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Sarah Cobey

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentEcology & Evolution
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    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.


    Collapse Biography 
    Collapse education and training
    Princeton UniversityAB2002Ecology & Evolution
    University of Michigan, Ann ArborPhD2009Ecology & Evolution
    Harvard School of Public HealthPostdoctoral2013Infectious disease dynamics
    Collapse awards and honors
    2002Sigma Xi Society, Princeton University
    2002Phi Beta Kappa, Princeton University
    2002Senior Book Prize, Ecology & Evolution, Princeton University
    2005NSF Graduate Research Fellowship, University of Michigan
    2011NIH Kirchstein National Research Service Award, Harvard School of Public Health
    2014James S. McDonnell Foundation Complex Systems Scholar Award, University of Chicago
    2014NIH New Innovator Award, University of Chicago
    2016Neubauer Faculty Development Fellowship, University of Chicago

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    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. 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.
      View in: PubMed
    2. 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.
      View in: PubMed
    3. 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.
      View in: PubMed
    4. 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.
      View in: PubMed
    5. Cobey S, Grad YH. Response to Skowronski and De Serres. Clin Infect Dis. 2018 10 15; 67(9):1476. PMID: 29688302.
      View in: PubMed
    6. Cobey S. Repeated Vaccination May Protect Children From Influenza Infection. JAMA Netw Open. 2018 10 05; 1(6):e183730. PMID: 30646259.
      View in: PubMed
    7. 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.
      View in: PubMed
    8. Wen FT, Bell SM, Bedford T, Cobey S. Estimating Vaccine-Driven Selection in Seasonal Influenza. Viruses. 2018 09 18; 10(9). PMID: 30231576.
      View in: PubMed
    9. 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 in: PubMed
    10. Wilson PC, Cobey S. Characterization of the immunologic repertoire: A quick start guide. Immunol Rev. 2018 07; 284(1):5-8. PMID: 29944764.
      View in: PubMed
    11. Lewnard JA, Cobey S. Immune History and Influenza Vaccine Effectiveness. Vaccines (Basel). 2018 May 21; 6(2). PMID: 29883414.
      View in: PubMed
    12. Vieira MC, Zinder D, Cobey S. Selection and Neutral Mutations Drive Pervasive Mutability Losses in Long-Lived Anti-HIV B-Cell Lineages. Mol Biol Evol. 2018 05 01; 35(5):1135-1146. PMID: 29688540.
      View in: PubMed
    13. Ranjeva SL, Baskerville EB, Dukic V, Villa LL, Lazcano-Ponce E, Giuliano AR, Dwyer G, Cobey S. Recurring infection with ecologically distinct HPV types can explain high prevalence and diversity. Proc Natl Acad Sci U S A. 2017 12 19; 114(51):13573-13578. PMID: 29208707.
      View in: PubMed
    14. Zost SJ, Parkhouse K, Gumina ME, Kim K, Diaz Perez S, Wilson PC, Treanor JJ, Sant AJ, Cobey S, Hensley SE. Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies elicited by egg-adapted vaccine strains. Proc Natl Acad Sci U S A. 2017 11 21; 114(47):12578-12583. PMID: 29109276.
      View in: PubMed
    15. Cobey S. Sick if you do, sick if you don't. Nat Ecol Evol. 2017 11; 1(11):1602-1603. PMID: 28963490.
      View in: PubMed
    16. Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch M. Host population structure and treatment frequency maintain balancing selection on drug resistance. J R Soc Interface. 2017 08; 14(133). PMID: 28835542.
      View in: PubMed
    17. Baskerville EB, Cobey S. Does influenza drive absolute humidity? Proc Natl Acad Sci U S A. 2017 03 21; 114(12):E2270-E2271. PMID: 28298534.
      View in: PubMed
    18. Cobey S, Hensley SE. Immune history and influenza virus susceptibility. Curr Opin Virol. 2017 02; 22:105-111. PMID: 28088686.
      View in: PubMed
    19. Cobey S, Baskerville EB. Limits to Causal Inference with State-Space Reconstruction for Infectious Disease. PLoS One. 2016; 11(12):e0169050. PMID: 28030639.
      View in: PubMed
    20. Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. Viral factors in influenza pandemic risk assessment. Elife. 2016 11 11; 5. PMID: 27834632.
      View in: PubMed
    21. Wen F, Bedford T, Cobey S. Explaining the geographical origins of seasonal influenza A (H3N2). Proc Biol Sci. 2016 09 14; 283(1838). PMID: 27629034.
      View in: PubMed
    22. Childs LM, Baskerville EB, Cobey S. Trade-offs in antibody repertoires to complex antigens. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 05; 370(1676). PMID: 26194759.
      View in: PubMed
    23. Cobey S, Wilson P, Matsen FA. The evolution within us. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 05; 370(1676). PMID: 26194749.
      View in: PubMed
    24. Pessia A, Grad Y, Cobey S, Puranen JS, Corander J. K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets. Microb Genom. 2015 Jul; 1(1):e000025. PMID: 28348810.
      View in: PubMed
    25. Perron GG, Inglis RF, Pennings PS, Cobey S. Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health. Evol Appl. 2015 Mar; 8(3):211-22. PMID: 25861380.
      View in: PubMed
    26. Cobey S. Pathogen evolution and the immunological niche. Ann N Y Acad Sci. 2014 Jul; 1320:1-15. PMID: 25040161.
      View in: PubMed
    27. Ampofo WK, Baylor N, Cobey S, Cox NJ, Daves S, Edwards S, Ferguson N, Grohmann G, Hay A, Katz J, Kullabutr K, Lambert L, Levandowski R, Mishra AC, Monto A, Siqueira M, Tashiro M, Waddell AL, Wairagkar N, Wood J, Zambon M, Zhang W. Improving influenza vaccine virus selection: report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010. Influenza Other Respir Viruses. 2013 Sep; 7 Suppl 2:52-3. PMID: 24034484.
      View in: PubMed
    28. Shogan BD, Smith DP, Packman AI, Kelley ST, Landon EM, Bhangar S, Vora GJ, Jones RM, Keegan K, Stephens B, Ramos T, Kirkup BC, Levin H, Rosenthal M, Foxman B, Chang EB, Siegel J, Cobey S, An G, Alverdy JC, Olsiewski PJ, Martin MO, Marrs R, Hernandez M, Christley S, Morowitz M, Weber S, Gilbert J. The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15(th), 2013. Stand Genomic Sci. 2013 Jul 30; 8(3):571-9. PMID: 24501640.
      View in: PubMed
    29. Cobey S, Lipsitch M. Pathogen diversity and hidden regimes of apparent competition. Am Nat. 2013 Jan; 181(1):12-24. PMID: 23234842.
      View in: PubMed
    30. Cobey S, Lipsitch M. Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes. Science. 2012 Mar 16; 335(6074):1376-80. PMID: 22383809.
      View in: PubMed
    31. Flanagan ML, Parrish CR, Cobey S, Glass GE, Bush RM, Leighton TJ. Anticipating the species jump: surveillance for emerging viral threats. Zoonoses Public Health. 2012 May; 59(3):155-63. PMID: 21914152.
      View in: PubMed
    32. Improving influenza vaccine virus selection: report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010. Influenza Other Respir Viruses. 2012 Mar; 6(2):142-52, e1-5. PMID: 21819547.
      View in: PubMed
    33. Bedford T, Cobey S, Pascual M. Strength and tempo of selection revealed in viral gene genealogies. BMC Evol Biol. 2011 Jul 25; 11:220. PMID: 21787390.
      View in: PubMed
    34. Goldstein E, Cobey S, Takahashi S, Miller JC, Lipsitch M. Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method. PLoS Med. 2011 Jul; 8(7):e1001051. PMID: 21750666.
      View in: PubMed
    35. Cobey S, Pascual M. Consequences of host heterogeneity, epitope immunodominance, and immune breadth for strain competition. J Theor Biol. 2011 Feb 07; 270(1):80-7. PMID: 21093455.
      View in: PubMed
    36. Bedford T, Cobey S, Beerli P, Pascual M. Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS Pathog. 2010 May 27; 6(5):e1000918. PMID: 20523898.
      View in: PubMed
    37. Cobey S, Pascual M, Dieckmann U. Ecological factors driving the long-term evolution of influenza's host range. Proc Biol Sci. 2010 Sep 22; 277(1695):2803-10. PMID: 20444714.
      View in: PubMed
    38. Cobey S, Koelle K. Capturing escape in infectious disease dynamics. Trends Ecol Evol. 2008 Oct; 23(10):572-7. PMID: 18715671.
      View in: PubMed
    39. Koelle K, Cobey S, Grenfell B, Pascual M. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science. 2006 Dec 22; 314(5807):1898-903. PMID: 17185596.
      View in: PubMed
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