Preprints

Age-specific differences in the dynamics of protective immunity to influenza, bioRxiv
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
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Vaccination and the evolution of seasonal influenza, bioRxiv
Frank T. Wen, Anup Malani, and Sarah Cobey
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2018

Repeated vaccination may protect children from influenza infection, JAMA Network Open
Sarah Cobey
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Estimating vaccine-driven selection in seasonal influenza, Viruses
Frank T. Wen, Sidney M. Bell, Trevor Bedford, and Sarah Cobey
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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
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Characterization of the immunologic repertoire: A quick start guide, Immunological Reviews
Patrick C. Wilson and Sarah Cobey
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Immune history and influenza vaccine effectiveness, Vaccines
Joseph A. Lewnard and Sarah Cobey
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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
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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
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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
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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
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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
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Immune history and influenza virus susceptibility, Current Opinion in Virology
Sarah Cobey and Scott E. Hensley
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Does influenza drive absolute humidity?, Proceedings of the National Academy of Sciences
Edward B. Baskerville and Sarah Cobey
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Sick if you do, sick if you don’t, Nature Ecology & Evolution
Sarah Cobey
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2016

Limits to causal inference with state-space reconstruction for infectious disease, PLOS One
Sarah Cobey and Edward B. Baskerville
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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
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Explaining the geographical origins of seasonal influenza A (H3N2), Proceedings of the Royal Society B
Frank Wen, Trevor Bedford, and Sarah Cobey
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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
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The evolution within us, Philosophical Transactions of the Royal Society B
Sarah Cobey, Patrick Wilson, and Frederick A. Matsen IV
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Tradeoffs in antibody repertoires to complex antigens, Philosophical Transactions of the Royal Society B
Lauren M. Childs, Edward B. Baskerville, and Sarah Cobey
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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
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2014

Pathogen evolution and the immunological niche, Annals of the New York Academy of Sciences
Sarah Cobey
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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
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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
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Pathogen coexistence through hidden regimes of apparent competition (2013), American Naturalist
Sarah Cobey and Marc Lipsitch
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Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes (2012), Science
Sarah Cobey and Marc Lipsitch
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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
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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
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Strength and tempo of selection revealed in viral gene genealogies (2011), BMC Evolutionary Biology
Trevor Bedford, Sarah Cobey, and Mercedes Pascual
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Consequences of host heterogeneity, epitope immunodominance, and immune breadth for strain competition (2011), Journal of Theoretical Biology
Sarah Cobey and Mercedes Pascual
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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
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Global migration dynamics underlie evolution and persistence of human influenza A (H3N2) (2010), PLOS Pathogens
Trevor Bedford, Sarah Cobey, Peter Beerli, and Mercedes Pascual
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Capturing escape in infectious disease dynamics (2008), Trends in Ecology and Evolution
Sarah Cobey and Katia Koelle
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Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans (2006), Science
Katia Koelle*, Sarah Cobey*, Bryan Grenfell, and Mercedes Pascual
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Sea lampreys in the Great Lakes (2005), Ecological Networks
Sarah Cobey
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