Publications

Complete Bibliography

Visit Google Scholar and ResearcherID to view Dr. Jesse Bloom's complete publication record.


Publications

2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 20092007 | 2006 | 2005 | 2004 | 2003 | 2001

2018

Katherine S. Xue and Jesse D. Bloom. "Reconciling disparate estimates of viral genetic diversity during human influenza infections." bioRxiv. DOI: 10.1101/364430 (2018).

Heather M. Machkovech, Jesse D. Bloom#, Arvind R. Subramaniam#. "Comprehensive profiling of translation initiation in influenza virus infected cells." bioRxiv. DOI 10.1101/326967 (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).

Sarah K. Hilton and Jesse D. Bloom. "Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral divergence." bioRxiv. DOI: 10.1101/302703 (2018).

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." bioRxiv. DOI: 10.1101/298364 (2018).
Computer code to reproduce analyses and paper: https://github.com/jbloomlab/Perth2009-DMS-Manuscript

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).
Computer code to reproduce analyses and paper: https://github.com/jbloomlab/EnvMutationalShiftsPaper    

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
Computer code to reproduce analyses and paper: https://github.com/jbloomlab/HA_antibody_ease_of_escape

Katherine S. Xue, Louise H. Moncla, Trevor Bedford, and Jesse D. Bloom. "Within-host evolution of human influenza virus." Trends in Microbiology. DOI 10.1016/j.tim.2018.02.007 (2018).

Alistair B. Russell, Cole Trapnell, and Jesse D. Bloom. "Extreme heterogeneity of influenza virus infection in single cells." eLife. 7:e32303 (2018)
Computer code to reproduce analyses and paper: https://github.com/jbloomlab/flu_single_cell

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
Coverage in The Atlantic
Coverage in WIRED
Katherine's broad-audience write-up in The Conversation

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
phydms software  

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
Preview article in Cell Host and Microbe | PDF

Eva-Maria Strauch, ..., Kathryn A. Hooper, ..., Jesse D. Bloom, ..., and David Baker. "Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site." Nature Biotechnology. (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
Spotlight article in Trends in Microbiology | 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
Hutch news article
the Molecular Ecologist blog

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
dms_tools software

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

Susanne L. Linderman, Benjamin S. Chambers, Seth J. Zost, Kaela Parkhouse, Yang Li, Christin Herrmann, Ali H. Ellebedy, Donald M. Carter, Sarah F. Andrews, Nai-Ying Zheng, Min Huang, Yunping Huang, Donna Strauss, Beth H. Shaz, Richard L. Hodinka, Gustavo Reyes-Teran, Ted M. Ross, Patrick C. Wilson, Rafi Ahmed, Jesse D. Bloom, and Scott E. Hensley. "Potential antigenic explanation for atypical H1N1 infections among middle-aged adults during the 2013-2014 influenza season." Proc. Natl. Acad. Sci. USA. 111:15798-15803 (2014) | PDF

Colin A. Russell, Peter M. Kasson, Ruben O. Donis, Steven Riley, Andrew Rambaut, ... [19 other authors] ..., Jesse D. Bloom. "Improving pandemic influenza risk assessment." eLife. 3:e03883 (2014) | 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
Phylogenetic analysis of lactamase (software, data, description)
Phylogenetic analysis of nucleoprotein (software, data, description)

Bargavi Thyagarajan and Jesse D. Bloom. "The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin." eLife. 3:e03300 (2014) | PDF
Computational analysis of deep-sequencing data (software, data, description)
Phylogenetic analysis (software, data, description)
Deep-sequencing data, SRA accession SRP040983

Jesse D. Bloom. "An experimentally determined evolutionary model dramatically improves phylogenetic fit." Molecular Biology and Evolution. 30:1956-1978 (2014) | PDF
Computational analysis of deep-sequencing data (software, data, and description)
Phylogenetic analysis (software, data, and description)
Deep-sequencing data, SRA accession SRP036064

L. Ian Gong and Jesse D. Bloom. "Epistatically interacting substitutions are enriched during adaptive protein evolution." PLoS Genetics. 10:e1004328 (2014) | PDF   
Software to build mutational trajectories
Software to map epitopes

Jeff Butler, Kathryn A. Hooper, Stephen Petrie, Raphael Lee, Sebastian Maurer-Stroh, Lucia Reh, Teagan Guarnaccia, Chantal Baas, Lumin Xue, Sophie Vitesnik, Sook-Kwan Leang, Jodie McVernon, Anne Kelso, Ian G. Barr, James M. McCaw, Jesse D. Bloom, and Aeron C. Hurt. "Estimating the Fitness Advantage Conferred by Permissive Neuraminidase Mutations in Recent Oseltamivir-Resistant A(H1N1)pdm09 Influenza Viruses." PLoS Pathogens. 10:e1004065 (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
Article of Significant Interest Selected from This Issue by the Editors

Alejandro B. Balazs, Jesse D. Bloom, Christin M. Hong, Dinesh S. Rao & David Baltimore. "Broad protection against influenza infection by vectored immunoprophylaxis in mice." Nature Biotechnology. 31:647-652 (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
eLife insight article
Faculty of 1000 review
Software to build mutational trajectory
eLife selects four outstanding papers, showcases early-career investigators

2012

David A. Liberles, Sarah A. Teichmann, Ivet Bahar, Ugo Bastolla, Jesse D. Bloom, et al. "The interface of protein structure, protein biophysics, and molecular evolution." Protein Science. 6:769-785 (2012) | PDF

Oliver Lieleg, Corinna Lieleg, Jesse D. Bloom, Christopher B. Buck, and Katharina Ribbeck. "Mucin biopolymers as broad-spectrum antiviral agents." Biomacromolecules. 6:1724-1732 (2012) | PDF

Dennis L. Chao, Jesse D. Bloom, Beth F. Kochin, Rustom Antia, and Ira M. Longini Jr. "The global spread of drug-resistant influenza." Journal of the Royal Society, Interface. 69:648-656 (2012) | 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
PIPS software

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
Perspectives article at Science
Faculty of 1000 review

Christian Jackel, Jesse D. Bloom, Peter Kast, Frances H. Arnold, and Donald Hilvert. “Consensus protein design without phylogenetic bias.” J. Mol. Biol. 399:541-546 (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
PIPS software

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

Jijun Dong, Jesse D. Bloom, Vladimir Goncharov, Madhuri Chattopadhyay, Glenn L. Millhauser, David G. Lynn, Thomas Scheibel, and Susan Lindquist. “Probing the role of PrP repeats in the conformational conversion and amyloid assembly of chimeric yeast proteins.” J. Biol. Chem. 282:34204-34212 (2007) | PDF

Yougen Li, Andrew M. Sawayama, Chris D. Snow, Jesse D. Bloom, and Frances H. Arnold. “A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments.” Nature Biotechnology. 25:1051-1056 (2007) | PDF
Faculty of 1000 review

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
Faculty of 1000 review

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
Faculty of 1000 review

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
Faculty of 1000 review

Christopher R. Otey, Marco Landwehr, Jeffrey B. Endelman, Kaori Hiraga, Jesse D. Bloom, and Frances H. Arnold. “Structure-guided recombination creates an artificial family of cytochromes P450.” PLoS Biology. 4:e112 (2006) | PDF

2005

D. Allan Drummond, Jesse D. Bloom, Christoph Adami, Claus O. Wilke, and Frances H. Arnold. “Why highly expressed proteins evolve slowly.” Proc. Natl. Acad. Sci. USA. 102:14388-14343 (2005) | PDF
Faculty of 1000 review

Claus O. Wilke, Jesse D. Bloom, D. Allan Drummond, and Alpan Raval. “Predicting the tolerance of proteins to random amino acid substitution.” Biophysical J. 89:3714-3720 (2005) | 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
Faculty of 1000 review

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

Thomas Scheibel, Jesse D. Bloom, and Susan L. Lindquist. “The elongation of yeast prion fibers involves separable steps of association and conversion.” Proc. Natl. Acad. Sci. USA. 101:2287-2292 (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

2001

Thomas Scheibel, A. S. Kowal, Jesse D. Bloom, and Susan L. Lindquist. “Bidirectional amyloid fiber growth for a yeast prion.” Current Biology. 11:366-369 (2001) | PDF