Papers

Papers from the Bloom Lab team. See also Google Scholar for a complete list of publications.

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Key Papers

These papers exemplify key current areas of research in the lab.

Complete definition of how mutations affect antibodies used to prevent RSV

Functional and antigenic landscape of the Nipah virus receptor binding protein

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains

Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance

PLoS Biology. 2024

Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades

Fitness effects of mutations to SARS-CoV-2 proteins

Virus Evolution. 2023

All Papers

Below is a complete list of primary research papers from our group.

Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines
Andrea N Loes, Rosario AL Tarabi, Shuk H Li, Reilly K Atkinson, John Huddleston, Caroline Kikawa, Tachianna Griffiths, Elizabeth M Drapeau, Sook-San Wong, Samuel MS Cheng, Nancy HL Leung, Sarah Cobey, Benjamin J Cowling, Trevor Bedford, Scott E Hensley, Jesse D Bloom
bioRxiv. 2026. doi:10.64898/2026.02.23.707528
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Mutations to the HCoV-229E spike have counterbalancing effects on serum antibody neutralization and receptor binding
Sheri Harari, Rachel T Eguia, Bernadeta Dadonaite, Caelan E Radford, Cameron Stewart, David Veesler, Jesse D Bloom
bioRxiv. 2026. doi:10.64898/2026.02.22.707297
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Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection
Caroline Kikawa, John Huddleston, Sam A Turner, Andrea N Loes, Jiaojiao Liu, Sydney Gang, Tachianna Griffiths, Elizabeth M Drapeau, Benjamin J Cowling, Faith Ho, Nancy HL Leung, Janet A Englund, Kirsten Lacombe, Shinji Watanabe, Hideki Hasegawa, Michael Busch, Mario Lanteri, Mars Stone, Bryan Spencer, Richard A Neher, Derek J Smith, Trevor Bedford, Scott E Hensley, Jesse D Bloom
bioRxiv. 2026. doi:10.64898/2026.02.18.706711
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Complete definition of how mutations affect antibodies used to prevent RSV
Cassandra AL Simonich, Teagan E McMahon, Lucas Kampman, Helen Y Chu, Jesse D Bloom
bioRxiv. 2026. doi:10.64898/2026.02.12.705519
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Functional and antigenic constraints on the Nipah virus fusion protein
Brendan B Larsen, Sheri Harari, Risako Gen, Cameron Stewart, David Veesler, Jesse D Bloom
Proc Natl Acad Sci USA. 2026. doi:10.1073/pnas.25295051
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Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures
Jenny J Ahn, Timothy C Yu, Bernadeta Dadonaite, Caelan E Radford, Jesse D Bloom
bioRxiv. 2026. doi:10.64898/2026.01.05.697808
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Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza hemagglutinin
Timothy C Yu, Caroline Kikawa, Bernadeta Dadonaite, Andrea N Loes, Janet A Englund, Jesse D Bloom
Nature Ecology & Evolution. 2025. doi:10.1038/s41559-025-02895-1
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Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025
Caroline Kikawa, John Huddleston, Andrea N Loes, Sam A Turner, Jover Lee, Ian G Barr, Benjamin J Cowling, Janet A Englund, Alexander L Greninger, Ruth Harvey, Hideki Hasegawa, Faith Ho, Kirsten Lacombe, Nancy HL Leung, Nicola S Lewis, Heidi Peck, Shinji Watanabe, Derek J Smith, Trevor Bedford, Jesse D Bloom
Virus Evolution. 2025. doi:10.1093/ve/veaf086
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Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants
Bernadeta Dadonaite, Sheri Harari, Brendan B Larsen, Lucas Kampman, Alex Harteloo, Anna Elias-Warren, Helen Y Chu, Jesse D Bloom
Journal of Virology. 2025. doi:10.1128/jvi.01423-25
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Determinants of human versus mosquito cell entry by the Chikungunya virus envelope proteins
Xiaohui Ju, William W Hannon, Tomasz Kaszuba, Caelan E Radford, Brendan B Larsen, Samantha S Nelson, Christopher A Nelson, Israel Baltazar-Perez, Ofer Zimmerman, Daved H Fremont, Michael S Diamond, Jesse D Bloom
bioRxiv. 2025. doi:10.1101/2025.08.25.672233
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RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera
Cassandra AL Simonich, Teagan A McMahon, Xiaohui Ju, Timothy C Yu, Natalie Brunette, Terry Stevens-Ayers, Michael J Boeckh, Neil P King, Alexander L Greninger, Jesse D Bloom
Journal of Virology. 2025. doi:10.1128/jvi.00531-25
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Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations
Arjun K Aditham, Caelan E Radford, Caleb R Carr, Naveen Jasti, Neil P King, Jesse D Bloom
Cell Host & Microbe. 2025. doi:10.1016/j.chom.2025.04.018
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Comprehensive maps of escape mutations from antibodies 10-1074 and 3BNC117 for Envs from two divergent HIV strains
Caelan E Radford, Jesse D Bloom
Journal of Virology. 2025. doi:10.1128/jvi.00195-25
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SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individuals
Bernadeta Dadonaite, Allison R Burrell, Jenni Logue, Helen Y Chu, Daniel C Payne, David B Haslam, Mary A Staat, Jesse D Bloom
Journal of Virology. 2025. doi:10.1128/jvi.00109-25
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Functional and antigenic landscape of the Nipah virus receptor binding protein
Brendan B Larsen, Teagan McMahon, Jack T Brown, Zhaoqian Wang, Caelan E Radford, James E Crowe, David Veesler, Jesse D Bloom
Cell. 2025. doi:10.1016/j.cell.2025.02.030
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High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains
Caroline Kikawa, Andrea N Loes, John Huddleston, Marlin D Figgins, Philippa Steinberg, Tachianna Griffiths, Elizabeth M Drapeau, Heidi Peck, Ian G Barr, Janet A Englund, Scott E Hensley, Trevor Bedford, Jesse D Bloom
eLife. 2025. doi:10.7554/eLife.106811.4
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Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance
Bernadeta Dadonaite, Jenny J Ahn, Jordan T Ort, Jin Yu, Colleen Furey, Annie Dosey, William W Hannon, Amy Vincent Baker, Richard J Webby, Neil P King, Yan Liu, Scott E Hensley, Thomas P Peacock, Louise H Moncla, Jesse D Bloom
PLoS Biology. 2024. doi:10.1371/journal.pbio.3002916
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High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains
Andrea N Loes, Rosario Araceli L Tarabi, John Huddleston, Lisa Touyon, Sook San Wong, Samuel MS Cheng, Nancy HL Leung, William W Hannon, Trevor Bedford, Sarah Cobey, Benjamin J Cowling, Jesse D Bloom
Journal of Virology. 2024. doi:10.1128/jvi.00689-24
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Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Nguyen Van Vinh Chau, Andrea N Loes, John Huddleston, Timothy C Yu, Mai Quynh Le, Nguyen TD Nhat, Nguyen Thi Le Thanh, Alexander L Greninger, Helen Y Chu, Janet A Englund, Trevor Bedford, Frederick A Matsen IV, Maciej F Boni, Jesse D Bloom
Cell Host & Microbe. 2024. doi:10.1016/j.chom.2024.06.015
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dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets
William W Hannon, Jesse D Bloom
Journal of Open Source Software. 2024. doi:10.21105/joss.06129
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Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex
Caleb R Carr*, Katharine HD Crawford*, Michael Murphy, Jared G Galloway, Hugh K Haddox, Frederick A Matsen, Kristian G Andersen, Neil P King, Jesse D Bloom
Immunity. 2024. doi:10.1016/j.immuni.2024.06.013
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Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades
Bernadeta Dadonaite, Jack Brown, Teagan E McMahon, Ariana G Farrell, Marlin D Figgins, Daniel Asarnow, Cameron Stewart, Jimin Lee, Jenni Logue, Trevor Bedford, Ben Murrell, Helen Y Chu, David Veesler, Jesse D Bloom
Nature. 2024. doi:10.1038/s41586-024-07636-1
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Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market
Jesse D Bloom
Virus Evolution. 2024. doi:10.1093/ve/vead089
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The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies
Caroline Kikawa, Catiana H Cartwright-Acar, Jackson B Stuart, Maya Contreras, Lisa M Levoir, Matthew J Evans, Jesse D Bloom, Leslie Goo
Journal of Virology. 2023. doi:10.1128/jvi.01414-23
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Fitness effects of mutations to SARS-CoV-2 proteins
Jesse D Bloom, Richard A Neher
Virus Evolution. 2023. doi:10.1093/ve/veae026
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Influenza virus transcription and progeny production are poorly correlated in single cells
David J Bacsik, Bernadeta Dadonaite, Andrew Butler, Allison J Greaney, Nicholas S Heaton, Jesse D Bloom
eLife. 2023. doi:10.7554/eLife.86852.2
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Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning
Caelan E Radford, Philipp Schommers, Lutz Gieselmann, Katharine HD Crawford, Bernadeta Dadonaite, Timothy C Yu, Adam S Dingens, Julie Overbaugh, Florian Klein, Jesse D Bloom
Cell Host & Microbe. 2023. doi:10.1016/j.chom.2023.05.025
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Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market
Jesse D Bloom
Virus Evolution. 2023. doi:10.1093/ve/vead050
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Evolution of the SARS-CoV-2 mutational spectrum
Jesse D Bloom, Annabel C Beichman, Richard A Neher, Kelley Harris
Molecular Biology and Evolution. 2023. doi:10.1093/molbev/msad085
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A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike
Bernadeta Dadonaite*, Katharine HD Crawford*, Caelan E Radford*, Ariana G Farrell, C Yu Timothy, William W Hannon, Panpan Zhou, Raiees Andrabi, Dennis R Burton, Lihong Liu, David D Ho, Helen Y Chu, Richard A Neher, Jesse D Bloom
Cell. 2023. doi:10.1016/j.cell.2023.02.001
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Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains
Tyler N Starr*, Allison J Greaney*, Cameron M Stewart, Alexandra C Walls, William W Hannon, David Veesler, Jesse D Bloom
PLoS pathogens. 2022. doi:10.1371/journal.ppat.1010951
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Receptor-binding domain (RBD) antibodies contribute more to SARS-CoV-2 neutralization when target cells express high levels of ACE2
Ariana Ghez Farrell*, Bernadeta Dadonaite*, Allison J Greaney, Rachel Eguia, Andrea N Loes, Nicholas M Franko, Jennifer Logue, Juan Manuel Carreño, Anass Abbad, Helen Y Chu, Kenneth A Matreyek, Jesse D Bloom
Viruses. 2022. doi:10.3390/v14092061
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Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution
Tyler N Starr*, Allison J Greaney*, William W Hannon, Andrea N Loes, Kevin Hauser, Josh R Dillen, Elena Ferri, Ariana Ghez Farrell, Bernadeta Dadonaite, Matthew McCallum, Kenneth A Matreyek, Davide Corti, David Veesler, Gyorgy Snell, Jesse D Bloom
Science. 2022. doi:10.1126/science.abo7896
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Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat
William W Hannon, Pavitra Roychoudhury, Hong Xie, Lasata Shrestha, Amin Addetia, Keith R Jerome, Alexander L Greninger, Jesse D Bloom
Virus Evolution. 2022. doi:10.1093/ve/veac052
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A biophysical model of viral escape from polyclonal antibodies
Timothy C Yu, Zorian T Thornton, William W Hannon, William S DeWitt, Caelan E Radford, Frederick A Matsen IV, Jesse D Bloom
Virus Evolution. 2022. doi:10.1093/ve/veac110
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The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes
Allison J Greaney, Rachel T Eguia, Tyler N Starr, Khadija Khan, Nicholas Franko, Jennifer K Logue, Sandra M Lord, Cate Speake, Helen Y Chu, Alex Sigal, Jesse D Bloom
PLoS Pathogens. 2022. doi:10.1371/journal.ppat.1010592
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ACE2 binding is an ancestral and evolvable trait of sarbecoviruses
Tyler N Starr, Samantha K Zepeda, Alexandra C Walls, Allison J Greaney, Sergey Alkhovsky, David Veesler, Jesse D Bloom
Nature. 2022. doi:10.1038/s41586-022-04464-z
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A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy
Allison J Greaney, Tyler N Starr, Rachel T Eguia, Andrea N Loes, Khadija Khan, Farina Karim, Sandile Cele, John E Bowen, Jennifer K Logue, Davide Corti, David Veesler, Helen Y Chu, Alex Sigal, Jesse D Bloom
PLoS pathogens. 2022. doi:10.1371/journal.ppat.1010248
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Dynamics of infection-elicited SARS-CoV-2 antibodies in children over time
Lauren E Gentles, Leanne Kehoe, Katharine HD Crawford, Kirsten Lacombe, Jane Dickerson, Caitlin Wolf, Joanna Yuan, Susanna Schuler, John T Watson, Sankan Nyanseor, Melissa Briggs-Hagen, Sharon Saydah, Claire M Midgley, Kimberly Pringle, Helen Chu, Jesse D Bloom, Janet A Englund
medRxiv. 2022. doi:10.1101/2022.01.14.22269235
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An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain
Allison J Greaney, Tyler N Starr, Jesse D Bloom
Virus Evolution. 2022. doi:10.1093/ve/veac021
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Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic
Jesse D Bloom
mBio. 2021. doi:10.1093/molbev/msab246
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SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape
Tyler N Starr, Nadine Czudnochowski, Zhuoming Liu, Fabrizia Zatta, Young-Jun Park, Amin Addetia, Dora Pinto, Martina Beltramello, Patrick Hernandez, Allison J Greaney, Roberta Marzi, William G Glass, Ivy Zhang, Adam S Dingens, John E Bowen, M Alejandra Tortorici, Alexandra C Walls, Jason A Wojcechowskyj, Anna De Marco, Laura E Rosen, Jiayi Zhou, Martin Montiel-Ruiz, Hannah Kaiser, Josh R Dillen, Heather Tucker, Jessica Bassi, Chiara Silacci-Fregni, Michael P Housley, Julia di Iulio, Gloria Lombardo, Maria Agostini, Nicole Sprugasci, Katja Culap, Stefano Jaconi, Marcel Meury, Exequiel Dellota Jr, Rana Abdelnabi, Shi-Yan Caroline Foo, Elisabetta Cameroni, Spencer Stumpf, Tristan I Croll, Jay C Nix, Colin Havenar-Daughton, Luca Piccoli, Fabio Benigni, Johan Neyts, Amalio Telenti, Florian A Lempp, Matteo S Pizzuto, John D Chodera, Christy M Hebner, Herbert W Virgin, Sean PJ Whelan, David Veesler, Davide Corti, Jesse D Bloom, Gyorgy Snell
Nature. 2021. doi:10.1038/s41586-021-03807-6
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Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
Allison J Greaney, Tyler N Starr, Christopher O Barnes, Yiska Weisblum, Fabian Schmidt, Marina Caskey, Christian Gaebler, Alice Cho, Marianna Agudelo, Shlomo Finkin, Zijun Wang, Daniel Poston, Frauke Muecksch, Theodora Hatziioannou, Paul D Bieniasz, Davide F Robbiani, Michel C Nussenzweig, Pamela J Bjorkman, Jesse D Bloom
Nature Communications. 2021. doi:10.1038/s41467-021-24435-8
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Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection
Allison J Greaney, Andrea N Loes, Lauren E Gentles, Katharine HD Crawford, Tyler N Starr, Keara D Malone, Helen Y Chu, Jesse D Bloom
Science translational medicine. 2021. doi:10.1126/scitranslmed.abi9915
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Comprehensive profiling of mutations to influenza virus PB2 that confer resistance to the cap-binding inhibitor pimodivir
Shirleen YQ Soh, Keara D Malone, Rachel T Eguia, Jesse D Bloom
Viruses. 2021. doi:10.3390/v13071196
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Co-dominant neutralizing epitopes make anti-measles immunity resistant to viral evolution
Allison J Greaney, Frances C Welsh, Jesse D Bloom
Cell Reports Medicine. 2021. doi:10.1016/j.xcrm.2021.100257
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Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016
Tyler N Starr, Allison J Greaney, Adam S Dingens, Jesse D Bloom
Cell Reports Medicine. 2021. doi:10.1016/j.xcrm.2021.100255
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A human coronavirus evolves antigenically to escape antibody immunity
Rachel T Eguia, Katharine HD Crawford, Terry Stevens-Ayers, Laurel Kelnhofer-Millevolte, Alexander L Greninger, Janet A Englund, Michael J Boeckh, Jesse D Bloom
PLoS pathogens. 2021. doi:10.1371/journal.ppat.1009453
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Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies
Allison J Greaney, Andrea N Loes, Katharine HD Crawford, Tyler N Starr, Keara D Malone, Helen Y Chu, Jesse D Bloom
Cell host & microbe. 2021. doi:10.1016/j.chom.2021.02.003
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Prospective mapping of viral mutations that escape antibodies used to treat COVID-19
Tyler N Starr*, Allison J Greaney*, Amin Addetia, William W Hannon, Manish C Choudhary, Adam S Dingens, Jonathan Z Li, Jesse D Bloom
Science. 2021. doi:10.1126/science.abf9302
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Dynamics of neutralizing antibody titers in the months after severe acute respiratory syndrome coronavirus 2 infection
Katharine HD Crawford, Adam S Dingens, Rachel Eguia, Caitlin R Wolf, Naomi Wilcox, Jennifer K Logue, Kiel Shuey, Amanda M Casto, Brooke Fiala, Samuel Wrenn, Deleah Pettie, Neil P King, Alexander L Greninger, Helen Y Chu, Jesse D Bloom
The Journal of infectious diseases. 2021. doi:10.1093/infdis/jiaa618
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High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination
Adam S Dingens, Payal Pratap, Keara Malone, Sarah K Hilton, Thomas Ketas, Christopher A Cottrell, Julie Overbaugh, John P Moore, PJ Klasse, Andrew B Ward, Jesse D Bloom
eLife. 2021. doi:10.7554/eLife.64281
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Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition
Allison J Greaney*, Tyler N Starr*, Pavlo Gilchuk, Seth J Zost, Elad Binshtein, Andrea N Loes, Sarah K Hilton, John Huddleston, Rachel Eguia, Katharine HD Crawford, Adam S Dingens, Rachel S Nargi, Rachel E Sutton, Naveenchandra Suryadevara, Paul W Rothlauf, Zhuoming Liu, Sean PJ Whelan, Robert H Carnahan, James E Crowe, Jesse D Bloom
Cell host & microbe. 2021. doi:10.1016/j.chom.2020.11.007
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Attenuated influenza virions expressing the SARS-CoV-2 receptor-binding domain induce neutralizing antibodies in mice
Andrea N Loes, Lauren E Gentles, Allison J Greaney, Katharine HD Crawford, Jesse D Bloom
Viruses. 2020. doi:10.3390/v12090987
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Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding
Tyler N Starr*, Allison J Greaney*, Sarah K Hilton, Daniel Ellis, Katharine HD Crawford, Adam S Dingens, Mary Jane Navarro, John E Bowen, Alejandra M Tortorici, Alexandra C Walls, Neil P King, David Veesler, Jesse D Bloom
Cell. 2020. doi:10.1016/j.cell.2020.08.012
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Serological identification of SARS-CoV-2 infections among children visiting a hospital during the initial Seattle outbreak
Adam S Dingens, Katharine HD Crawford, Amanda Adler, Sarah L Steele, Kirsten Lacombe, Rachel Eguia, Fatima Amanat, Alexandra C Walls, Caitlin R Wolf, Michael Murphy, Deleah Pettie, Lauren Carter, Xuan Qin, Neil P King, David Veesler, Florian Krammer, Jane A Dickerson, Helen Y Chu, Janet A Englund, Jesse D Bloom
Nature communications. 2020. doi:10.1038/s41467-020-18178-1
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dms-view: Interactive visualization tool for deep mutational scanning data
Sarah K Hilton*, John Huddleston*, Allison Black, Khrystyna North, Adam S Dingens, Trevor Bedford, Jesse D Bloom
JOSS. 2020. doi:10.21105/joss.02353
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Antibody neutralization of an influenza virus that uses neuraminidase for receptor binding
Lauren E Gentles, Hongquan Wan, Maryna C Eichelberger, Jesse D Bloom
Viruses. 2020. doi:10.3390/v12060597
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Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 spike protein for neutralization assays
Katharine HD Crawford, Rachel Eguia, Adam S Dingens, Andrea N Loes, Keara D Malone, Caitlin R Wolf, Helen Y Chu, M Alejandra Tortorici, David Veesler, Michael Murphy, Deleah Pettie, Neil P King, Alejandro B Balazs, Jesse D Bloom
Viruses. 2020. doi:10.3390/v12050513
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When two are better than one: Modeling the mechanisms of antibody mixtures
Tal Einav, Jesse D Bloom
PLoS computational biology. 2020. doi:10.1371/journal.pcbi.1007830
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Identification of HIV-1 envelope mutations that enhance entry using macaque CD4 and CCR5
Jeremy I Roop, Noah A Cassidy, Adam S Dingens, Jesse D Bloom, Julie Overbaugh
Viruses. 2020. doi:10.3390/v12020241
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Linking influenza virus evolution within and between human hosts
Katherine S Xue, Jesse D Bloom
Virus evolution. 2020. doi:10.1093/ve/veaa010
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Reconciling disparate estimates of viral genetic diversity during human influenza infections
Katherine S Xue, Jesse D Bloom
Nature genetics. 2019. doi:10.1038/s41588-019-0349-3
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Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin
Juhye M Lee, Rachel Eguia, Seth J Zost, Saket Choudhary, Patrick C Wilson, Trevor Bedford, Terry Stevens-Ayers, Michael Boeckh, Aeron C Hurt, Seema S Lakdawala, Scott E Hensley, Jesse D Bloom
eLife. 2019. doi:10.7554/eLife.49324
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Single-cell virus sequencing of influenza infections that trigger innate immunity
Alistair B Russell, Elizaveta Elshina, Jacob R Kowalsky, Aartjan JW Te Velthuis, Jesse D Bloom
Journal of virology. 2019. doi:10.1128/jvi.00500-19
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Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide
Adam S Dingens, Dana Arenz, Julie Overbaugh, Jesse D Bloom
Viruses. 2019. doi:10.3390/v11050439
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Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans
YQ Shirleen Soh, Louise H Moncla, Rachel Eguia, Trevor Bedford, Jesse D Bloom
eLife. 2019. doi:10.7554/eLife.45079
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An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies distinguishes functional and structural epitopes
Adam S Dingens, Dana Arenz, Haidyn Weight, Julie Overbaugh, Jesse D Bloom
Immunity. 2019. doi:10.1016/j.immuni.2018.12.017
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alignparse: A Python package for parsing complex features from high-throughput long-read sequencing
Katharine HD Crawford, Jesse D Bloom
JOSS. 2019. doi:10.21105/joss.01915
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Comprehensive profiling of translation initiation in influenza virus infected cells
Heather M Machkovech, Jesse D Bloom, Arvind R Subramaniam
PLoS pathogens. 2019. doi:10.1371/journal.ppat.1007518
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Within-host evolution of human influenza virus
Katherine S Xue, Louise H Moncla, Trevor Bedford, Jesse D Bloom
Trends in Microbiology. 2018. doi:10.1016/j.tim.2018.02.007
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Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants
Juhye M Lee, John Huddleston, Michael B Doud, Kathryn A Hooper, Nicholas C Wu, Trevor Bedford, Jesse D Bloom
PNAS. 2018. doi:10.1073/pnas.1806133115
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Complete functional mapping of infection-and vaccine-elicited antibodies against the fusion peptide of HIV
Adam S Dingens, Priyamvada Acharya, Hugh K Haddox, Reda Rawi, Kai Xu, Gwo-Yu Chuang, Hui Wei, Baoshan Zhang, John R Mascola, Bridget Carragher, Clinton S Potter, Julie Overbaugh, Peter D Kwong, Jesse D Bloom
PLoS pathogens. 2018. doi:10.1371/journal.ppat.1007159
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Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence
Sarah K Hilton, Jesse D Bloom
Virus evolution. 2018. doi:10.1093/ve/vey033
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How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin
Michael B Doud*, Juhye M Lee*, Jesse D Bloom
Nature communications. 2018. doi:10.1038/s41467-018-03665-3
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Mapping mutational effects along the evolutionary landscape of HIV envelope
Hugh K Haddox*, Adam S Dingens*, Sarah K Hilton, Julie Overbaugh, Jesse D Bloom
eLife. 2018. doi:10.7554/eLife.34420
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Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples
Katherine S Xue, Alexander L Greninger, Ailyn Pérez-Osorio, Jesse D Bloom
MSphere. 2018. doi:10.1128/mspheredirect.00552-17
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Extreme heterogeneity of influenza virus infection in single cells
Alistair B Russell, Cole Trapnell, Jesse D Bloom
eLife. 2018. doi:10.7554/eLife.32303
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Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models
Jesse D Bloom
Biology direct. 2017. doi:10.1186/s13062-016-0172-z
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phydms: Software for phylogenetic analyses informed by deep mutational scanning
Sarah K Hilton, Michael B Doud, Jesse D Bloom
PeerJ. 2017. doi:10.7717/peerj.3657
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Parallel evolution of influenza across multiple spatiotemporal scales
Katherine S Xue, Terry Stevens-Ayers, Angela P Campbell, Janet A Englund, Steven A Pergam, Michael Boeckh, Jesse D Bloom
eLife. 2017. doi:10.7554/eLife.26875.001
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Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody
Adam S Dingens, Hugh K Haddox, Julie Overbaugh, Jesse D Bloom
Cell host & microbe. 2017. doi:10.1016/j.chom.2017.05.003
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Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA
Orr Ashenberg, Jai Padmakumar, Michael B Doud, Jesse D Bloom
PLoS pathogens. 2017. doi:10.1371/journal.ppat.1006288
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Complete mapping of viral escape from neutralizing antibodies
Michael B Doud, Scott E Hensley, Jesse D Bloom
PLoS pathogens. 2017. doi:10.1371/journal.ppat.1006271
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Experimental estimation of the effects of all amino-acid mutations to HIV’s envelope protein on viral replication in cell culture
Hugh K Haddox, Adam S Dingens, Jesse D Bloom
PLoS pathogens. 2016. doi:10.1371/journal.ppat.1006114
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Accurate measurement of the effects of all amino-acid mutations on influenza hemagglutinin
Michael B Doud, Jesse D Bloom
Viruses. 2016. doi:10.3390/v8060155
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Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture
Katherine S Xue, Kathryn A Hooper, Anja R Ollodart, Adam S Dingens, Jesse D Bloom
eLife. 2016. doi:10.7554/eLife.13974.001
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Software for the analysis and visualization of deep mutational scanning data
Jesse D Bloom
BMC bioinformatics. 2015. doi:10.1186/s12859-015-0590-4
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Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages
Heather M Machkovech, Trevor Bedford, Marc A Suchard, Jesse D Bloom
Journal of virology. 2015. doi:10.1128/jvi.01571-15
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Site-specific amino acid preferences are mostly conserved in two closely related protein homologs
Michael B Doud, Orr Ashenberg, Jesse D Bloom
Molecular biology and evolution. 2015. doi:10.1093/molbev/msv167
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Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice
Kathryn A Hooper, James E Crowe Jr, Jesse D Bloom
Journal of virology. 2015. doi:10.1128/jvi.00012-15
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An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs
Jesse D Bloom
Molecular biology and evolution. 2014. doi:10.1093/molbev/msu220
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An experimentally determined evolutionary model dramatically improves phylogenetic fit
Jesse D Bloom
Molecular Biology and Evolution. 2014. doi:10.1093/molbev/msu173
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The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
Bargavi Thyagarajan, Jesse D Bloom
eLife. 2014. doi:10.7554/eLife.03300
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Epistatically interacting substitutions are enriched during adaptive protein evolution
Lizhi Ian Gong, Jesse D Bloom
PLoS genetics. 2014. doi:10.1371/journal.pgen.1004328
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Mutational effects on stability are largely conserved during protein evolution
Orr Ashenberg, Lizhi Ian Gong, Jesse D Bloom
PNAS. 2013. doi:10.1073/pnas.1314781111
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A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein
Kathryn A Hooper, Jesse D Bloom
Journal of virology. 2013. doi:10.1128/jvi.01889-13
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Stability-mediated epistasis constrains the evolution of an influenza protein
Lizhi Ian Gong, Marc A Suchard, Jesse D Bloom
Journal of virology. 2013. doi:10.7554/eLife.00631.001
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