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 May 05; 333549221091826. View in: PubMed
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. View in: PubMed
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 Feb 24. View in: PubMed
Wen FT, Malani A, Cobey S. The Potential Beneficial Effects of Vaccination on Antigenically Evolving Pathogens. Am Nat. 2022 02; 199(2):223-237. View in: PubMed
Grubaugh ND, Cobey S. Of variants and vaccines. Cell. 2021 12 22; 184(26):6222-6223. View in: PubMed
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, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Correction: Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2021 Dec; 17(12):e1009679. View in: PubMed
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 May 03; 74(9):1534-1542. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2020 12; 16(12):e1008409. View in: PubMed
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). View in: PubMed
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. View in: PubMed
Arevalo P, McLean HQ, Belongia EA, Cobey S. Earliest infections predict the age distribution of seasonal influenza A cases. Elife. 2020 07 07; 9. View in: PubMed
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, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. medRxiv. 2020 Aug 28. View in: PubMed
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, López A, 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. CpG-creating mutations are costly in many human viruses. Evol Ecol. 2020; 34(3):339-359. View in: PubMed
Cobey S. Modeling infectious disease dynamics. Science. 2020 May 15; 368(6492):713-714. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
Cobey S. Repeated Vaccination May Protect Children From Influenza Infection. JAMA Netw Open. 2018 10 05; 1(6):e183730. View in: PubMed
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. View in: PubMed
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. View in: PubMed
Wen FT, Bell SM, Bedford T, Cobey S. Estimating Vaccine-Driven Selection in Seasonal Influenza. Viruses. 2018 09 18; 10(9). View in: PubMed
Wilson PC, Cobey S. Characterization of the immunologic repertoire: A quick start guide. Immunol Rev. 2018 07; 284(1):5-8. View in: PubMed
Lewnard JA, Cobey S. Immune History and Influenza Vaccine Effectiveness. Vaccines (Basel). 2018 May 21; 6(2). View in: PubMed
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. View in: PubMed
Cobey S, Grad YH. Response to Skowronski and De Serres. Clin Infect Dis. 2018 10 15; 67(9):1476. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
Cobey S. Sick if you do, sick if you don't. Nat Ecol Evol. 2017 11; 1(11):1602-1603. View in: PubMed
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). View in: PubMed
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. View in: PubMed
Baskerville EB, Cobey S. Does influenza drive absolute humidity? Proc Natl Acad Sci U S A. 2017 03 21; 114(12):E2270-E2271. View in: PubMed
Cobey S, Hensley SE. Immune history and influenza virus susceptibility. Curr Opin Virol. 2017 02; 22:105-111. View in: PubMed
Cobey S, Baskerville EB. Limits to Causal Inference with State-Space Reconstruction for Infectious Disease. PLoS One. 2016; 11(12):e0169050. View in: PubMed
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. View in: PubMed
Wen F, Bedford T, Cobey S. Explaining the geographical origins of seasonal influenza A (H3N2). Proc Biol Sci. 2016 09 14; 283(1838). View in: PubMed
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). View in: PubMed
Cobey S, Wilson P, Matsen FA. The evolution within us. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 05; 370(1676). View in: PubMed
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. View in: PubMed
Cobey S. Pathogen evolution and the immunological niche. Ann N Y Acad Sci. 2014 Jul; 1320:1-15. View in: PubMed
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. View in: PubMed
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. View in: PubMed
Cobey S, Lipsitch M. Pathogen diversity and hidden regimes of apparent competition. Am Nat. 2013 Jan; 181(1):12-24. View in: PubMed
Cobey S, Lipsitch M. Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes. Science. 2012 Mar 16; 335(6074):1376-80. View in: PubMed
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. View in: PubMed
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. View in: PubMed
Bedford T, Cobey S, Pascual M. Strength and tempo of selection revealed in viral gene genealogies. BMC Evol Biol. 2011 Jul 25; 11:220. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
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. View in: PubMed
Cobey S, Koelle K. Capturing escape in infectious disease dynamics. Trends Ecol Evol. 2008 Oct; 23(10):572-7. View in: PubMed
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. View in: PubMed