Biol., 2009)

Software for the analysis and visualization of deep mutational scanning data. - Jesse D. Bloom (BMC Bioinform., 2015)

alignparse: A Python package for parsing complex features from high-throughput long-read sequencing. - Katharine Crawford; Jesse D. Bloom (J. Open Source Softw., 2019)

dms-view: Interactive visualization tool for deep mutational scanning data. - Sarah Hilton; John Huddleston; Allison Black; Khrystyna North; Adam S. Dingens; Trevor Bedford; Jesse D. Bloom (J. Open Source Softw., 2020)

When two are better than one: Modeling the mechanisms of antibody mixtures. - Tal Einav; Jesse D. Bloom (PLoS Comput. Biol., 2020)

dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets. - William W. Hannon; Jesse D. Bloom (J. Open Source Softw., 2024)