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)

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. 2020 Sep 3;182(5):1295-1310.e20. doi: 10.1016/j.cell.2020.08.012. Epub 2020 Aug 11. PMID: 32841599; PMCID: PMC7418704. | PDF

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, Helen Y. Chu, Jesse D. Bloom. Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection. Journal of Infectious Diseases. 2020 Sep 30:jiaa618. doi: 10.1093/infdis/jiaa618. Epub ahead of print. PMID: 33000143. | PDF

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. 2020 Sep 5;12(9):E987. doi: 10.3390/v12090987. PMID: 32899480.PDF

Tal Einav, Lauren E. Gentles, Jesse D. Bloom. SnapShot: Influenza by the Numbers. Cell. 2020 Jul 23;182(2):532-532.e1. doi: 10.1016/j.cell.2020.05.004. PMID: 32707094. PDF

Lauren E. Gentles, Hongquan Wan, Maryna C. Eichelberger, Jesse D. Bloom. Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Viruses. 2020 May 30;12(6):597. doi: 10.3390/v12060597. PMID: 32486222; PMCID: PMC7354634. PDF

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. Nature Communications. 2020 Sep 1;11(1):4378. doi: 10.1038/s41467-020-18178-1. PMID: 32873791; PMCID: PMC7463158. | PDF

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. 2020 May 6;12(5):513. doi: 10.3390/v12050513. PMID: 32384820; PMCID: PMC7291041. PDF

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. bioRxiv 2020.05.14.096842; doi: https://doi.org/10.1101/2020.05.14.096842 PDF

Tal Einav and Jesse D. Bloom. When two are better than one: Modeling the mechanisms of antibody mixtures. PLoS Comput Biol. 2020 May 4;16(5):e1007830. doi: 10.1371/journal.pcbi.1007830. PMID: 32365091; PMCID: PMC7224563. PDF

Katherine S. Xue and Jesse D. BloomLinking influenza virus evolution within and between human hosts. Virus Evol. 2020 Feb 17;6(1):veaa010. doi: 10.1093/ve/veaa010. PMID: 32082616; PMCID: PMC7025719. | PDF

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. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. bioRxiv 2020.09.10.292078; doi: https://doi.org/10.1101/2020.09.10.292078  | PDF

2019

Katharine H.D. Crawford and Jesse D. Bloom. "alignparse: A Python package for parsing complex features from high-throughput long-read sequencing." Journal of Open Source Software. 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." Journal of Virology. 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." Journal of Virology. 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." Nature Genetics. DOI: 10.1038/s41588-019-0349-3 (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 Pathogens. 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 Pathogens. 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 Evolution. 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." Nature Communications. 9:1386 (2018) | PDF

Katherine S. Xue, Louise H. Moncla, Trevor Bedford, and Jesse D. Bloom. "Within-host evolution of human influenza virus." Trends in Microbiology. 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 and 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 Pathogens. 13:e1006288 (2017) | PDF

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

Jesse D. Bloom. "Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models." Biology 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 Pathogens. 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." Journal of Virology. 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." Molecular Biology and Evolution. 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." Journal of Virology. 89:3737-3745 (2015) | PDF

2014

Jesse D. Bloom. "An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs." Molecular Biology and Evolution. 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." Molecular Biology and Evolution. 30:1956-1978 (2014) | PDF

L. Ian Gong and Jesse D. Bloom. "Epistatically interacting substitutions are enriched during adaptive protein evolution." PLoS Genetics. 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." Journal of Virology. 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 Baltimore. “Permissive 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. Arnold. “In 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 Biology. 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.” Biology 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.) Molecular Systems Biology. 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.” Biophysical 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 Evolutionary Biology. 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 Evolutionary Biology. 3:21 (2003) | PDF