Preprints

Chance and contingency in B cell evolution limit the similarity of antibody responses to infection across individuals, bioRxiv
Marcos C Vieira, Anna-Karin E. Palm, Christopher T. Stamper, Micah E. Tepora, Khoa D. Nguyen, Tho D. Pham, Scott D. Boyd, Patrick C. Wilson, Sarah Cobey
urlpdf

Time-varying transmission heterogeneity of SARS and COVID-19 in Hong Kong, Research Square
Dillon Adam, Katelyn Gostic, Tim Tsang, Peng Wu, Wey Wen Lim, Amy Yeung, Jessica Wong, Eric Lau, Zhanwei Du, Dongxuan Chen, Lai-Ming Ho, Mario Martín-Sánchez, Simon Cauchemez, Sarah Cobey, Gabriel Leung, Benjamin Cowling
urlpdf

SARS-CoV-2 testing in Florida, Illinois, and Maryland: access and barriers, medRxiv
Steven J. Clipman, Amy Wesolowski, Shruti H. Mehta, Smisha Agarwal, Sarah Cobey, Derek A.T. Cummings, Dustin G. Gibson, Alain B. Labrique, Gregory D. Kirk, Sunil S. Solomon
urlpdf

2022

Getting the most out of noisy surveillance data, Nature Computational Science
Lauren McGough
urlpdf

Original antigenic sin and childhood immune responses against SARS-CoV-2, Science
Sarah Cobey and Scott E. Hensley
urlpdf

PARIS and SPARTA: Finding the Achilles’ Heel of SARS-CoV-2, mSphere
Viviana Simon, Vamsi Kota, Ryan F. Bloomquist, Hannah B. Hanley, David Forgacs, Savita Pahwa, Suresh Pallikkuth, Loren G. Miller, Joanna Schaenman, Michael R. Yeaman, David Manthei, Joshua Wolf, Aditya H. Gaur, Jeremie H. Estepp, Komal Srivastava, Juan Manuel Carreño, Frans Cuevas, Ali H. Ellebedy, Aubree Gordon, Riccardo Valdez, Sarah Cobey, Elaine F. Reed, Ravindra Kolhe, Paul G. Thomas, Stacey Schultz-Cherry, Ted M. Ross
urlpdf

Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA, Nature Communications
Reese Richardson, Emile Jorgensen, Philip Arevalo, Tobias M. Holden, Katelyn M. Gostic, Massimo Pacilli, Isaac Ghinai, Shannon Lightner, Sarah Cobey, Jaline Gerardin
urlpdf

SARS-CoV-2 infection among pregnant people at labor and delivery and changes in Infection rates in the general population: lessons learned from Illinois, Public Health Reports
Sonal Goyal, Jaline Gerardin, Sarah Cobey, Crystal Son, Owen McCarthy, Arielle Dror, Shannon Lightner, Ngozi O. Ezike, Wayne A. Duffus, Amanda C. Bennett
urlpdf

Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission, Nature Communications
Yun Lin, Bingyi Yang, Sarah Cobey, Eric H. Y. Lau, Dillon C. Adam, Jessica Y. Wong, Helen S. Bond, Justin K. Cheung, Faith Ho, Huizhi Gao, Sheikh Taslim Ali, Nancy H. L. Leung, Tim K. Tsang, Peng Wu, Gabriel M. Leung, Benjamin J. Cowling
urlpdf

Modeling comparative cost-effectiveness of SARS-CoV-2 vaccine dose fractionation in India, Nature Medicine
Zhanwei Du, Lin Wang, Abhishek Pandey, Wey Wen Lim, Matteo Chinazzi, Ana Pastore y. Piontti, Eric H. Y. Lau, Peng Wu, Anup Malani, Sarah Cobey, Benjamin J. Cowling
urlpdf

The potential beneficial effects of vaccination on the evolution of antigenically evolving pathogens, American Naturalist
Frank T. Wen, Anup Malani, and Sarah Cobey
urlpdf

2021

Of variants and vaccines, Cell
Nathan D. Grubaugh and Sarah Cobey
urlpdf

Improvements in Severe Acute Respiratory Syndrome Coronavirus 2 testing cascade in the United States: data from serial cross-sectional assessments, Clinical Infectious Diseases
Steven J Clipman, Amy Wesolowski, Shruti H Mehta, Sarah Cobey, Derek A T Cummings, Sunil S Solomon
urlpdf

Fractionation of COVID-19 vaccine doses could extend limited supplies and reduce mortality, Nature Medicine
Benjamin J. Cowling, Wey Wen Lim, and Sarah Cobey
urlpdf

Influenza immune escape under heterogeneous host immune histories, Trends in Microbiology
Rachel J. Oidtman, Philip Arevalo, Qifang Bi, Lauren McGough, Christopher Joel Russo, Diana Vera Cruz, Marcos Costa Vieira, and Katelyn M. Gostic
url

Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases, Nature Communications
Marcos C. Vieira, Celeste M. Donato, Philip Arevalo, Guus F. Rimmelzwaan, Timothy Wood, Liza Lopez, Q. Sue Huang, Vijaykrishna Dhanasekaran, Katia Koelle, and Sarah Cobey
urlpdf

Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020, BMC Public Health
Tobias M. Holden, Reese A. K. Richardson, Philip Arevalo, Wayne A. Duffus, Manuela Runge, Elena Whitney, Leslie Wise, Ngozi O. Ezike, Sarah Patrick, Sarah Cobey and Jaline Gerardin
urlpdf

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

Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination, Nature Reviews Immunology
Sarah Cobey, Daniel B. Larremore, Yonatan H. Grad, and Marc Lipsitch
url

COVID-19 infection, reinfection, and vaccine effectiveness in Arizona frontline and essential workers: Protocol for a longitudinal cohort study, JMIR Research Protocols
Karen Lutrick, Katherine D Ellingson, Zoe Baccam, Patrick Rivers, Shawn Beitel, Joel Parker, James Hollister, Xiaoxiao Sun, Joe K Gerald, Kenneth Komatsu, Elizabeth Kim, Bonnie LaFleur, Lauren Grant, Young M Yoo, Archana Kumar, Julie Mayo Lamberte, Benjamin J Cowling, Sarah Cobey, Natalie J Thornburg, Jennifer K Meece, Preeta Kutty, Janko Nikolich-Zugich, Mark G Thompson, Jefferey L Burgess
urlpdf

An egg-derived sulfated N-Acetyllactosamine glycan is an antigenic decoy of influenza virus vaccines, mBio
Jenna J. Guthmiller, Henry A. Utset, Carole Henry, Lei Li, Nai-Ying Zheng, Weina Sun, Marcos C. Vieira, Seth Zost, Min Huang, Scott E. Hensley, Sarah Cobey, Peter Palese, and Patrick C. Wilson
urlpdf

Model-informed COVID-19 vaccine prioritization strategies by age and serostatus, Science
Kate M Bubar, Kyle Reinholt, Stephen M Kissler, Marc Lipsitch, Sarah Cobey, Yonatan Grad, and Daniel B Larremore
urlpdf

2020

Preexisting immunity shapes distinct antibody landscapes after influenza virus infection and vaccination in humans, Science Translational Medicine
Haley L. Dugan, Jenna J. Guthmiller, Philip Arevalo, Min Huang, Yao-Qing Chen, Karlynn E. Neu, Carole Henry, Nai-Ying Zheng, Linda Yu-Ling Lan, Micah E. Tepora, Olivia Stovicek, Dalia Bitar, Anna-Karin E. Palm, Christopher T. Stamper, Siriruk Changrob, Henry A. Utset, Lynda Coughlan, Florian Krammer, Sarah Cobey, Patrick C. Wilson
urlpdf

Practical considerations for measuring the effective reproductive number, Rt, PLOS Computational Biology
Katelyn M Gostic, Lauren McGough, Edward Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James Munday, Nikos Bosse, Katharine Sherratt, Robin M Thompson, Laura F White, Jana Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, and Sarah Cobey
urlpdfcode

Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility, Nature Communications
Sigrid Gouma, Kangchon Kim, Madison E Weirick, Megan E Gumina, Angela Branche, David J Topham, Emily T Martin, Arnold S Monto, Sarah Cobey, and Scott E Hensley
urlpdfgithub

Earliest infections predict the age distribution of seasonal influenza A cases, eLife
Philip Arevalo, Huong Q. McLean, Edward A. Belongia, and Sarah Cobey
urlpdfcode

Modeling infectious disease dynamics, Science
Sarah Cobey
url

2019

Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season, Clinical Infectious Diseases
Sigrid Gouma, Seth J. Zost, Kaela Parkhouse, Angela Branche, David J Topham, Sarah Cobey, Scott E Hensley
url

Age-specific differences in the dynamics of protective immunity to influenza, Nature Communications
Sylvia Ranjeva, Rahul Subramanian, Vicky J. Fang, Gabriel M. Leung, Dennis K. M. Ip, Ranawaka A.P.M. Perera, J. S. Malik Peiris, Benjamin J. Cowling*, and Sarah Cobey*
urlpdfcode

Influenza virus vaccination elicits poorly adapted B cell responses in elderly individuals, Cell Host & Microbe
Carole Henry, Nai-Ying Zheng, Min Huang, Alexandra Cabanov, Karla Thatcher Rojas, Kaval Kaur, Sarah F. Andrews, Anna-Karin E. Palm, Yao-Qing Chen, Yang Li, Katerina Hoskova, Henry A. Utset, Marcos C. Vieira, Jens Wrammert, Rafi Ahmed, Jeanne Holden-Wiltse, David J. Topham, John J. Treanor, Hildegund C. Ertl, Kenneth E. Schmader, Sarah Cobey, Florian Krammer, Scott E. Hensley, Harry Greenberg, Xiao-Song He, and Patrick C.Wilson
url

2018

Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination, The Journal of Clinical Investigation
Karlynn E. Neu, Jenna J. Guthmiller, Min Huang, Jennifer La, Marcos C. Vieira, Kangchon Kim, Nai-Ying Zheng, Mario Cortese, Micah E. Tepora, Natalie J. Hamel, Karla Thatcher Rojas, Carole Henry, Dustin Shaw, Charles L. Dulberger, Bali Pulendran, Sarah Cobey, Aly A. Khan, Patrick C. Wilson
url

Repeated vaccination may protect children from influenza infection, JAMA Network Open
Sarah Cobey
url

Estimating vaccine-driven selection in seasonal influenza, Viruses
Frank T. Wen, Sidney M. Bell, Trevor Bedford, and Sarah Cobey
urlpdfcode

Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a vaccine, PLOS Computational Biology
Francisco Y. Cai, Thomas Fussell, Sarah Cobey, and Marc Lipsitch
urlpdf

Characterization of the immunologic repertoire: A quick start guide, Immunological Reviews
Patrick C. Wilson and Sarah Cobey
urlpdf

Immune history and influenza vaccine effectiveness, Vaccines
Joseph A. Lewnard and Sarah Cobey
urlpdf

Selection and neutral mutations drive pervasive mutability losses in long-lived B cell lineages, Molecular Biology and Evolution
Marcos C. Vieira, Daniel Zinder, and Sarah Cobey
urlpdfcode

Poor immunogenicity, not vaccine strain egg adaptation, may explain the low H3N2 influenza vaccine effectiveness in 2012-2013, Clinical Infectious Diseases
Sarah Cobey, Sigrid Gouma, Kaela Parkhouse, Benjamin S. Chambers, Hildegund C. Ertl, Kenneth E. Schmader, Rebecca A. Halpin, Xudong Lin, Timothy B. Stockwell, Suman R. Das, Emily Landon, Vera Tesic, Ilan Youngster, Benjamin A. Pinsky, David E. Wentworth, Scott E. Hensley, and Yonatan H. Grad
urlpdfpress releaseresponse to Skowronski and De Serres

2017

Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies to egg-adapted vaccine strains, Proceedings of the National Academy of Sciences
Seth J. Zost, Kaela Parkhouse, Megan E. Gumina, Kangchon Kim, Sebastian Diaz Perez, Patrick C. Wilson, John J. Treanor, Andrea J. Sant, Sarah Cobey, and Scott E. Hensley
urlpdfcodepress releaseF1000 recommendation

Recurring infection with ecologically distinct human papillomavirus (HPV) types can explain high prevalence and diversity, Proceedings of the National Academy of Sciences
Sylvia Ranjeva, Edward B. Baskerville, Vanja Dukic, Luisa L. Villa, Eduardo Lazcano-Ponce, Anna R. Giuliano, Greg Dwyer, and Sarah Cobey
urlpdfcodepress release

Host population structure and treatment frequency maintain balancing selection on drug resistance, Journal of the Royal Society Interface
Sarah Cobey, Edward B. Baskerville, Caroline Colijn, William Hanage, Christophe Fraser, and Marc Lipsitch
urlpdfcode

Immune history and influenza virus susceptibility, Current Opinion in Virology
Sarah Cobey and Scott E. Hensley
urlpdflocal file

Does influenza drive absolute humidity?, Proceedings of the National Academy of Sciences
Edward B. Baskerville and Sarah Cobey
urlpdfcode

Sick if you do, sick if you don’t, Nature Ecology & Evolution
Sarah Cobey
url

2016

Limits to causal inference with state-space reconstruction for infectious disease, PLOS One
Sarah Cobey and Edward B. Baskerville
urlpdfcode

Viral factors in influenza pandemic risk assessment, eLife
Marc Lipsitch, Wendy Barclay, Rahul Raman, Charles J. Russell, Jessica A. Belser, Sarah Cobey, Peter M. Kasson, James O. Lloyd-Smith, Sebastian Maurer-Stroh, Steven Riley, Catherine A. A. Beauchemin, Trevor Bedford, Thomas C. Friedrich, Andreas Handel, Sander Herfst, Pablo R. Murcia, Benjamin Roche, Claus O. Wilke, and Colin A. Russell
urlpdf

Explaining the geographical origins of seasonal influenza A (H3N2), Proceedings of the Royal Society B
Frank Wen, Trevor Bedford, and Sarah Cobey
urlpdfcodepress releaselocal file

2015

K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets, Microbial Genomics
Alberto Pessia, Yonatan Grad, Sarah Cobey, Juha Santeri Puranen, and Jukka Corander
urlpdf

The evolution within us, Philosophical Transactions of the Royal Society B
Sarah Cobey, Patrick Wilson, and Frederick A. Matsen IV
urlpdf

Tradeoffs in antibody repertoires to complex antigens, Philosophical Transactions of the Royal Society B
Lauren M. Childs, Edward B. Baskerville, and Sarah Cobey
urlpdfcode

Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health, Evolutionary Applications
Gabriel G. Perron, R. Fredrik Inglis, Pleuni S. Pennings, and Sarah Cobey
urlpdf

2014

Pathogen evolution and the immunological niche, Annals of the New York Academy of Sciences
Sarah Cobey
urlpdf

Pre-2014

Improving influenza vaccine virus selection: Report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010 (2013), Influenza and Other Respiratory Diseases
WHO Writing Group, William K. Ampofo, Norman Baylor, Sarah Cobey, Nancy J. Cox, Sharon Daves, Steven Edwards, Neil Ferguson, Gary Grohmann, Alan Hay, Jacqueline Katz, Kornnika Kullabutr, Linda Lambert, Roland Levandowski, A. C. Mishra, Arnold Monto, Marilda Siqueira, Masato Tashiro, Anthony L. Waddell, Niteen Wairagkar, John Wood, Maria Zambon, and Wenqing Zhang
urlpdf

The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15th, 2013 (2013), Standards in Genomic Sciences
Benjamin D. Shogan, Daniel P. Smith, Aaron I. Packman, Scott T. Kelley, Emily M Landon, Seema Bhangar, Gary J. Vora, Rachael M. Jones, Kevin Keegan, Brent Stephens, Tiffanie Ramos, Benjamin C. Kirkup, Jr., Hal Levin, Mariana Rosenthal, Betsy Foxman, Eugene B. Chang, Jeffrey Siegel, Sarah Cobey, Gary An, John C. Alverdy, Paula J. Olsiewski, Mark O. Martin, Rachel Marrs, Mark Hernandez, Scott Christley, Michael Morowitz, Stephen Weber, and Jack Gilbert
urlpdf

Pathogen coexistence through hidden regimes of apparent competition (2013), American Naturalist
Sarah Cobey and Marc Lipsitch
urlpdfcodelocal file

Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes (2012), Science
Sarah Cobey and Marc Lipsitch
urlpdfcodeF1000 recommendationlocal file

Anticipating the species jump: Surveillance for emerging viral threats (2011), Zoonoses and Public Health
M. L. Flanagan, C. Parrish, S. Cobey, G. E. Glass, R. M. Bush, and T. J. Leighton
urlpdflocal file

Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method (2011), PLOS Medicine
Edward Goldstein, Sarah Cobey, Saki Takahashi, Joel C. Miller, and Marc Lipsitch
urlpdf

Strength and tempo of selection revealed in viral gene genealogies (2011), BMC Evolutionary Biology
Trevor Bedford, Sarah Cobey, and Mercedes Pascual
urlpdf

Consequences of host heterogeneity, epitope immunodominance, and immune breadth for strain competition (2011), Journal of Theoretical Biology
Sarah Cobey and Mercedes Pascual
urlpdflocal file

Ecological factors driving the long-term evolution of influenza’s host range (2010), Proceedings of the Royal Society B
Sarah Cobey, Mercedes Pascual, and Ulf Dieckmann
urlpdf

Global migration dynamics underlie evolution and persistence of human influenza A (H3N2) (2010), PLOS Pathogens
Trevor Bedford, Sarah Cobey, Peter Beerli, and Mercedes Pascual
urlpdf

Capturing escape in infectious disease dynamics (2008), Trends in Ecology and Evolution
Sarah Cobey and Katia Koelle
urlpdflocal file

Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans (2006), Science
Katia Koelle*, Sarah Cobey*, Bryan Grenfell, and Mercedes Pascual
urlpdflocal file

Sea lampreys in the Great Lakes (2005), Ecological Networks
Sarah Cobey
url