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Sarah E. Cobey

TitleProfessor
InstitutionUniversity of Chicago
DepartmentEcology and Evolution
AddressChicago IL 60637
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    Collapse Overview 
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    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.
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    Collapse Biography 
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    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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. McGough L, Cobey S, McGough L, Cobey S. A speed limit on serial strain replacement from original antigenic sin. bioRxiv. 2024 Jan 04. PMID: 38260288; PMCID: PMC10802292.
      Citations:    
    2. Kim K, Gouma S, Vieira MC, Weirick ME, Hensley SE, Cobey S. Measures of population immunity can predict the dominant clade of influenza A (H3N2) and reveal age-associated differences in susceptibility and specificity. medRxiv. 2023 Oct 27. PMID: 37961288; PMCID: PMC10635207.
      Citations:    
    3. US Flu Vaccine Effectiveness Network Investigators, Bi Q, Dickerman BA, McLean HQ, Martin ET, Gaglani M, Wernli KJ, Balasubramani GK, Flannery B, Lipsitch M, Cobey S. Reduced effectiveness of repeat influenza vaccination: distinguishing among within-season waning, recent clinical infection, and subclinical infection. medRxiv. 2023 Sep 27. PMID: 37016669; PMCID: PMC10071822.
      Citations:    
    4. Vieira MC, Palm AE, Stamper CT, Tepora ME, Nguyen KD, Pham TD, Boyd SD, Wilson PC, Cobey S. Germline-encoded specificities and the predictability of the B cell response. PLoS Pathog. 2023 08; 19(8):e1011603. PMID: 37624867; PMCID: PMC10484431.
      Citations:    Fields:    Translation:AnimalsCells
    5. Tsang TK, Chen S, Wang Y, Lau EHY, Cowling BJ, Gostic KM, Arevalo P, Cobey S. Investigation of the Impact of Childhood Immune Imprinting on Birth Year-Specific Risk of Clinical Infection During Influenza A Virus Epidemics in Hong Kong. J Infect Dis. 2023 07 14; 228(2):169-172. PMID: 36637115; PMCID: PMC10345470.
      Citations:    Fields:    Translation:HumansCellsPHPublic Health
    6. Shaw DG, Aguirre-Gamboa R, Vieira MC, Gona S, DiNardi N, Wang A, Dumaine A, Gelderloos-Arends J, Earley ZM, Meckel KR, Ciszewski C, Castillo A, Monroe K, Torres J, Shah SC, Colombel JF, Itzkowitz S, Newberry R, Cohen RD, Rubin DT, Quince C, Cobey S, Jonkers IH, Weber CR, Pekow J, Wilson PC, Barreiro LB, Jabri B. Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis. Nat Med. 2023 Jun; 29(6):1520-1529. PMID: 37322120; PMCID: PMC10287559.
      Citations: 3     Fields:    Translation:Humans
    7. Richardson R, Jorgensen E, Arevalo P, Holden TM, Gostic KM, Pacilli M, Ghinai I, Lightner S, Cobey S, Gerardin J. Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA. Nat Commun. 2022 09 22; 13(1):5547. PMID: 36138039; PMCID: PMC9499975.
      Citations: 1     Fields:    Translation:HumansCellsPHPublic Health
    8. Pierce CA, Herold KC, Herold BC, Chou J, Randolph A, Kane B, McFarland S, Gurdasani D, Pagel C, Hotez P, Cobey S, Hensley SE. COVID-19 and children. Science. 2022 09 09; 377(6611):1144-1149. PMID: 36074833; PMCID: PMC10324476.
      Citations: 16     Fields:    Translation:HumansCellsPHPublic Health
    9. Simon V, Kota V, Bloomquist RF, Hanley HB, Forgacs D, Pahwa S, Pallikkuth S, Miller LG, Schaenman J, Yeaman MR, Manthei D, Wolf J, Gaur AH, Estepp JH, Srivastava K, Cuevas F, PARIS/SPARTA Study Group,, Ellebedy AH, Gordon A, Valdez R, Cobey S, Reed EF, Kolhe R, Thomas PG, Schultz-Cherry S, Ross TM, Krammer F, Carreño JM. PARIS and SPARTA: Finding the Achilles' Heel of SARS-CoV-2. mSphere. 2022 06 29; 7(3):e0017922. PMID: 35586986; PMCID: PMC9241545.
      Citations: 12     Fields:    Translation:HumansCells
    10. Goyal S, Gerardin J, Cobey S, Son C, McCarthy O, Dror A, Lightner S, Ezike NO, Duffus WA, Bennett AC. 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 Rep. 2022 Jul-Aug; 137(4):672-678. PMID: 35510756; PMCID: PMC9257515.
      Citations:    Fields:    Translation:HumansCells
    11. Clipman SJ, Wesolowski A, Mehta SH, Cobey S, Cummings DAT, Solomon SS. Improvements in Severe Acute Respiratory Syndrome Coronavirus 2 Testing Cascade in the United States: Data From Serial Cross-sectional Assessments. Clin Infect Dis. 2022 05 03; 74(9):1534-1542. PMID: 34374758; PMCID: PMC9070851.
      Citations: 3     Fields:    Translation:HumansCells
    12. Lin Y, Yang B, Cobey S, Lau EHY, Adam DC, Wong JY, Bond HS, Cheung JK, Ho F, Gao H, Ali ST, Leung NHL, Tsang TK, Wu P, Leung GM, Cowling BJ. Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission. Nat Commun. 2022 03 03; 13(1):1155. PMID: 35241662; PMCID: PMC8894407.
      Citations: 8     Fields:    Translation:HumansCellsPHPublic Health
    13. Du Z, Wang L, Pandey A, Lim WW, Chinazzi M, Piontti APY, Lau EHY, Wu P, Malani A, Cobey S, Cowling BJ. Modeling comparative cost-effectiveness of SARS-CoV-2 vaccine dose fractionation in India. Nat Med. 2022 05; 28(5):934-938. PMID: 35210596; PMCID: PMC9117137.
      Citations: 18     Fields:    Translation:HumansCellsPHPublic Health
    14. Wen FT, Malani A, Cobey S. The Potential Beneficial Effects of Vaccination on Antigenically Evolving Pathogens. Am Nat. 2022 02; 199(2):223-237. PMID: 35077280.
      Citations: 2     Fields:    Translation:HumansPHPublic Health
    15. Grubaugh ND, Cobey S. Of variants and vaccines. Cell. 2021 12 22; 184(26):6222-6223. PMID: 34942096; PMCID: PMC8693473.
      Citations: 12     Fields:    Translation:HumansCells
    16. Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S, Scire J. Correction: Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2021 Dec; 17(12):e1009679. PMID: 34879070; PMCID: PMC8654153.
      Citations:    Fields:    
    17. Cowling BJ, Lim WW, Cobey S. Fractionation of COVID-19 vaccine doses could extend limited supplies and reduce mortality. Nat Med. 2021 08; 27(8):1321-1323. PMID: 34226735.
      Citations: 17     Fields:    Translation:HumansCells
    18. Vieira MC, Donato CM, Arevalo P, Rimmelzwaan GF, Wood T, Lopez L, Huang QS, Dhanasekaran V, Koelle K, Cobey S. Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases. Nat Commun. 2021 07 14; 12(1):4313. PMID: 34262041; PMCID: PMC8280188.
      Citations: 13     Fields:    Translation:HumansCells
    19. Guthmiller JJ, Utset HA, Henry C, Li L, Zheng NY, Sun W, Costa Vieira M, Zost S, Huang M, Hensley SE, Cobey S, Palese P, Wilson PC. An Egg-Derived Sulfated N-Acetyllactosamine Glycan Is an Antigenic Decoy of Influenza Virus Vaccines. mBio. 2021 06 29; 12(3):e0083821. PMID: 34126773; PMCID: PMC8263001.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    20. Holden TM, Richardson RAK, Arevalo P, Duffus WA, Runge M, Whitney E, Wise L, Ezike NO, Patrick S, Cobey S, Gerardin J. Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020. BMC Public Health. 2021 06 10; 21(1):1105. PMID: 34107947; PMCID: PMC8189821.
      Citations: 13     Fields:    Translation:HumansCellsPHPublic Health
    21. Lutrick K, Ellingson KD, Baccam Z, Rivers P, Beitel S, Parker J, Hollister J, Sun X, Gerald JK, Komatsu K, Kim E, LaFleur B, Grant L, Yoo YM, Kumar A, Mayo Lamberte J, Cowling BJ, Cobey S, Thornburg NJ, Meece JK, Kutty P, Nikolich-Zugich J, Thompson MG, Burgess JL. COVID-19 Infection, Reinfection, and Vaccine Effectiveness in a Prospective Cohort of Arizona Frontline/Essential Workers: The AZ HEROES Research Protocol. JMIR Res Protoc. 2021 May 26. PMID: 34057904; PMCID: PMC8386365.
      Citations: 16     
    22. Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, van Nimwegen E, Worobey M, Relman DA. Investigate the origins of COVID-19. Science. 2021 05 14; 372(6543):694. PMID: 33986172; PMCID: PMC9520851.
      Citations: 44     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    23. Holden TM, Richardson RAK, Arevalo P, Duffus WA, Runge M, Whitney E, Wise L, Ezike NO, Patrick S, Cobey S, Gerardin J. Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020. medRxiv. 2021 Apr 20. PMID: 33907762; PMCID: PMC8077585.
      Citations:    
    24. Cobey S, Larremore DB, Grad YH, Lipsitch M. Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination. Nat Rev Immunol. 2021 05; 21(5):330-335. PMID: 33795856; PMCID: PMC8014893.
      Citations: 54     Fields:    Translation:HumansCellsPHPublic Health
    25. Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. Science. 2021 02 26; 371(6532):916-921. PMID: 33479118; PMCID: PMC7963218.
      Citations: 308     Fields:    Translation:HumansCellsPHPublic Health
    26. Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. medRxiv. 2021 Jan 08. PMID: 33330882; PMCID: PMC7743091.
      Citations:    
    27. Clipman SJ, Wesolowski A, Mehta SH, Agarwal S, Cobey SE, Cummings DAT, Gibson DG, Labrique AB, Kirk GD, Solomon SS. SARS-CoV-2 Testing in Florida, Illinois, and Maryland: Access and Barriers. medRxiv. 2020 Dec 24. PMID: 33398298; PMCID: PMC7781341.
      Citations: 2     
    28. Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Wallinga J, Funk S, Lipsitch M, Cobey S, Huisman JS, Scire J, Bonhoeffer S, Stadler T. Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2020 12; 16(12):e1008409. PMID: 33301457; PMCID: PMC7728287.
      Citations: 195     Fields:    Translation:HumansCellsPHPublic Health
    29. Dugan HL, Guthmiller JJ, Arevalo P, Huang M, Chen YQ, Neu KE, Henry C, Zheng NY, Lan LY, Tepora ME, Stovicek O, Bitar D, Palm AE, Stamper CT, Changrob S, Utset HA, Coughlan L, Krammer F, Cobey S, Wilson PC. Preexisting immunity shapes distinct antibody landscapes after influenza virus infection and vaccination in humans. Sci Transl Med. 2020 12 09; 12(573). PMID: 33298562; PMCID: PMC8115023.
      Citations: 50     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    30. 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. 2020 09 12; 71(6):1447-1453. PMID: 31598646; PMCID: PMC7486837.
      Citations: 19     Fields:    Translation:HumansCells
    31. Gouma S, Kim K, Weirick ME, Gumina ME, Branche A, Topham DJ, Martin ET, Monto AS, Cobey S, Hensley SE. Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility. Nat Commun. 2020 09 11; 11(1):4566. PMID: 32917903; PMCID: PMC7486384.
      Citations: 27     Fields:    Translation:HumansCells
    32. Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar PM, Hellewell J, Meakin S, Munday J, Bosse NI, Sherrat K, Thompson RN, White LF, Wallinga J, Funk S, Lipsitch M, Cobey S, Huisman JS, Scire J, Bonhoeffer S, Stadler T. Practical considerations for measuring the effective reproductive number, Rt. medRxiv. 2020 Aug 28. PMID: 32607522; PMCID: PMC7325187.
      Citations:    
    33. Arevalo P, McLean HQ, Belongia EA, Cobey S. Earliest infections predict the age distribution of seasonal influenza A cases. Elife. 2020 07 07; 9. PMID: 32633233; PMCID: PMC7367686.
      Citations: 36     Fields:    Translation:HumansCellsPHPublic Health
    34. Cobey S. Modeling infectious disease dynamics. Science. 2020 May 15; 368(6492):713-714. PMID: 32332062.
      Citations: 66     Fields:    Translation:HumansCellsPHPublic Health
    35. Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan FL, Chemel AK, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED, Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PS, López A. CpG-creating mutations are costly in many human viruses. Evol Ecol. 2020; 34(3):339-359. PMID: 32508375; PMCID: PMC7245597.
      Citations: 8     
    36. 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; PMCID: PMC6458119.
      Citations: 56     Fields:    Translation:HumansCells
    37. 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; PMCID: PMC6452894.
      Citations: 83     Fields:    Translation:HumansCells
    38. 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; PMCID: PMC6307935.
      Citations: 27     Fields:    Translation:HumansCellsPHPublic Health
    39. Cobey S, Grad YH. Response to Skowronski and De Serres. Clin Infect Dis. 2018 10 15; 67(9):1476. PMID: 29688302; PMCID: PMC6186850.
      Citations:    Fields:    Translation:Cells
    40. Cobey S. Repeated Vaccination May Protect Children From Influenza Infection. JAMA Netw Open. 2018 10 05; 1(6):e183730. PMID: 30646259.
      Citations:    Fields:    Translation:HumansPHPublic Health
    41. 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; PMCID: PMC6181404.
      Citations: 4     Fields:    Translation:HumansCells
    42. Wen FT, Bell SM, Bedford T, Cobey S. Estimating Vaccine-Driven Selection in Seasonal Influenza. Viruses. 2018 09 18; 10(9). PMID: 30231576; PMCID: PMC6165116.
      Citations: 3     Fields:    Translation:HumansCellsPHPublic Health
    43. 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; PMCID: PMC6051447.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    44. Wilson PC, Cobey S. Characterization of the immunologic repertoire: A quick start guide. Immunol Rev. 2018 07; 284(1):5-8. PMID: 29944764.
      Citations:    Fields:    Translation:HumansCellsPHPublic Health
    45. Lewnard JA, Cobey S. Immune History and Influenza Vaccine Effectiveness. Vaccines (Basel). 2018 May 21; 6(2). PMID: 29883414; PMCID: PMC6027411.
      Citations: 94     
    46. 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; PMCID: PMC5913683.
      Citations: 7     Fields:    Translation:HumansCells
    47. Ranjeva SL, Baskerville EB, Dukic V, Giuliano AR, Dwyer G, Cobey S, Villa LL, Lazcano-Ponce E. 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; PMCID: PMC5754802.
      Citations: 32     Fields:    Translation:HumansCells
    48. 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; PMCID: PMC5703309.
      Citations: 254     Fields:    Translation:HumansAnimalsCells
    49. Cobey S. Sick if you do, sick if you don't. Nat Ecol Evol. 2017 11; 1(11):1602-1603. PMID: 28963490.
      Citations:    Fields:    
    50. 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; PMCID: PMC5582124.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    51. 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; PMCID: PMC5373373.
      Citations: 10     Fields:    Translation:Humans
    52. Cobey S, Hensley SE. Immune history and influenza virus susceptibility. Curr Opin Virol. 2017 02; 22:105-111. PMID: 28088686; PMCID: PMC5467731.
      Citations: 140     Fields:    Translation:HumansCells
    53. Cobey S, Baskerville EB. Limits to Causal Inference with State-Space Reconstruction for Infectious Disease. PLoS One. 2016; 11(12):e0169050. PMID: 28030639; PMCID: PMC5193453.
      Citations: 13     Fields:    Translation:Humans
    54. 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; PMCID: PMC5156527.
      Citations: 56     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    55. 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; PMCID: PMC5031657.
      Citations: 11     Fields:    Translation:HumansCells
    56. 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; PMCID: PMC4528422.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    57. 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; PMCID: PMC4528412.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    58. Pessia A, Grad Y, Cobey S, Corander J, Puranen JS. K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets. Microb Genom. 2015 Jul; 1(1):e000025. PMID: 28348810; PMCID: PMC5320600.
      Citations: 8     Fields:    
    59. 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; PMCID: PMC4380916.
      Citations: 15     
    60. Cobey S. Pathogen evolution and the immunological niche. Ann N Y Acad Sci. 2014 Jul; 1320:1-15. PMID: 25040161; PMCID: PMC4141700.
      Citations: 27     Fields:    Translation:HumansAnimals
    61. WHO Writing Group, 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 2:52-53. PMID: 24034484; PMCID: PMC5909392.
      Citations: 8     Fields:    Translation:HumansCells
    62. 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; PMCID: PMC3910697.
      Citations: 6     
    63. Cobey S, Lipsitch M. Pathogen diversity and hidden regimes of apparent competition. Am Nat. 2013 Jan; 181(1):12-24. PMID: 23234842; PMCID: PMC3716377.
      Citations: 23     Fields:    Translation:HumansCells
    64. 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; PMCID: PMC3341938.
      Citations: 86     Fields:    Translation:HumansCells
    65. 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; PMCID: PMC4948863.
      Citations: 17     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    66. WHO Writing Group, 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. 2012 Mar; 6(2):142-52, e1-5. PMID: 21819547; PMCID: PMC4954460.
      Citations: 38     Fields:    Translation:HumansCellsPHPublic Health
    67. 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; PMCID: PMC3199772.
      Citations: 45     Fields:    Translation:HumansCells
    68. 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; PMCID: PMC3130020.
      Citations: 105     Fields:    Translation:HumansCellsPHPublic Health
    69. 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; PMCID: PMC3042250.
      Citations: 11     Fields:    Translation:HumansCells
    70. 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; PMCID: PMC2877742.
      Citations: 96     Fields:    Translation:HumansCells
    71. 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; PMCID: PMC2981989.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    72. Cobey S, Koelle K. Capturing escape in infectious disease dynamics. Trends Ecol Evol. 2008 Oct; 23(10):572-7. PMID: 18715671.
      Citations: 14     Fields:    Translation:Cells
    73. 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.
      Citations: 238     Fields:    Translation:HumansCellsPHPublic Health
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