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.

All Papers

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

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
bioRxiv. 2024. doi:10.1101/2024.12.17.628970
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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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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
bioRxiv. 2024. doi:10.1101/2024.04.17.589977
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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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