PageSourceSearch

https://jbloomlab.github.io/papers/

html jbloomlab.github.io collected 2026-10-03 09:22:27 UTC 148,385 bytes, 27 lines download raw bytes

1<!DOCTYPE html>
2<html lang="en-US" dir="ltr">
3  <head>
4    <meta charset="utf-8">
5    <meta name="viewport" content="width=device-width,initial-scale=1">
6    <title>Bloom Lab</title>
7    <meta name="description" content="We study the evolution of viruses.">
8    <meta name="generator" content="VitePress v1.1.0">
9    <link rel="preload stylesheet" href="/assets/style.RVaGtGCs.css" as="style">
10    
11    
11<script type="module" src="/assets/app.DYXolgqF.js"></script>
11
12    <link rel="modulepreload" href="/assets/chunks/framework.BOAZPCR7.js">
13    <link rel="modulepreload" href="/assets/chunks/theme.DDzl6J9S.js">
14    <link rel="modulepreload" href="/assets/papers_index.md.OHKOyLXE.lean.js">
15    <meta name="google-site-verification" content="ZIQn6aYwzgvrO-eWI5MYIU5R21R5LnUk95UPij-RXWQ">
16    <meta name="keywords" content="Jesse Bloom, Bloom Lab, Fred Hutch Cancer Center, Deep Mutational Scanning, Virus Evolution, Lentiviral Psuedotyping">
17    <link rel="icon" href="/images/icon.png">
18    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.min.css">
19    
19<script id="check-mac-os">document.documentElement.classList.toggle("mac",/Mac|iPhone|iPod|iPad/i.test(navigator.platform));</script>
19
20    <link rel="canonical" href="https://jbloomlab.org/papers/">
21  </head>
22  <body>
23    <div id="app"><div id="app" class="flex flex-col min-h-screen"><nav class="p-4 mb-4"><div class="flex justify-between items-center w-full px-4 select-none"><a href="/" class="flex items-center no-underline"><img src="/images/icon.png" alt="Logo" class="h-8 w-8 mr-2"><span class="title text-lg font-bold text-custom-orange collapse sm:visible">Bloom Lab</span></a><button class="flex md:hidden text-gray-600"><span class="i-menu h-6 w-6"></span></button><div class="flex bg-custom-soft backdrop-blur-md md:backdrop-blur-none flex-col md:flex-row bg-opacity-75 md:bg-transparent md:flex md:items-center md:px-0 px-3 md:pb-0 pb-10 md:static absolute md:w-auto w-full md:h-auto h-full md:pt-0 pt-10 top-14 z-50 md:flex hidden left-[-100%]"><!--[--><a href="/research/" class="text-gray-600 text-xl md:text-lg px-4 py-4 md:py-2 flex items-center justify-center md:flex-none md:items-stretch md:justify-start" data-v-1c4acd03>Research</a><a href="/posts/" class="text-gray-600 text-xl md:text-lg px-4 py-4 md:py-2 flex items-center justify-center md:flex-none md:items-stretch md:justify-start" data-v-1c4acd03>Blog</a><a href="/papers/" class="text-custom-orange text-xl md:text-lg px-4 py-4 md:py-2 flex items-center justify-center md:flex-none md:items-stretch md:justify-start" data-v-1c4acd03>Papers</a><a href="/people/" class="text-gray-600 text-xl md:text-lg px-4 py-4 md:py-2 flex items-center justify-center md:flex-none md:items-stretch md:justify-start" data-v-1c4acd03>Team</a><a href="/projects/" class="text-gray-600 text-xl md:text-lg px-4 py-4 md:py-2 flex items-center justify-center md:flex-none md:items-stretch md:justify-start" data-v-1c4acd03>Software</a><!--]--></div></div></nav><main class="flex-1 max-w-3xl mx-auto px-4 sm:px-6 lg:max-w-5xl xl:px-0"><div class="divide-y divide-gray-200"><div class="pt-6 pb-8 space-y-2 md:space-y-5"><h1 class="text-3xl leading-9 font-bold text-gray-800 tracking-tight sm:text-4xl sm:leading-10 md:text-6xl md:leading-14"> Papers </h1><p class="text-xl leading-8 text-gray-800"> Papers from the Bloom Lab team. See also <a href="https://scholar.google.com/citations?user=S12x_eQAAAAJ&amp;hl" target="_blank">Google Scholar</a> for a complete list of publications. </p><div class="p-multiselect p-component p-inputwrapper w-full md:w-80" style="" data-pc-name="multiselect" data-pc-section="root"><div class="p-hidden-accessible" data-pc-section="hiddeninputcontainer" data-p-hidden-accessible="true"><input type="text" readonly placeholder="Filter by Keywords" tabindex="0" role="combobox" aria-haspopup="listbox" aria-expanded="false" aria-controls="undefined_list" data-pc-section="hiddeninput"></div><div class="p-multiselect-label-container" data-pc-section="labelcontainer"><div class="p-multiselect-label p-placeholder" data-pc-section="label"><!--[--><!--[-->Filter by Keywords<!--]--><!--]--></div></div><div class="p-multiselect-dropdown" data-pc-section="dropdown"><!--[--><svg width="14" height="14" viewBox="0 0 14 14" fill="none" xmlns="http://www.w3.org/2000/svg" class="p-icon p-multiselect-dropdown-icon" aria-hidden="true" data-pc-section="dropdownicon"><path d="M7.01744 10.398C6.91269 10.3985 6.8089 10.378 6.71215 10.3379C6.61541 10.2977 6.52766 10.2386 6.45405 10.1641L1.13907 4.84913C1.03306 4.69404 0.985221 4.5065 1.00399 4.31958C1.02276 4.13266 1.10693 3.95838 1.24166 3.82747C1.37639 3.69655 1.55301 3.61742 1.74039 3.60402C1.92777 3.59062 2.11386 3.64382 2.26584 3.75424L7.01744 8.47394L11.769 3.75424C11.9189 3.65709 12.097 3.61306 12.2748 3.62921C12.4527 3.64535 12.6199 3.72073 12.7498 3.84328C12.8797 3.96582 12.9647 4.12842 12.9912 4.30502C13.0177 4.48162 12.9841 4.662 12.8958 4.81724L7.58083 10.1322C7.50996 10.2125 7.42344 10.2775 7.32656 10.3232C7.22968 10.3689 7.12449 10.3944 7.01744 10.398Z" fill="currentColor"></path></svg><!--]--></div><!----></div></div><div class="selected-publications mb-8"><h2 class="text-3xl leading-8 font-bold text-gray-800 tracking-tight mt-4 mb-4">Key Papers</h2><h3 class="text-lg leading-7 text-gray-600 tracking-tight mt-4 mb-4">These papers exemplify key current areas of research in the lab.</h3><div class="grid grid-cols-2 gap-4"><!--[--><div class="hover:shadow-lg hover:shadow-custom-orange flex flex-col gap-px rounded-lg w-full h-full overflow-hidden transition-shadow duration-300 ease-in-out"><a href="/papers/2026_simonich_dms.html" class="flex-grow bg-custom-soft no-underline p-4"><div class=""><h3 class="m-0 text-gray-800 font-semibold text-lg leading-6 ease-in-out pb-2">Mutational constraints on RSV F and its neutralization by antibodies</h3><a href="https://www.nature.com/articles/s41586-026-11030-4" target="_blank" class="m-0 font-medium text-gray-600 pt-1 text-base no-underline">Nature. 2026</a></div></a></div><div class="hover:shadow-lg hover:shadow-custom-orange flex flex-col gap-px rounded-lg w-full h-full overflow-hidden transition-shadow duration-300 ease-in-out"><a href="/papers/2026_dadonaite.html" class="flex-grow bg-custom-soft no-underline p-4"><div class=""><h3 class="m-0 text-gray-800 font-semibold text-lg leading-6 ease-in-out pb-2">Defining the molecular interaction between influenza hemagglutinin and MHC-II</h3><a href="https://doi.org/10.64898/2026.07.17.738765" target="_blank" class="m-0 font-medium text-gray-600 pt-1 text-base no-underline">bioRxiv. 2026</a></div></a></div><div class="hover:shadow-lg hover:shadow-custom-orange flex flex-col gap-px rounded-lg w-full h-full overflow-hidden transition-shadow duration-300 ease-in-out"><a href="/papers/2025_kikawa.html" class="flex-grow bg-custom-soft no-underline p-4"><div class=""><h3 class="m-0 text-gray-800 font-semibold text-lg leading-6 ease-in-out pb-2">High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains</h3><a href="https://doi.org/10.7554/eLife.106811.4" target="_blank" class="m-0 font-medium text-gray-600 pt-1 text-base no-underline">eLife. 2026</a></div></a></div><div class="hover:shadow-lg hover:shadow-custom-orange flex flex-col gap-px rounded-lg w-full h-full overflow-hidden transition-shadow duration-300 ease-in-out"><a href="/papers/2025_larsen.html" class="flex-grow bg-custom-soft no-underline p-4"><div class=""><h3 class="m-0 text-gray-800 font-semibold text-lg leading-6 ease-in-out pb-2">Functional and antigenic landscape of the Nipah virus receptor binding protein</h3><a href="https://doi.org/10.1016/j.cell.2025.02.030" target="_blank" class="m-0 font-medium text-gray-600 pt-1 text-base no-underline">Cell. 2025</a></div></a></div><div class="hover:shadow-lg hover:shadow-custom-orange flex flex-col gap-px rounded-lg w-full h-full overflow-hidden transition-shadow duration-300 ease-in-out"><a href="/papers/2024_dadonaite_b.html" class="flex-grow bg-custom-soft no-underline p-4"><div class=""><h3 class="m-0 text-gray-800 font-semibold text-lg leading-6 ease-in-out pb-2">Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance</h3><a href="https://doi.org/10.1371/journal.pbio.3002916" target="_blank" class="m-0 font-medium text-gray-600 pt-1 text-base no-underline">PLoS Biology. 2024</a></div></a></div><div class="hover:shadow-lg hover:shadow-custom-orange flex flex-col gap-px rounded-lg w-full h-full overflow-hidden transition-shadow duration-300 ease-in-out"><a href="/papers/2024_dadonaite_a.html" class="flex-grow bg-custom-soft no-underline p-4"><div class=""><h3 class="m-0 text-gray-800 font-semibold text-lg leading-6 ease-in-out pb-2">Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades</h3><a href="https://www.nature.com/articles/s41586-024-07636-1" target="_blank" class="m-0 font-medium text-gray-600 pt-1 text-base no-underline">Nature. 2024</a></div></a></div><!--]--></div></div><div class="all-publications"><h2 class="text-3xl leading-8 font-bold text-gray-800 tracking-tight mt-4 mb-4">All Papers</h2><h3 class="text-lg leading-7 text-gray-600 tracking-tight mt-4 mb-4">Below is a complete list of primary research papers from our group.</h3><div class="flex"><ul class="flex-1 divide-y divide-gray-200"><!--[--><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2026_simonich_dms.png" alt="Image for Mutational constraints on RSV F and its neutralization by antibodies" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2026_simonich_dms.html">Mutational constraints on RSV F and its neutralization by antibodies</a></h2><div class="max-w-none text-gray-700 hidden lg:block">
23Cassandra AL Simonich, Teagan E McMahon, Gavin Juviler, Lucas Kampman, Helen Y Chu, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Nature</span>. 2026. <a href="https://www.nature.com/articles/s41586-026-11030-4" target="_blank">doi:10.1038/s41586-026-11030-4</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2026_simonich_dms.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2026_kikawa_b.jpg" alt="Image for Near real-time data on the human neutralizing antibody landscape to influenza virus in summer of 2026 shows antigenic advance of H3N2 subclade K region D mutants and H1N1 D.3.1.1 Sa mutants" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2026_kikawa_b.html">Near real-time data on the human neutralizing antibody landscape to influenza virus in summer of 2026 shows antigenic advance of H3N2 subclade K region D mutants and H1N1 D.3.1.1 Sa mutants</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Caroline Kikawa, Andrew Butler, John Huddleston, Sam A Turner, Heidi Peck, Janet A Englund, Kirsten Lacombe, Michael Busch, Mario Lanteri, Mars Stone, Bryan Spencer, Alexander L Greninger, Derek J Smith, Stephanie Wallace, Helen S Marshall, Shidan Tosif, Scott E Hensley, Ian G Barr, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">bioRxiv</span>. 2026. <a href="https://doi.org/10.64898/2026.09.15.751855" target="_blank">doi:10.64898/2026.09.15.751855</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2026_kikawa_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2026_kikawa.jpg" alt="Image for Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2026_kikawa.html">Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Caroline Kikawa, John Huddleston, Sam A Turner, Andrea N Loes, Jiaojiao Liu, Sydney Gang, Tachianna Griffiths, Elizabeth M Drapeau, Benjamin J Cowling, Faith Ho, Nancy HL Leung, Janet A Englund, Kirsten Lacombe, Shinji Watanabe, Hideki Hasegawa, Michael Busch, Mario Lanteri, Mars Stone, Bryan Spencer, Richard A Neher, Derek J Smith, Trevor Bedford, Scott E Hensley, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2026. <a href="https://doi.org/10.1093/ve/veag046" target="_blank">doi:10.1093/ve/veag046</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2026_kikawa.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2026_dadonaite.png" alt="Image for Defining the molecular interaction between influenza hemagglutinin and MHC-II" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2026_dadonaite.html">Defining the molecular interaction between influenza hemagglutinin and MHC-II</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Bernadeta Dadonaite, Annie Dosey, Jenny J Ahn, Timothy C Yu, Sara A Sunshine, Ariana G Farrell, Neil P King, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">bioRxiv</span>. 2026. <a href="https://doi.org/10.64898/2026.07.17.738765" target="_blank">doi:10.64898/2026.07.17.738765</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2026_dadonaite.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2026_loes.jpg" alt="Image for Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2026_loes.html">Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Andrea N Loes, Rosario AL Tarabi, Shuk H Li, Reilly K Atkinson, John Huddleston, Caroline Kikawa, Tachianna Griffiths, Elizabeth M Drapeau, Sook-San Wong, Samuel MS Cheng, Nancy HL Leung, Sarah Cobey, Benjamin J Cowling, Trevor Bedford, Scott E Hensley, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of Virology</span>. 2026. <a href="https://journals.asm.org/doi/10.1128/jvi.00317-26" target="_blank">doi:10.1128/jvi.00317-26</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2026_loes.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2026_ahn.jpg" alt="Image for Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2026_ahn.html">Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jenny J Ahn, Timothy C Yu, Bernadeta Dadonaite, Caelan E Radford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2026. <a href="https://doi.org/10.1093/ve/veag018" target="_blank">doi:10.1093/ve/veag018</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2026_ahn.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_kikawa.jpg" alt="Image for High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_kikawa.html">High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Caroline Kikawa, Andrea N Loes, John Huddleston, Marlin D Figgins, Philippa Steinberg, Tachianna Griffiths, Elizabeth M Drapeau, Heidi Peck, Ian G Barr, Janet A Englund, Scott E Hensley, Trevor Bedford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2026. <a href="https://doi.org/10.7554/eLife.106811.4" target="_blank">doi:10.7554/eLife.106811.4</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_kikawa.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2026_harari.png" alt="Image for Mutations to the HCoV-229E spike have counterbalancing effects on serum antibody neutralization and receptor binding" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2026_harari.html">Mutations to the HCoV-229E spike have counterbalancing effects on serum antibody neutralization and receptor binding</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Sheri Harari, Rachel T Eguia, Bernadeta Dadonaite, Caelan E Radford, Cameron Stewart, David Veesler, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">bioRxiv</span>. 2026. <a href="https://doi.org/10.64898/2026.02.22.707297" target="_blank">doi:10.64898/2026.02.22.707297</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2026_harari.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_larsen_f.jpg" alt="Image for Functional and antigenic constraints on the Nipah virus fusion protein" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_larsen_f.html">Functional and antigenic constraints on the Nipah virus fusion protein</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Brendan B Larsen, Sheri Harari, Risako Gen, Cameron Stewart, David Veesler, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Proc Natl Acad Sci USA</span>. 2026. <a href="https://www.pnas.org/doi/10.1073/pnas.2529505123" target="_blank">doi:10.1073/pnas.25295051</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_larsen_f.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_yu.jpg" alt="Image for Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza hemagglutinin" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_yu.html">Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza hemagglutinin</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Timothy C Yu, Caroline Kikawa, Bernadeta Dadonaite, Andrea N Loes, Janet A Englund, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Nature Ecology &amp; Evolution</span>. 2025. <a href="https://www.nature.com/articles/s41559-025-02895-1" target="_blank">doi:10.1038/s41559-025-02895-1</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_yu.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_kikawa_b.jpg" alt="Image for Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_kikawa_b.html">Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Caroline Kikawa, John Huddleston, Andrea N Loes, Sam A Turner, Jover Lee, Ian G Barr, Benjamin J Cowling, Janet A Englund, Alexander L Greninger, Ruth Harvey, Hideki Hasegawa, Faith Ho, Kirsten Lacombe, Nancy HL Leung, Nicola S Lewis, Heidi Peck, Shinji Watanabe, Derek J Smith, Trevor Bedford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2025. <a href="https://doi.org/10.1093/ve/veaf086" target="_blank">doi:10.1093/ve/veaf086</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_kikawa_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4">
23<img src="/assets/papers/2025_dadonaite_b.png" alt="Image for Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_dadonaite_b.html">Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Bernadeta Dadonaite, Sheri Harari, Brendan B Larsen, Lucas Kampman, Alex Harteloo, Anna Elias-Warren, Helen Y Chu, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of Virology</span>. 2025. <a href="https://journals.asm.org/doi/10.1128/jvi.01423-25" target="_blank">doi:10.1128/jvi.01423-25</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}
23" href="/papers/2025_dadonaite_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_xu.png" alt="Image for Determinants of human versus mosquito cell entry by the Chikungunya virus envelope proteins" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_xu.html">Determinants of human versus mosquito cell entry by the Chikungunya virus envelope proteins</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Xiaohui Ju, William W Hannon, Tomasz Kaszuba, Caelan E Radford, Brendan B Larsen, Samantha S Nelson, Christopher A Nelson, Israel Baltazar-Perez, Ofer Zimmerman, Daved H Fremont, Michael S Diamond, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">bioRxiv</span>. 2025. <a href="https://doi.org/10.1101/2025.08.25.672233" target="_blank">doi:10.1101/2025.08.25.672233</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_xu.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_simonich.jpg" alt="Image for RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_simonich.html">RSV F evolution escapes some monoclonal antibodies but does not strongly erode neutralization by human polyclonal sera</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Cassandra AL Simonich, Teagan A McMahon, Xiaohui Ju, Timothy C Yu, Natalie Brunette, Terry Stevens-Ayers, Michael J Boeckh, Neil P King, Alexander L Greninger, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of Virology</span>. 2025. <a href="https://journals.asm.org/doi/10.1128/jvi.00531-25" target="_blank">doi:10.1128/jvi.00531-25</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_simonich.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2024_aditham.png" alt="Image for Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_aditham.html">Deep mutational scanning of rabies glycoprotein defines mutational constraint and antibody-escape mutations</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Arjun K Aditham, Caelan E Radford, Caleb R Carr, Naveen Jasti, Neil P King, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Cell Host &amp; Microbe</span>. 2025. <a href="https://doi.org/10.1016/j.chom.2025.04.018" target="_blank">doi:10.1016/j.chom.2025.04.018</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_aditham.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_radford.jpg" alt="Image for Comprehensive maps of escape mutations from antibodies 10-1074 and 3BNC117 for Envs from two divergent HIV strains" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_radford.html">
23Comprehensive maps of escape mutations from antibodies 10-1074 and 3BNC117 for Envs from two divergent HIV strains</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Caelan E Radford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of Virology</span>. 2025. <a href="https://doi.org/10.1128/jvi.00195-25" target="_blank">doi:10.1128/jvi.00195-25</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_radford.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_dadonaite.png" alt="Image for SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individuals" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_dad
23onaite.html">SARS-CoV-2 neutralizing antibody specificities differ dramatically between recently infected infants and immune-imprinted individuals</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Bernadeta Dadonaite, Allison R Burrell, Jenni Logue, Helen Y Chu, Daniel C Payne, David B Haslam, Mary A Staat, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of Virology</span>. 2025. <a href="https://doi.org/10.1128/jvi.00109-25" target="_blank">doi:10.1128/jvi.00109-25</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_dadonaite.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2025_larsen.jpg" alt="Image for Functional and antigenic landscape of the Nipah virus receptor binding protein" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2025_larsen.html">Functional and antigenic landscape of the Nipah virus receptor binding protein</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Brendan B Larsen, Teagan McMahon, Jack T Brown, Zhaoqian Wang, Caelan E Radford, James E Crowe, David Veesler, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Cell</span>. 2025. <a href="https://doi.org/10.1016/j.cell.2025.02.030" target="_blank">doi:10.1016/j.cell.2025.02.030</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2025_larsen.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2024_dadonaite_b.png" alt="Image for Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2024_dadonaite_b.html">Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">PLoS Biology</span>. 2024. <a href="https://doi.org/10.1371/journal.pbio.3002916" target="_blank">doi:10.1371/journal.pbio.3002916</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2024_dadonaite_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2024_loes.jpg" alt="Image for High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2024_loes.html">High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Journal of Virology</span>. 2024. <a href="https://doi.org/10.1128/jvi.00689-24" target="_blank">doi:10.1128/jvi.00689-24</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2024_loes.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2024_welsh.jpg" alt="Image for Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2024_welsh.html">Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Cell Host &amp; Microbe</span>. 2024. <a href="https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(24)00233-6" target="_blank">doi:10.1016/j.chom.2024.06.015</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2024_welsh.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2024_hannon.jpg" alt="Image for dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2024_hannon.html">dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets</a></h2><div class="max-w-none text-gray-700 hidden lg:block">William W Hannon, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of Open Source Software</span>. 2024. <a href="https://joss.theoj.org/papers/10.21105/joss.06129" target="_blank">doi:10.21105/joss.06129</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2024_hannon.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2024_carr.jpg" alt="Image for Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2024_carr.html">Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Immunity</span>. 2024. <a href="https://www.cell.com/immunity/fulltext/S1074-7613(24)00319-4" target="_blank">doi:10.1016/j.immuni.2024.06.013</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2024_carr.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2024_dadonaite_a.jpg" alt="Image for Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2024_dadonaite_a.html">Full-spike deep mutational scanning helps predict the evolutionary success of SARS-CoV-2 clades</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Nature</span>. 2024. <a href="https://www.nature.com/articles/s41586-024-07636-1" target="_blank">doi:10.1038/s41586-024-07636-1</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2024_dadonaite_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2024_bloom.jpg" alt="Image for Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2024_bloom.html">Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2024. <a href="https://academic.oup.com/ve/article/10/1/vead089/7504441" target="_blank">doi:10.1093/ve/vead089</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2024_bloom.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2023_kikawa.jpg" alt="Image for The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2023_kikawa.html">The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Caroline Kikawa, Catiana H Cartwright-Acar, Jackson B Stuart, Maya Contreras, Lisa M Levoir, Matthew J Evans, Jesse D Bloom, Leslie Goo</div><div class="max-w-none text-gray-500"><span class="italic">Journal of Virology</span>. 2023. <a href="https://journals.asm.org/doi/full/10.1128/jvi.01414-23" target="_blank">doi:10.1128/jvi.01414-23</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2023_kikawa.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2023_bloom_c.jpg" alt="Image for Fitness effects of mutations to SARS-CoV-2 proteins" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2023_bloom_c.html">Fitness effects of mutations to SARS-CoV-2 proteins</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom, Richard A Neher</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2023. <a href="https://academic.oup.com/ve/article/9/2/vead055/7265011" target="_blank">doi:10.1093/ve/veae026</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2023_bloom_c.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2023_bacsik.jpg" alt="Image for Influenza virus transcription and progeny production are poorly correlated in single cells" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2023_bacsik.html">Influenza virus transcription and progeny production are poorly correlated in single cells</a></h2><div class="max-w-none text-gray-700 hidden lg:block">David J Bacsik, Bernadeta Dadonaite, Andrew Butler, Allison J Greaney, Nicholas S Heaton, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2023. <a href="https://elifesciences.org/articles/86852" target="_blank">doi:10.7554/eLife.86852.2</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2023_bacsik.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2023_radford.png" alt="Image for Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2023_radford.html">Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div clas
23s="max-w-none text-gray-500"><span class="italic">Cell Host &amp; Microbe</span>. 2023. <a href="https://www.cell.com/cell-host-microbe/pdf/S1931-3128(23)00218-4.pdf" target="_blank">doi:10.1016/j.chom.2023.05.025</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2023_radford.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2023_bloom_a.jpg" alt="Image for Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2023_bloom_a.html">Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2023. <a href="https://academic.oup.com/ve/article/9/2/vead050/7249794" target="_blank">doi:10.1093/ve/vead050</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2023_bloom_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2023_bloom_b.jpg" alt="Image for Evolution of the SARS-CoV-2 mutational spectrum" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2023_bloom_b.html">Evolution of the SARS-CoV-2 mutational spectrum</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom, Annabel C Beichman, Richard A Neher, Kelley Harris</div><div class="max-w-none text-gray-500"><span class="italic">Molecular Biology and Evolution</span>. 2023. <a href="https://academic.oup.com/mbe/article/40/4/msad085/7113660" target="_blank">doi:10.1093/molbev/msad085</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2023_bloom_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2023_dadonaite_crawford_radford.png" alt="Image for A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2023_dadonaite_crawford_radford.html">A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Cell</span>. 2023. <a href="https://www.cell.com/cell/pdf/S0092-8674(23)00103-4.pdf" target="_blank">doi:10.1016/j.cell.2023.02.001</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2023_dadonaite_crawford_radford.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_starr_greaney_a.png" alt="Image for 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" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_starr_greaney_a.html">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</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Tyler N Starr*, Allison J Greaney*, Cameron M Stewart, Alexandra C Walls, William W Hannon, David Veesler, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PLoS pathogens</span>. 2022. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010951" target="_blank">doi:10.1371/journal.ppat.1010951</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_starr_greaney_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_farrell.png" alt="Image for Receptor-binding domain (RBD) antibodies contribute more to SARS-CoV-2 neutralization when target cells express high levels of ACE2" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_farrell.html">Receptor-binding domain (RBD) antibodies contribute more to SARS-CoV-2 neutralization when target cells express high levels of ACE2</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Viruses</span>. 2022. <a href="https://www.mdpi.com/1999-4915/14/9/2061" target="_blank">doi:10.3390/v14092061</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_farrell.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_starr_greaney_b.jpg" alt="Image for Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_starr_greaney_b.html">Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Science</span>. 2022. <a href="https://www.science.org/doi/full/10.1126/science.abo7896" target="_blank">doi:10.1126/science.abo7896</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_starr_greaney_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_hannon.jpg" alt="Image for Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat" 
23class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_hannon.html">Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat</a></h2><div class="max-w-none text-gray-700 hidden lg:block">William W Hannon, Pavitra Roychoudhury, Hong Xie, Lasata Shrestha, Amin Addetia, Keith R Jerome, Alexander L Greninger, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2022. <a href="https://academic.oup.com/ve/article/8/2/veac052/6609212" target="_blank">doi:10.1093/ve/veac052</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_hannon.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_yu.jpg" alt="Image for A biophysical model of viral escape from polyclonal antibodies" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_yu.html">A biophysical model of viral escape from polyclonal antibodies</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Timothy C Yu, Zorian T Thornton, William W Hannon, William S DeWitt, Caelan E Radford, Frederick A Matsen IV, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2022. <a href="https://academic.oup.com/ve/article/8/2/veac110/6889254" target="_blank">doi:10.1093/ve/veac110</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_yu.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_greaney_a.png" alt="Image for The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_greaney_a.html">The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">PLoS Pathogens</span>. 2022. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010592" target="_blank">doi:10.1371/journal.ppat.1010592</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_greaney_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_starr_a.jpg" alt="Image for ACE2 binding is an ancestral and evolvable trait of sarbecoviruses" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_starr_a.html">ACE2 binding is an ancestral and evolvable trait of sarbecoviruses</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Tyler N Starr, Samantha K Zepeda, Alexandra C Walls, Allison J Greaney, Sergey Alkhovsky, David Veesler, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Nature</span>. 2022. <a href="https://www.nature.com/articles/s41586-022-04464-z" target="_blank">doi:10.1038/s41586-022-04464-z</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_starr_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_greaney_b.png" alt="Image for A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_greaney_b.html">A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">PLoS pathogens</span>. 2022. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010248" target="_blank">
23doi:10.1371/journal.ppat.1010248</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_greaney_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_gentles.jpg" alt="Image for Dynamics of infection-elicited SARS-CoV-2 antibodies in children over time" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_gentles.html">Dynamics of infection-elicited SARS-CoV-2 antibodies in children over time</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">medRxiv</span>. 2022. <a href="https://www.medrxiv.org/content/10.1101/2022.01.14.22269235v1" target="_blank">doi:10.1101/2022.01.14.22269235</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_gentles.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2022_greaney_c.jpg" alt="Image for An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2022_greaney_c.html">An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Allison J Greaney, Tyler N Starr, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus Evolution</span>. 2022. <a href="https://academic.oup.com/ve/article/8/1/veac021/6549895" target="_blank">doi:10.1093/ve/veac021</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2022_greaney_c.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_bloom_a.jpg" alt="Image for Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_bloom_a.html">Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">mBio</span>. 2021. <a href="https://academic.oup.com/mbe/article/38/12/5211/6353034" target="_blank">doi:10.1093/molbev/msab246</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_bloom_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_starr_greaney_a.jpg" alt="Image for SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_starr_greaney_a.html">SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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, G
23yorgy Snell</div><div class="max-w-none text-gray-500"><span class="italic">Nature</span>. 2021. <a href="https://www.nature.com/articles/s41586-021-03807-6" target="_blank">doi:10.1038/s41586-021-03807-6</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_starr_greaney_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_greaney_a.jpg" alt="Image for Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_greaney_a.html">Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Nature Communications</span>. 2021. <a href="https://www.nature.com/articles/s41467-021-24435-8" target="_blank">doi:10.1038/s41467-021-24435-8</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_greaney_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_greaney_b.jpg" alt="Image for Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_greaney_b.html">Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Allison J Greaney, Andrea N Loes, Lauren E Gentles, Katharine HD Crawford, Tyler N Starr, Keara D Malone, Helen Y Chu, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Science translational medicine</span>. 2021. <a href="https://www.science.org/doi/full/10.1126/scitranslmed.abi9915" target="_blank">doi:10.1126/scitranslmed.abi9915</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_greaney_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_soh.png" alt="Image for Comprehensive profiling of mutations to influenza virus PB2 that confer resistance to the cap-binding inhibitor pimodivir" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_soh.html">Comprehensive profiling of mutations to influenza virus PB2 that confer resistance to the cap-binding inhibitor pimodivir</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Shirleen YQ Soh, Keara D Malone, Rachel T Eguia, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Viruses</span>. 2021. <a href="https://www.mdpi.com/1999-4915/13/7/1196" target="_blank">doi:10.3390/v13071196</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_soh.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_greaney_welsh.jpg" alt="Image for Co-dominant neutralizing epitopes make anti-measles immunity resistant to viral evolution" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_greaney_welsh.html">Co-dominant neutralizing epitopes make anti-measles immunity resistant to viral evolution</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Allison J Greaney, Frances C Welsh, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Cell Reports Medicine</span>. 2021. <a href="https://www.sciencedirect.com/science/article/pii/S2666379121000732?via%3Dihub" target="_blank">doi:10.1016/j.xcrm.2021.100257</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_greaney_welsh.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_starr_b.jpg" alt="Image for Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_starr_b.html">Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Tyler N Starr, Allison J Greaney, Adam S Dingens, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Cell Reports Medicine</span>. 2021. <a href="https://www.cell.com/cell-reports-medicine/pdf/S2666-3791(21)00071-9.pdf" target="_blank">doi:10.1016/j.xcrm.2021.100255</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_starr_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_eguia.png" alt="Image for A human coronavirus evolves antigenically to escape antibody immunity" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_eguia.html">A human coronavirus evolves antigenically to escape antibody immunity</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Rachel T Eguia, Katharine HD Crawford, Terry Stevens-Ayers, Laurel Kelnhofer-Millevolte, Alexander L Greninger, Janet A Englund, Michael J Boeckh, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PLoS pathogens</span>. 2021. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009453" target="_blank">doi:10.1371/journal.ppat.1009453</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_eguia.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_greaney_c.jpg" alt="Image for Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_greaney_c.html">
23Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Allison J Greaney, Andrea N Loes, Katharine HD Crawford, Tyler N Starr, Keara D Malone, Helen Y Chu, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Cell host &amp; microbe</span>. 2021. <a href="https://www.cell.com/cell-host-microbe/pdf/S1931-3128(21)00082-2.pdf" target="_blank">doi:10.1016/j.chom.2021.02.003</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_greaney_c.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_starr_greaney.jpg" alt="Image for Prospective mapping of viral mutations that escape antibodies used to treat COVID-19" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_starr_greaney.html">Prospective mapping of viral mutations that escape antibodies used to treat COVID-19</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Tyler N Starr*, Allison J Greaney*, Amin Addetia, William W Hannon, Manish C Choudhary, Adam S Dingens, Jonathan Z Li, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Science</span>. 2021. <a href="https://www.science.org/doi/full/10.1126/science.abf9302" target="_blank">doi:10.1126/science.abf9302</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_starr_greaney.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_crawford.jpg" alt="Image for Dynamics of neutralizing antibody titers in the months after severe acute respiratory syndrome coronavirus 2 infection" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_crawford.html">Dynamics of neutralizing antibody titers in the months after severe acute respiratory syndrome coronavirus 2 infection</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">The Journal of infectious diseases</span>. 2021. <a href="https://academic.oup.com/jid/article/223/2/197/5916372" target="_blank">doi:10.1093/infdis/jiaa618</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_crawford.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_dingens.jpg" alt="Image for High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_dingens.html">High-resolution mapping of the neutralizing and binding specificities of pol
23yclonal sera post-HIV Env trimer vaccination</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2021. <a href="https://elifesciences.org/articles/64281" target="_blank">doi:10.7554/eLife.64281</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_dingens.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2021_greaney_d.jpg" alt="Image for Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2021_greaney_d.html">Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Cell host &amp; microbe</span>. 2021. <a href="https://www.cell.com/cell-host-microbe/pdf/S1931-3128(20)30624-7.pdf" target="_blank">doi:10.1016/j.chom.2020.11.007</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2021_greaney_d.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_loes.jpg" alt="Image for Attenuated influenza virions expressing the SARS-CoV-2 receptor-binding domain induce neutralizing antibodies in mice" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_loes.html">Attenuated influenza virions expressing the SARS-CoV-2 receptor-binding domain induce neutralizing antibodies in mice</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Andrea N Loes, Lauren E Gentles, Allison J Greaney, Katharine HD Crawford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Viruses</span>. 2020. <a href="https://www.mdpi.com/1999-4915/12/9/987" target="_blank">doi:10.3390/v12090987</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_loes.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_starr_a.jpg" alt="Image for Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_starr_a.html">Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Cell</span>. 2020. <a href="https://www.sciencedirect.com/science/article/pii/S0092867420310035?via%3Dihub" target="_blank">doi:10.1016/j.cell.2020.08.012</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_starr_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_dingens.jpg" alt="Image for Serological identification of SARS-CoV-2 infections among children visiting a hospital during the initial Seattle outbreak" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_dingens.html">Serological identification of SARS-CoV-2 infections among children visiting a hospital during the initial Seattle outbreak</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Nature communications</span>. 2020. <a href="https://www.nature.com/articles/s41467-020-18178-1" target="_blank">doi:10.1038/s41467-020-18178-1</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_dingens.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_hilton.png" alt="Image for dms-view: Interactive visualization tool for deep mutational scanning data" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_hilton.html">dms-view: Interactive visualization tool for deep mutational scanning data</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Sarah K Hilton*, John Huddleston*, Allison Black, Khrystyna North, Adam S Dingens, Trevor Bedford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">JOSS</span>. 2020. <a href="https://joss.theoj.org/papers/10.21105/joss.02353" target="_blank">doi:10.21105/joss.02353</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_hilton.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_gentles.png" alt="Image for Antibody neutralization of an influenza virus that uses neuraminidase for receptor binding" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_gentles.html">Antibody neutralization of an influenza virus that uses neuraminidase for receptor binding</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Lauren E Gentles, Hongquan Wan, Maryna C Eichelberger, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Viruses</span>. 2020. <a href="https://www.mdpi.com/1999-4915/12/6/597" target="_blank">doi:10.3390/v12060597</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_gentles.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_crawford.jpg" alt="Image for Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 spike protein for neutralization assays" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_crawford.html">Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 spike protein for neutralization assays</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">Viruses</span>. 2020. <a href="https://www.mdpi.com/1999-4915/12/5/513" target="_blank">doi:10.3390/v12050513</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_crawford.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_einav_b.png" alt="Image for When two are better than one: Modeling the mechanisms of antibody mixtures" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_einav_b.html">
23When two are better than one: Modeling the mechanisms of antibody mixtures</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Tal Einav, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PLoS computational biology</span>. 2020. <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007830" target="_blank">doi:10.1371/journal.pcbi.1007830</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_einav_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_roop.jpg" alt="Image for Identification of HIV-1 envelope mutations that enhance entry using macaque CD4 and CCR5" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_roop.html">Identification of HIV-1 envelope mutations that enhance entry using macaque CD4 and CCR5</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jeremy I Roop, Noah A Cassidy, Adam S Dingens, Jesse D Bloom, Julie Overbaugh</div><div class="max-w-none text-gray-500"><span class="italic">Viruses</span>. 2020. <a href="https://www.mdpi.com/1999-4915/12/2/241" target="_blank">doi:10.3390/v12020241</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_roop.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2020_xue.jpg" alt="Image for Linking influenza virus evolution within and between human hosts" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2020_xue.html">Linking influenza virus evolution within and between human hosts</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Katherine S Xue, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus evolution</span>. 2020. <a href="https://academic.oup.com/ve/article/6/1/veaa010/5739536" target="_blank">doi:10.1093/ve/veaa010</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2020_xue.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2019_xue_a.jpg" alt="Image for Reconciling disparate estimates of viral genetic diversity during human influenza infections" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2019_xue_a.html">Reconciling disparate estimates of viral genetic diversity during human influenza infections</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Katherine S Xue, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Nature genetics</span>. 2019. <a href="https://www.nature.com/articles/s41588-019-0349-3" target="_blank">doi:10.1038/s41588-019-0349-3</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2019_xue_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2019_lee.jpg" alt="Image for Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2019_lee.html">Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2019. <a href="https://elifesciences.org/articles/49324" target="_blank">
23doi:10.7554/eLife.49324</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2019_lee.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2019_russell.jpg" alt="Image for Single-cell virus sequencing of influenza infections that trigger innate immunity" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2019_russell.html">Single-cell virus sequencing of influenza infections that trigger innate immunity</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Alistair B Russell, Elizaveta Elshina, Jacob R Kowalsky, Aartjan JW Te Velthuis, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of virology</span>. 2019. <a href="https://journals.asm.org/doi/full/10.1128/jvi.00500-19" target="_blank">doi:10.1128/jvi.00500-19</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2019_russell.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2019_dingens_a.jpg" alt="Image for Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2019_dingens_a.html">Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Adam S Dingens, Dana Arenz, Julie Overbaugh, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Viruses</span>. 2019. <a href="https://www.mdpi.com/1999-4915/11/5/439" target="_blank">doi:10.3390/v11050439</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2019_dingens_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2019_soh.jpg" alt="Image for Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2019_soh.html">Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans</a></h2><div class="max-w-none text-gray-700 hidden lg:block">YQ Shirleen Soh, Louise H Moncla, Rachel Eguia, Trevor Bedford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2019. <a href="https://doi.org/10.7554/eLife.45079" target="_blank">doi:10.7554/eLife.45079</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2019_soh.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2019_dingens_b.jpg" alt="Image for An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies distinguishes functional and structural epitopes" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2019_dingens_b.html">An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies distinguishes functional and structural epitopes</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Adam S Dingens, Dana Arenz, Haidyn Weight, Julie Overbaugh, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Immunity</span>. 2019. <a href="https://www.sciencedirect.com/science/article/pii/S107476131830565X?via%3Dihub" target="_blank">doi:10.1016/j.immuni.2018.12.017</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2019_dingens_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2019_crawford.png" alt="Image for alignparse: A Python package for parsing complex features from high-throughput long-read sequencing" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2019_crawford.html">alignparse: A Python package for parsing complex features from high-throughput long-read sequencing</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Katharine HD Crawford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">JOSS</span>. 2019. <a href="https://doi.org/10.21105%2Fjoss.01915" target="_blank">doi:10.21105/joss.01915</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2019_crawford.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2019_machkovech.png" alt="Image for Comprehensive profiling of translation initiation in influenza virus infected cells" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2019_machkovech.html">
23Comprehensive profiling of translation initiation in influenza virus infected cells</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Heather M Machkovech, Jesse D Bloom, Arvind R Subramaniam</div><div class="max-w-none text-gray-500"><span class="italic">PLoS pathogens</span>. 2019. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007518" target="_blank">doi:10.1371/journal.ppat.1007518</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2019_machkovech.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2018_xue_a.jpg" alt="Image for Within-host evolution of human influenza virus" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2018_xue_a.html">Within-host evolution of human influenza virus</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Katherine S Xue, Louise H Moncla, Trevor Bedford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Trends in Microbiology</span>. 2018. <a href="https://www.cell.com/trends/microbiology/fulltext/S0966-842X(18)30043-X" target="_blank">doi:10.1016/j.tim.2018.02.007</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2018_xue_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2018_lee.jpg" alt="Image for Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2018_lee.html">Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Juhye M Lee, John Huddleston, Michael B Doud, Kathryn A Hooper, Nicholas C Wu, Trevor Bedford, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PNAS</span>. 2018. <a href="https://www.pnas.org/doi/abs/10.1073/pnas.1806133115" target="_blank">doi:10.1073/pnas.1806133115</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2018_lee.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2018_dingens.png" alt="Image for Complete functional mapping of infection-and vaccine-elicited antibodies against the fusion peptide of HIV" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2018_dingens.html">Complete functional mapping of infection-and vaccine-elicited antibodies against the fusion peptide of HIV</a></h2><div class="max-w-none text-gray-700 hidden lg:block">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</div><div class="max-w-none text-gray-500"><span class="italic">PLoS pathogens</span>. 2018. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007159" target="_blank">doi:10.1371/journal.ppat.1007159</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2018_dingens.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2018_hilton.jpg" alt="Image for Modeling site-specific am
23ino-acid preferences deepens phylogenetic estimates of viral sequence divergence" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2018_hilton.html">Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Sarah K Hilton, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Virus evolution</span>. 2018. <a href="https://academic.oup.com/ve/article/4/2/vey033/5163287" target="_blank">doi:10.1093/ve/vey033</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2018_hilton.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2018_doud.jpg" alt="Image for How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2018_doud.html">How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Michael B Doud*, Juhye M Lee*, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Nature communications</span>. 2018. <a href="https://www.nature.com/articles/s41467-018-03665-3" target="_blank">doi:10.1038/s41467-018-03665-3</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2018_doud.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2018_haddox.jpg" alt="Image for Mapping mutational effects along the evolutionary landscape of HIV envelope" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2018_haddox.html">Mapping mutational effects along the evolutionary landscape of HIV envelope</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Hugh K Haddox*, Adam S Dingens*, Sarah K Hilton, Julie Overbaugh, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2018. <a href="https://elifesciences.org/articles/34420" target="_blank">doi:10.7554/eLife.34420</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2018_haddox.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2018_xue_b.jpg" alt="Image for Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2018_xue_b.html">Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Katherine S Xue, Alexander L Greninger, Ailyn Pérez-Osorio, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">MSphere</span>. 2018. <a href="https://journals.asm.org/doi/full/10.1128/mspheredirect.00552-17" target="_blank">doi:10.1128/mspheredirect.00552-17</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2018_xue_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2018_russell.jpg" alt="Image for Extreme heterogeneity of influenza virus infection in single cells" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2018_russell.html">Extreme heterogeneity of influenza virus infection in single cells</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Alistair B Russell, Cole Trapnell, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2018. <a href="https://elifesciences.org/articles/32303" target="_blank">doi:10.7554/eLife.32303</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2018_russell.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2017_bloom.jpg" alt="Image for Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2017_bloom.html">Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Biology direct</span>. 2017. <a href="https://link.springer.com/article/10.1186/s13062-016-0172-z" target="_blank">doi:10.1186/s13062-016-0172-z</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2017_bloom.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2017_hilton.jpg" alt="Image for phydms: Software for phylogenetic analyses informed by deep mutational scanning" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2017_hilton.html">phydms: Software for phylogenetic analyses informed by deep mutational scanning</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Sarah K Hilton, Michael B Doud, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PeerJ</span>. 2017. <a href="https://peerj.com/articles/3657/" target="_blank">doi:10.7717/peerj.3657</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2017_hilton.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2017_xue.jpg" alt="Image for Parallel evolution of influenza across multiple spatiotemporal scales" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2017_xue.html">Parallel evolution of influenza across multiple spatiotemporal scales</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Katherine S Xue, Terry Stevens-Ayers, Angela P Campbell, Janet A Englund, Steven A Pergam, Michael Boeckh, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2017. <a href="https://elifesciences.org/articles/26875" target="_blank">doi:10.7554/eLife.26875.001</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2017_xue.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2017_dingens.jpg" alt="Image for Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2017_dingens.html">
23Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Adam S Dingens, Hugh K Haddox, Julie Overbaugh, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Cell host &amp; microbe</span>. 2017. <a href="https://www.cell.com/cell-host-microbe/pdf/S1931-3128(17)30196-8.pdf" target="_blank">doi:10.1016/j.chom.2017.05.003</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2017_dingens.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2017_ashenberg.png" alt="Image for Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2017_ashenberg.html">Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Orr Ashenberg, Jai Padmakumar, Michael B Doud, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PLoS pathogens</span>. 2017. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006288" target="_blank">doi:10.1371/journal.ppat.1006288</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2017_ashenberg.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2017_doud.png" alt="Image for Complete mapping of viral escape from neutralizing antibodies" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2017_doud.html">Complete mapping of viral escape from neutralizing antibodies</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Michael B Doud, Scott E Hensley, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PLoS pathogens</span>. 2017. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006271" target="_blank">doi:10.1371/journal.ppat.1006271</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2017_doud.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2016_haddox.png" alt="Image for Experimental estimation of the effects of all amino-acid mutations to HIV’s envelope protein on viral replication in cell culture" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2016_haddox.html">Experimental estimation of the effects of all amino-acid mutations to HIV’s envelope protein on viral replication in cell culture</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Hugh K Haddox, Adam S Dingens, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PLoS pathogens</span>. 2016. <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006114" target="_blank">doi:10.1371/journal.ppat.1006114</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2016_haddox.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2016_doud.jpg" alt="Image for Accurate measurement of the effects of all amino-acid mutations on influenza hemagglutinin" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2016_doud.html">Accurate measurement of the effects of all amino-acid mutations on influenza hemagglutinin</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Michael B Doud, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Viruses</span>. 2016. <a href="https://www.mdpi.com/1999-4915/8/6/155" target="_blank">doi:10.3390/v8060155</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2016_doud.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2016_xue.jpg" alt="Image for Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2016_xue.html">Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Katherine S Xue, Kathryn A Hooper, Anja R Ollodart, Adam S Dingens, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2016. <a href="https://elifesciences.org/articles/13974" target="_blank">doi:10.7554/eLife.13974.001</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2016_xue.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2015_bloom.jpg" alt="Image for Software for the analysis and visualization of deep mutational scanning data" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2015_bloom.html">Software for the analysis and visualization of deep mutational scanning data</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">BMC bioinformatics</span>. 2015. <a href="https://link.springer.com/article/10.1186/s12859-015-0590-4" target="_blank">doi:10.1186/s12859-015-0590-4</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2015_bloom.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2015_machkovech.jpg" alt="Image for Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and 
23Swine Viral Lineages" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2015_machkovech.html">Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Heather M Machkovech, Trevor Bedford, Marc A Suchard, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of virology</span>. 2015. <a href="https://journals.asm.org/doi/full/10.1128/jvi.01571-15" target="_blank">doi:10.1128/jvi.01571-15</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2015_machkovech.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2015_doud.jpg" alt="Image for Site-specific amino acid preferences are mostly conserved in two closely related protein homologs" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2015_doud.html">Site-specific amino acid preferences are mostly conserved in two closely related protein homologs</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Michael B Doud, Orr Ashenberg, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Molecular biology and evolution</span>. 2015. <a href="https://academic.oup.com/mbe/article/32/11/2944/982113" target="_blank">doi:10.1093/molbev/msv167</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2015_doud.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2015_hooper.jpg" alt="Image for Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2015_hooper.html">Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Kathryn A Hooper, James E Crowe Jr, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of virology</span>. 2015. <a href="https://journals.asm.org/doi/full/10.1128/jvi.00012-15" target="_blank">doi:10.1128/jvi.00012-15</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2015_hooper.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2014_bloom_a.jpg" alt="Image for An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2014_bloom_a.html">An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Molecular biology and evolution</span>. 2014. <a href="https://academic.oup.com/mbe/article/31/10/2753/1015257" target="_blank">doi:10.1093/molbev/msu220</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2014_bloom_a.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2014_bloom_b.jpg" alt="Image for An experimentally determined evolutionary model dramatically improves phylogenetic fit" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2014_bloom_b.html">An experimentally determined evolutionary model dramatically improves phylogenetic fit</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Molecular Biology and Evolution</span>. 2014. <a href="https://academic.oup.com/mbe/article/31/8/1956/2925795" target="_blank">doi:10.1093/molbev/msu173</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2014_bloom_b.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2014_thyagarajan.jpg" alt="Image for The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2014_thyagarajan.html">The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Bargavi Thyagarajan, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">eLife</span>. 2014. <a href="https://elifesciences.org/articles/3300" target="_blank">doi:10.7554/eLife.03300</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2014_thyagarajan.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2014_gong.png" alt="Image for Epistatically interacting substitutions are enriched during adaptive protein evolution" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2014_gong.html">Epistatically interacting substitutions are enriched during adaptive protein evolution</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Lizhi Ian Gong, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PLoS genetics</span>. 2014. <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004328" target="_blank">doi:10.1371/journal.pgen.1004328</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2014_gong.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2013_ashenberg.jpg" alt="Image for Mutational effects on stability are largely conserved during protein evolution" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2013_ashenberg.html">Mutational effects on stability are largely conserved during protein evolution</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Orr Ashenberg, Lizhi Ian Gong, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">PNAS</span>. 2013. <a href="https://www.pnas.org/doi/abs/10.1073/pnas.1314781111" target="_blank">doi:10.1073/pnas.1314781111</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2013_ashenberg.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2013_hooper.jpg" alt="Image for A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2013_hooper.html">A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Kathryn A Hooper, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of virology</span>. 2013. <a href="https://journals.asm.org/doi/full/10.1128/jvi.01889-13" target="_blank">doi:10.1128/jvi.01889-13</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2013_hooper.html">Read more →</a></div></div></div></li><li class="py-12"><div class="flex flex-col md:flex-row items-start"><div class="hidden md:block md:flex-none lg:w-48 lg:h-48 md:w-32 md:h-32 md:mr-4"><img src="/assets/papers/2013_gong.jpg" alt="Image for Stability-mediated epistasis constrains the evolution of an influenza protein" class="w-full h-auto object-cover rounded-lg"></div><div class="space-y-5 md:flex-grow"><div class="space-y-2"><h2 class="text-2xl leading-8 font-bold tracking-tight"><a class="text-gray-900 hover:text-gray-900 text-xl md:text-2xl no-underline" href="/papers/2013_gong.html">Stability-mediated epistasis constrains the evolution of an influenza protein</a></h2><div class="max-w-none text-gray-700 hidden lg:block">Lizhi Ian Gong, Marc A Suchard, Jesse D Bloom</div><div class="max-w-none text-gray-500"><span class="italic">Journal of virology</span>. 2013. <a href="https://elifesciences.org/articles/631" target="_blank">doi:10.7554/eLife.00631.001</a></div></div><div class="mt-4 md:mt-0 md:self-end"><a class="text-base leading-6 font-medium text-custom-orange no-underline" aria-label="read more about {{ paper.title }}" href="/papers/2013_gong.html">Read more →</a></div></div></div></li>
23<!--]--></ul></div></div></div></main><footer class="w-full p-4 bg-white text-center text-gray-400 text-sm"><p> Copyright © Jesse Bloom 2024-Present </p></footer></div></div>
24    
24<script>window.__VP_HASH_MAP__=JSON.parse("{\"index.md\":\"DPXu6HlU\",\"papers_2013_gong.md\":\"DQ2_iaSa\",\"papers_2013_ashenberg.md\":\"Dy_lq6VC\",\"papers_2014_bloom_b.md\":\"NdBLZwqR\",\"papers_2014_gong.md\":\"D6U3hSrc\",\"papers_2013_hooper.md\":\"OE9BAPOa\",\"papers_2015_doud.md\":\"DUDdTpYR\",\"papers_2015_hooper.md\":\"DjuqsHao\",\"papers_2015_machkovech.md\":\"Bv4xwsMQ\",\"papers_2016_doud.md\":\"BpehtoOt\",\"papers_2016_xue.md\":\"BkPMBzxe\",\"papers_2017_ashenberg.md\":\"C_8Xmhbd\",\"papers_2017_bloom.md\":\"D3odKrzn\",\"papers_2016_haddox.md\":\"BAPuxbcI\",\"papers_2017_hilton.md\":\"By-wezfO\",\"papers_2017_doud.md\":\"CdybD3Il\",\"papers_2017_dingens.md\":\"B5tmU7S1\",\"papers_2018_dingens.md\":\"DC9Q2LGc\",\"papers_2017_xue.md\":\"DZdIhBzj\",\"readme.md\":\"DM31n7di\",\"papers_2018_haddox.md\":\"Cq7ulGEC\",\"papers_2019_soh.md\":\"lW5rCTO0\",\"papers_2023_bloom_a.md\":\"CWgXKCqz\",\"papers_2020_loes.md\":\"Ddsx7g5E\",\"papers_2023_bloom_b.md\":\"DDWuMt-F\",\"papers_2019_russell.md\":\"6sceOOpJ\",\"papers_2019_lee.md\":\"DhePlFgq\",\"papers_2018_hilton.md\":\"CMCZjGz9\",\"papers_2020_dingens.md\":\"C-IOLxle\",\"papers_2019_dingens_a.md\":\"DEOOp8SB\",\"papers_2019_dingens_b.md\":\"DT8_Gxrn\",\"papers_2021_greaney_b.md\":\"BmfzOLif\",\"papers_2018_xue_a.md\":\"CdyaW5O3\",\"papers_2024_dadonaite_a.md\":\"B1vnwKrS\",\"papers_2018_lee.md\":\"Cr_aE_D3\",\"papers_2018_doud.md\":\"CqWnmt5Z\",\"papers_2020_gentles.md\":\"BnEVLRlz\",\"papers_2020_hilton.md\":\"DdFgNwZH\",\"papers_2022_farrell.md\":\"DFTVo4mW\",\"papers_2020_starr_a.md\":\"BzBMGQWy\",\"papers_2022_starr_greaney_b.md\":\"CaPqIpND\",\"papers_2014_bloom_a.md\":\"DcvJTeqh\",\"papers_2020_roop.md\":\"Si0B2MH8\",\"papers_2020_xue.md\":\"C7KDUeKs\",\"papers_2021_bloom_a.md\":\"DqnGDa5V\",\"papers_2021_starr_b.md\":\"Chk1hCK1\",\"papers_2021_dingens.md\":\"DhRtZdkh\",\"papers_2021_eguia.md\":\"Dm25k0_z\",\"papers_2021_greaney_a.md\":\"DfbrEqLO\",\"papers_2018_russell.md\":\"BS9bLjcL\",\"papers_2021_greaney_d.md\":\"CUTp-1o_\",\"papers_2020_einav_b.md\":\"CVYgdar5\",\"papers_2021_soh.md\":\"3xJwjFxX\",\"papers_2014_thyagarajan.md\":\"DIL4wrGh\",\"papers_2022_gentles.md\":\"nF8lzraI\",\"people_caelan-radford.md\":\"C31aklI7\",\"papers_2021_starr_greaney.md\":\"DRbz0xmC\",\"papers_2023_bacsik.md\":\"BPgyiKtE\",\"posts_2024-05-25_h5-dms.md\":\"BnGYHSL1\",\"posts_2024-11-20_escapecalc_update.md\":\"Bk6tJ1BR\",\"papers_2022_yu.md\":\"eEdVDuKL\",\"people_bernadeta-dadonaite.md\":\"rIfbGvjZ\",\"people_lindsey-doyle.md\":\"D6r4Yakm\",\"people_sheri-harari.md\":\"DGTIt-9t\",\"people_lizzie-plender.md\":\"DylgZNR4\",\"people_will-perlichek.md\":\"DAzIuBwi\",\"papers_2015_bloom.md\":\"DxXkmdsG\",\"papers_2021_crawford.md\":\"Dli_7GyE\",\"papers_2021_starr_greaney_a.md\":\"CVqRhvPC\",\"papers_2022_starr_greaney_a.md\":\"CjqMK9W-\",\"papers_2024_hannon.md\":\"B9gHkc-N\",\"papers_2024_loes.md\":\"CngF69aP\",\"papers_2024_welsh.md\":\"rJTE5wYS\",\"people_xiaohui-ju.md\":\"CFI0tNxq\",\"papers_2025_aditham.md\":\"l5bUFEqr\",\"posts_2024-09-24_flu_seqneut.md\":\"CKmzPb6c\",\"papers_2025_dadonaite_b.md\":\"DLDNelJ2\",\"papers_2025_kikawa.md\":\"DvQF2mO2\",\"papers_2025_kikawa_b.md\":\"C60r_IGK\",\"papers_2022_greaney_c.md\":\"BceMrKE8\",\"papers_2025_larsen.md\":\"DdTBIrwj\",\"papers_2025_larsen_f.md\":\"C04RCsH-\",\"papers_2025_simonich.md\":\"Ec3TbcHG\",\"papers_2025_xu.md\":\"Dk1X1HLV\",\"papers_2022_hannon.md\":\"DqwAvnOW\",\"papers_2025_yu.md\":\"DU5Njdwr\",\"papers_2026_ahn.md\":\"tg4dvOOS\",\"papers_2026_dadonaite.md\":\"C58vJd36\",\"papers_2026_harari.md\":\"BJR0_QBN\",\"papers_2026_kikawa.md\":\"iyEbK6Sz\",\"papers_2026_kikawa_b.md\":\"BYIqocCr\",\"papers_2026_loes.md\":\"DkCU2YJ2\",\"papers_2022_starr_a.md\":\"CkgIfhYD\",\"papers_2026_simonich_dms.md\":\"CjVneIkv\",\"papers_index.md\":\"OHKOyLXE\",\"papers_2020_crawford.md\":\"I3sMvIPC\",\"people_andrew-butler.md\":\"Bcs8B6o7\",\"posts_2025-03-12_h3-seqneut.md\":\"Imi11wrS\",\"people_brendan-larsen.md\":\"BsKHR_Jy\",\"posts_2025-03-12_rsv-evol-neut.md\":\"B7rQ_W8_\",\"posts_2025-05-27_yu-h3.md\":\"DG_Pvycg\",\"posts_2025-08-26_chikv_dms.md\":\"COLWYBTv\",\"papers_2021_greaney_welsh.md\":\"CoZBOoBR\",\"posts_2025-09-09_flu_seqneut.md\":\"BqlYKcg4\",\"posts_2026-02-20_flu_seqneut.md\":\"DMtSjl5C\",\"projects_dms-vep-pipeline-3.md\":\"DYNIxlKA\",\"papers_2022_greaney_a.md\":\"DuUTgxKD\",\"posts_index.md\":\"C4U6kLWr\",\"projects_alignparse.md\":\"BKLuDyeX\",\"projects_seqneut-pipeline.md\":\"Bxy9msH9\",\"posts_2025-08-18_kp311_dms.md\":\"F_NwjSxX\",\"papers_2022_greaney_b.md\":\"p-Tw8GRu\",\"projects_index.md\":\"BVCQlbZL\",\"projects_neutcurve.md\":\"DdrGfNiK\",\"projects_polyclonal.md\":\"DHWqK45A\",\"papers_2018_xue_b.md\":\"CwHhayD0\",\"posts_2026-07-23_ha_mhcii.md\":\"CUoDQdEm\",\"papers_2023_dadonaite_crawford_radford.md\":\"B9PLsy5Q\",\"people_wenlin-ren.md\":\"BiBZVBYm\",\"people_caleb-carr.md\":\"WIIvbQ-5\",\"people_caroline-kikawa.md\":\"CIoHlen8\",\"people_cassandra-simonich.md\":\"BEF7skSw\",\"people_catherine-jacob-dolan.md\":\"BpJotwRd\",\"people_gavin-juviler.md\":\"BBp9pj3a\",\"people_index.md\":\"dFIFbwt8\",\"research_research-aims.md\":\"32m7eud_\",\"people_john-huddleston.md\":\"BM0lTcvj\",\"papers_2025_radford.md\":\"C2J871Gq\",\"people_sara-sunshine.md\":\"B1rP-p1I\",\"posts_2024-12-18_rabv-g-dms.md\":\"DnKnOGTA\",\"people_lucas-kampman.md\":\"BofkCKZg\",\"papers_2024_bloom.md\":\"9KMbcDNZ\",\"people_jesse-bloom.md\":\"DxzQPDiI\",\"papers_2023_radford.md\":\"CvhRpxQi\",\"papers_2021_greaney_c.md\":\"DUqDg3UT\",\"papers_2019_xue_a.md\":\"D1bPFAFs\",\"papers_2023_kikawa.md\":\"BX5uAGai\",\"research_index.md\":\"ZqtWB0m-\",\"papers_2024_dadonaite_b.md\":\"BZHnKM88\",\"papers_2019_crawford.md\":\"CAscOCk4\",\"papers_2024_carr.md\":\"DG54nUav\",\"papers_2025_dadonaite.md\":\"4P_f68NP\",\"papers_2019_machkovech.md\":\"mtdpbeDg\",\"posts_2025-01-21_sars2-infant-sera.md\":\"BZC35RY6\",\"projects_dms-viz.md\":\"C2_kxF1z\",\"papers_2023_bloom_c.md\":\"Bmmp0_qS\"}");
24window.__VP_SITE_DATA__=JSON.parse("{\"lang\":\"en-US\",\"dir\":\"ltr\",\"title\":\"Bloom Lab\",\"description\":\"We study the evolution of viruses.\",\"base\":\"/\",\"head\":[],\"router\":{\"prefetchLinks\":true},\"appearance\":false,\"themeConfig\":{},\"locales\":{},\"scrollOffset\":134,\"cleanUrls\":false}");</script>
24
25    
26  </body>
27</html>

Line numbers count LF bytes from the start of the resource, as the search results do. Vendor segments are library code the classifier recognised; they are stored but not indexed. Bytes are shown as Latin1 characters, one per byte.