People

Sarah E. Cobey, PhD

Broadly, my group investigates the coevolution of pathogens and hosts’ adaptive immunity. We use computational and mathematical tools to test hypotheses and to advance theory. Our earlier work focused on the evolutionary consequences of immune-mediated competition between different pathogen strains, including pneumococcus, human papillomavirus, and especially influenza. More recently, our focus has expanded to include the related dynamics of the host immune response. We are investigating the evolution of antibody repertoires within hosts over time, in particular to identify the roles of infection history, chance, vaccination, and host genetics in generating the diversity of B cell responses. This research involves linking epidemiological and immunological observations of B cells to the antigenic and genetic evolution of influenza viruses. Consequently, it makes extensive use of longitudinal dynamical models of individuals and birth cohorts as well as techniques from molecular evolution to investigate coevolution across scales.



Understanding the dynamics of vaccination is another area of focus. We have investigated the actual and expected impacts of vaccines against pneumococcus, human papillomavirus, and influenza. With influenza, we have been investigating the impact of the vaccine on viral transmission and local evolution and how immune history might reduce the vaccine’s effectiveness and alter selective pressures. Improving vaccination strategies given hosts’ diverse immune histories and the potential for rapid evolution by the pathogen is a long-term aim of our work. Ultimately, we want to explain coevolution sufficiently well to enable prediction, or at least to determine when prediction is not feasible.

Harvard School of Public Health
Postdoctoral - Infectious disease dynamics
2013

University of Michigan, Ann Arbor
PhD - Ecology & Evolution
2009

Princeton University
AB - Ecology & Evolution
2002

Modeling infectious disease dynamics.
Cobey S. Modeling infectious disease dynamics. Science. 2020 May 15; 368(6492):713-714.
PMID: 32332062

Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season.
Gouma S, Zost SJ, Parkhouse K, Branche A, Topham DJ, Cobey S, Hensley SE. Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season. Clin Infect Dis. 2019 Oct 09.
PMID: 31598646

Age-specific differences in the dynamics of protective immunity to influenza.
Ranjeva S, Subramanian R, Fang VJ, Leung GM, Ip DKM, Perera RAPM, Peiris JSM, Cowling BJ, Cobey S. Age-specific differences in the dynamics of protective immunity to influenza. Nat Commun. 2019 04 10; 10(1):1660.
PMID: 30971703

Influenza Virus Vaccination Elicits Poorly Adapted B Cell Responses in Elderly Individuals.
Henry C, Zheng NY, Huang M, Cabanov A, Rojas KT, Kaur K, Andrews SF, Palm AE, Chen YQ, Li Y, Hoskova K, Utset HA, Vieira MC, Wrammert J, Ahmed R, Holden-Wiltse J, Topham DJ, Treanor JJ, Ertl HC, Schmader KE, Cobey S, Krammer F, Hensley SE, Greenberg H, He XS, Wilson PC. Influenza Virus Vaccination Elicits Poorly Adapted B Cell Responses in Elderly Individuals. Cell Host Microbe. 2019 03 13; 25(3):357-366.e6.
PMID: 30795982

Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination.
Neu KE, Guthmiller JJ, Huang M, La J, Vieira MC, Kim K, Zheng NY, Cortese M, Tepora ME, Hamel NJ, Rojas KT, Henry C, Shaw D, Dulberger CL, Pulendran B, Cobey S, Khan AA, Wilson PC. Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination. J Clin Invest. 2019 01 02; 129(1):93-105.
PMID: 30457979

Response to Skowronski and De Serres.
Cobey S, Grad YH. Response to Skowronski and De Serres. Clin Infect Dis. 2018 10 15; 67(9):1476.
PMID: 29688302

Repeated Vaccination May Protect Children From Influenza Infection.
Cobey S. Repeated Vaccination May Protect Children From Influenza Infection. JAMA Netw Open. 2018 10 05; 1(6):e183730.
PMID: 30646259

Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine.
Cai FY, Fussell T, Cobey S, Lipsitch M. Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine. PLoS Comput Biol. 2018 10; 14(10):e1006333.
PMID: 30273332

Estimating Vaccine-Driven Selection in Seasonal Influenza.
Wen FT, Bell SM, Bedford T, Cobey S. Estimating Vaccine-Driven Selection in Seasonal Influenza. Viruses. 2018 09 18; 10(9).
PMID: 30231576

Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012-2013.
Cobey S, Gouma S, Parkhouse K, Chambers BS, Ertl HC, Schmader KE, Halpin RA, Lin X, Stockwell TB, Das SR, Landon E, Tesic V, Youngster I, Pinsky BA, Wentworth DE, Hensley SE, Grad YH. Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012-2013. Clin Infect Dis. 2018 07 18; 67(3):327-333.
PMID: 29471464

View All Publications

Neubauer Faculty Development Fellowship
University of Chicago
2016

James S. McDonnell Foundation Complex Systems Scholar Award
University of Chicago
2014

NIH New Innovator Award
University of Chicago
2014

NIH Kirchstein National Research Service Award
Harvard School of Public Health
2011

NSF Graduate Research Fellowship
University of Michigan
2005

Sigma Xi Society
Princeton University
2002

Phi Beta Kappa
Princeton University
2002

Senior Book Prize, Ecology & Evolution
Princeton University
2002