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)


Katherine S. Xue and Jesse D. Bloom"Linking influenza virus evolution within and between human hosts." Virus Evolution. 6:veaa010 (2020) | PDF


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

Tal Einav and Jesse D. Bloom. "When two are better than one: Modeling the mechanisms of antibody mixtures." bioRxiv. DOI 10.1101/808394 (2019).

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


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


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


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


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


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   


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


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


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


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


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


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


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


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


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