Publications

All publications

For a complete list of publications, see Jesse Bloom's Google Scholar profile or NCBI bibliography.


Primary publications (Bloom lab is lead or co-lead)

2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2011 2010 | 2009 | 2007 | 2006 | 2005 | 2004 | 2003

2021

Jesse D Bloom. Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic. bioRxiv (2021)

Tyler N Starr, Samantha K Zepeda, Alexandra C Walls, Allison J Greaney, David Veesler, Jesse D Bloom. ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. bioRxiv (2021)

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. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. bioRxiv (2021)

Jesse D Bloom, Yujia Alina Chan, Ralph S Baric, Pamela J Bjorkman, Sarah Cobey, Benjamin E Deverman, David N Fisman, Ravindra Gupta, Akiko Iwasaki, Marc Lipsitch, Ruslan Medzhitov, Richard A Neher, Rasmus Nielsen, Nick Patterson, Tim Stearns, Erik van Nimwegen, Michael Worobey, David A Relman. Investigate the origins of COVID-19. Science. 373(6543):694-694 (2021)

Allison J Greaney, Andrea N Loes, Lauren E Gentles, Katharine HD Crawford, Tyler N Starr, Keara D Malone, Helen Y Chu, Jesse D Bloom. Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection. Science Translational Medicine. 13(600), (2021)

YQ Soh, Keara D Malone, Rachel T Eguia, Jesse D Bloom. Comprehensive profiling of mutations to influenza virus PB2 that confer resistance to the cap-binding inhibitor pimodivir. Viruses. 13(7):1196 (2021)

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. Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies. Nature Communications 12, 4196 (2021)

Allison J. Greaney, Frances C. Welsh, Jesse D. Bloom. Co-dominant neutralizing epitopes make anti-measles immunity resistant to viral evolution. Cell Reports Medicine, 2(4), (2021)

Rachel T. Eguia, Katharine H. D. Crawford, Terry Stevens-Ayers, Laurel Kelnhofer-Millevolte, Alexander L. Greninger, Janet A. Englund, Michael J. Boeckh, Jesse D. Bloom. A human coronavirus evolves antigenically to escape antibody immunity. PLoS Pathog 17(4): e1009453, (2021)

Tyler N. Starr, Allison J. Greaney, Adam S. Dingens, Jesse D. Bloom. Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Cell Reports Medicine. 2(4) (2021)

Allison J. Greaney, Andrea N. Loes, Lauren E. Gentles, Katharine H.D. Crawford, Tyler N. Starr, Keara D. Malone, Helen Y. Chu, Jesse D. Bloom. The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD. bioRxiv (2021)

Allison J. Greaney, Tyler N. Starr, Christopher O. Barnes, Yiska Weisblum, Fabian Schmidt, Marina Caskey, Christian Gaebler, 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. Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies. bioRxiv (2021)

Tyler N. Starr, Allison J. Greaney, Amin Addetia, William W. Hannon, Manish C. Choudhary, Adam S. Dingens, Jonathan Z. Li, Jesse D. Bloom. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. Science. 371(6531):850-854 (2021)

Allison J. Greaney, Andrea N. Loes, Katharine H.D. Crawford, Tyler N. Starr, Keara D. Malone, Helen Y. Chu, Jesse D. Bloom. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe. 29(3):322-324 (2021)

Katharine H.D. 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. Dynamics of Neutralizing Antibody Titers in the Months After Severe Acute Respiratory Syndrome Coronavirus 2 InfectionJ Infect Dis. 223(2):197-205 (2021)

Adam S. Dingens, Payal Pratap, Keara D. Malone, Sarah K. Hilton, Thomas Ketas, Christopher A. Cottrell, Julie M. Overbaugh, John P. Moore, P.J. Klasse, Andrew B. Ward, Jesse D. Bloom. High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination. eLife10:e64281 (2021) 

Allison J. Greaney, Tyler N. Starr, Pavlo Gilchuk, Seth J. Zost, Elad Binshtein, Andrea N. Loes, Sarah K. Hilton, John Huddleston, Rachel Eguia, Katharine H.D. Crawford, Adam S. Dingens, Rachel S. Nargi, Rachel E. Sutton, Naveenchandra Suryadevara, Paul W. Rothlauf, Zhuoming Liu, Sean P.J. Whelan, Robert H. Carnahan, James E Crowe Jr., Jesse D. Bloom.  Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition. Cell Host Microbe. 29(1):44-57.e9 (2021)

2020

Tyler N. Starr, Allison J. Greaney, Sarah K. Hilton, Katharine H.D. Crawford, Mary Jane Navarro, John E. Bowen, M. Alejandra Tortorici, Alexandra C. Walls, David Veesler, Jesse D. Bloom. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell. 182(5):1295-1310.e20 (2020)

Adam S. Dingens, Katharine H.D. 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, Helen Y. Chu, Janet A. Englund, Jesse D. Bloom. Serological identification of SARS-CoV-2 infections among children visiting a hospital during the initial Seattle outbreak. Nat Commun. 11(1):1-6 (2020) 

Andrea N. Loes, Lauren E. Gentles, Allison J. Greaney, Katharine H.D. Crawford, Jesse D. Bloom. Attenuated Influenza Virions Expressing the SARS- CoV-2 Receptor-Binding Domain Induce Neutralizing Antibodies in Mice. Viruses. 12(9):E987 (2020)

Sarah K. Hilton, John L. Huddleston, Allison Black, Khrystyna North, Adam S. Dingens, Trevor Bedford, Jesse D. Bloom. dms-view: Interactive visualization tool for deep mutational scanning data. J Open Source Softw. 5(52):2353 (2020)

Tal Einav, Lauren E. Gentles, Jesse D. Bloom. SnapShot: Influenza by the Numbers. Cell. 182(2):532-532.e1 (2020)

Adam S. Dingens, Katharine H.D. 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, Helen Y. Chu, Janet A. Englund, Jesse D. Bloom. Serological identification of SARS-CoV-2 infections among children visiting a hospital during the initial Seattle outbreak medRxiv. (2020) 

Lauren E. Gentles, Hongquan Wan, Maryna C. Eichelberger, Jesse D. Bloom. Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Viruses. 12(6):597 (2020)

Tal Einav and Jesse D. Bloom. When two are better than one: Modeling the mechanisms of antibody mixturesPLoS Comput Biol. 4;16(5):e1007830 (2020)

Katharine H.D. 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. Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays. Viruses. 12(5):513 (2020) 

Katherine S. Xue and Jesse D. BloomLinking influenza virus evolution within and between human hosts. Virus Evol. 6(1):veaa010 (2020)

2019

Katharine H.D. Crawford and Jesse D. Bloom. alignparse: A Python package for parsing complex features from high-throughput long-read sequencing. J Open Source Softw. 4:1915 (2019) | PDF

Marion Sourisseau*, Daniel J. P. Lawrence*, Megan C. Schwarz, Carina H. Storrs, Ethan C. Veit, Jesse D. Bloom#, and Matthew J. Evans#. Deep mutational scanning comprehensive maps how Zika virus mutations affect viral growth and antibody escape. J Virol. 93:e01291-19 (2019) | PDF

Juhye M. Lee, Rachel Eguia, Seth J. Zost, Saket Choudhary, Patrick C. Wilson, Trevor Bedford, Terry Stevens-Ayers, Michael Boeckh, Aeron Hurt, Seema S. Lakdawala, Scott E. Hensley, and Jesse D. Bloom. Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin. eLife. 8:e49324 (2019) | PDF

Alistair B. Russell, Elizaveta Elshina, Jacob Kowalsky, Aartjan J. W. te Velthuis, and Jesse D. Bloom. Single-cell virus sequencing of influenza infections that trigger innate immunity. J Virol. 93:e00500-19 (2019) | PDF

Y. Q. Shirleen Soh, Louise H. Moncla, Rachel Eguia, Trevor Bedford, and Jesse D. Bloom. Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans. eLife. 8:e45079 (2019) | PDF

Katherine S. Xue and Jesse D. Bloom. Reconciling disparate estimates of viral genetic diversity during human influenza infections. Nat Genet. 51:1298-1301 (2019) | PDF

Adam S. Dingens, Dana Arenz, Haidyn Weight, Julie Overbaugh#, and Jesse D. Bloom#An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies distinguishes functional and structural epitopes. Immunity. 50:520-532 (2019) | PDF

Adam S. Dingens, Dana Arenz, Julie Overbaugh#, and Jesse D. Bloom#. Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide. Viruses. 15:E439 (2019).

Heather M. Machkovech, Jesse D. Bloom#, Arvind R. Subramaniam#. Comprehensive profiling of translation initiation in influenza virus infected cells. PLoS Pathog. 15:e1007518 (2019) | PDF

2018

Adam S. Dingens*, Priyamvada Acharya*, Hugh K. Haddox, Reda Rawi, Kai Xu, Gwo-Yu Chuang, Hui Wei, Baoshan Zyang, John R. Mascola, Bridget Carragher, Clinton S. Potter, Julie Overbaugh, Peter D. Kwong#, and Jesse D. Bloom#Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV. PLoS Pathog. 14:e1007159 (2018) | PDF

Sarah K. Hilton and Jesse D. Bloom. Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence. Virus Evol. 4:vey033 (2018) | PDF

Juhye M. Lee*, John Huddleston*, Michael B. Doud, Kathryn A. Hooper, Nicholas C. Wu, Trevor Bedford#, and Jesse D. Bloom#Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. PNAS. 115:E8276-E8285 (2018) | PDF

Hugh K. Haddox*, Adam S. Dingens*, Sarah K. Hilton, Julie Overbaugh, and Jesse D. Bloom. Mapping mutational effects along the evolutionary landscape of HIV envelope. eLife. 7:e34420 (2018) | PDF

Michael B. Doud*, Juhye M. Lee*, and Jesse D. Bloom. How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin. Nat Commun. 9:1386 (2018) | PDF

Katherine S. Xue, Louise H. Moncla, Trevor Bedford, and Jesse D. Bloom. Within-host evolution of human influenza virus. Trends Microbiol. 26:781-793 (2018) | PDF

Alistair B. Russell, Cole Trapnell, and Jesse D. Bloom. Extreme heterogeneity of influenza virus infection in single cells. eLife. 7:e32303 (2018) | PDF

Katherine S. Xue, Alex L. Greninger, Ailyn Perez-Osorio, and Jesse D. Bloom. Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples. mSphere. 3:e00552-17 (2018) | PDF

2017

Katherine S. Xue, Terry Stevens-Ayers, Angela P. Campbell, Janet A. Englund, Steven A. Pergam, Michael Boeckh, and Jesse D. Bloom. Parallel evolution of influenza across multiple spatiotemporal scales. eLife. 6:e26875 (2017) | PDF

Sarah K. Hilton, Michael B. Doud, and Jesse D. Bloom. phydms: Software for phylogenetic analyses informed by deep mutational scanning. PeerJ. 5:e3657 (2017) | PDF

Adam S. Dingens, Hugh K. Haddox, Julie Overbaugh#, and Jesse D. Bloom#. Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody. Cell Host Microbe. 21:777-787 (2017) | PDF

Orr Ashenberg, Jai Padmakumar, Michael B. Doud, and Jesse D. Bloom. Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA. PLoS Pathog. 13:e1006288 (2017) | PDF

Michael B. Doud, Scott E. Hensley, and Jesse D. Bloom. Complete mapping of viral escape from neutralizing antibodies. PLoS Pathog. 13:e1006271 (2017) | PDF

Jesse D. Bloom. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct. 12:1 (2017) | PDF

2016

Hugh K. Haddox, Adam S. Dingens, and Jesse D. Bloom. Experimental estimation of the effects of all amino-acid mutations to HIV's envelope protein on viral replication in cell culture. PLoS Pathog. 12:e1006114 (2016)

Michael B. Doud and Jesse D. Bloom. Accurate measurement of the effects of all amino-acid mutations to influenza hemagglutinin. Viruses. 8:155 (2016) | PDF

Katherine S. Xue, Kathryn A. Hooper, Anja R. Ollodart, Adam S. Dingens, Jesse D. Bloom. Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture. eLife. 5:e13974 (2016) | PDF

2015

Heather M. Machkovech, Trevor Bedford, Marc Suchard, and Jesse D. Bloom. Positive selection in CD8+ T-cell epitopes of influenza nucleoprotein revealed by a comparative analysis of human and swine viral lineages. J Virol. 89:11275-11283 (2015) | PDF

Michael B. Doud*, Orr Ashenberg*, and Jesse D. Bloom. Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs. Mol Biol Evol. 32:2944-2960 (2015). (* indicates equal contribution) | PDF

Jesse D. Bloom. Software for the analysis and visualization of deep mutational scanning data. BMC Bioinformatics. 16:168 (2015) | PDF

Kathryn A. Hooper, James E. Crow Jr., and Jesse D. Bloom. Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. J Virol. 89:3737-3745 (2015) | PDF

2014

Jesse D. Bloom. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Mol Biol Evol. 31:2753-2769 (2014) | PDF

Bargavi Thyagarajan and Jesse D. Bloom. The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. eLife. 3:e03300 (2014) | PDF

Jesse D. Bloom. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol. 30:1956-1978 (2014) | PDF

L. Ian Gong and Jesse D. Bloom. Epistatically interacting substitutions are enriched during adaptive protein evolution. PLoS Genet. 10:e1004328 (2014) | PDF   

2013

Orr Ashenberg, L. Ian Gong, and Jesse D. Bloom. Mutational effects on stability are largely conserved during protein evolution. Proc Natl Acad Sci USA. 110:21071-21076 (2013) | PDF

Kathryn A. Hooper and Jesse D. Bloom. A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein. J Virol. 87:12531-12540 (2013) | PDF

L. Ian Gong, Marc A. Suchard, Jesse D. Bloom. Stability-mediated epistasis constrains the evolution of an influenza protein. eLife. 2:e00631 (2013) | PDF

2011

Jesse D. Bloom, Jagannath S. Nayak, and David Baltimore. A computational-experimental approach identifies mutations that enhance surface expression of an oseltamivir-resistant influenza neuraminidase. PLoS One. 6:e22201 (2011) | PDF

2010

Jesse D. Bloom, L. Ian Gong, and David BaltimorePermissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science. 5983:1272-1275 (2010) | PDF

2009

Jesse D. Bloom and Matthew J. Glassman. Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin. PLoS Comput. Biol. 5:e1000349 (2009) | PDF

Jesse D. Bloom and Frances H. ArnoldIn the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci USA. 106:995-1000 (2009) | PDF

2007

Jesse D. Bloom, Zhongyi Lu, David Chen, Alpan Raval, Ophelia S. Venturelli, and Frances H. Arnold. Evolution favors protein mutational robustness in sufficiently large populations. BMC Biol. 5:29 (2007) | PDF

Jesse D. Bloom, Philip A. Romero, Zhongyi Lu, and Frances H. Arnold. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Direct. 2:17 (2007) | PDF

Jesse D. Bloom, Frances H. Arnold, and Claus O. Wilke. Breaking proteins with mutations: threads and thresholds in evolution. (News and Views.) Mol Syst Biol. 3:76 (2007) | PDF

Jesse D. Bloom, Alpan Raval, and Claus O. Wilke. Thermodynamics of neutral protein evolution. Genetics. 175:255-266 (2007) | PDF

2006

Jesse D. Bloom, D. Allan Drummond, Frances H. Arnold, and Claus O. Wilke. Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol. 23:1751-1761 (2006) | PDF

Jesse D. Bloom, Sy T. Labthavikul, Christopher R. Otey, and Frances H. Arnold. Protein stability promotes evolvability. Proc Natl Acad Sci USA. 103:5869-5874 (2006) | PDF

2005

Jesse D. Bloom, Michelle M. Meyer, Peter Meinhold, Christopher R. Otey, David MacMillan, and Frances H. Arnold. Evolving strategies for enzyme engineering. Curr Opin Struct Biol. 15:447-452 (2005) | PDF

Jesse D. Bloom, Jonathan J. Silberg, Claus O. Wilke, D. Allan Drummond, Christoph Adami, and Frances H. Arnold. Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci USA. 102:606-611 (2005) | PDF

2004

Jesse D. Bloom, Claus O. Wilke, Frances H. Arnold, and Christoph Adami. A tradeoff between stability and the evolvability of function in a model protein. Biophys J. 86:2758-2764 (2004) | PDF

Jesse D. Bloom and Christoph Adami. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: response. BMC Evol Biol. 4:14 (2004) | PDF

2003

Jesse D. Bloom and Christoph Adami. Apparent dependence of protein evolutionary rate on number of protein-protein interactions is linked to biases in protein-protein interaction data sets. BMC Evol Biol. 3:21 (2003) | PDF