|Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans|
K Koelle, S Cobey, B Grenfell, M Pascual
Science 314 (5807), 1898-1903, 2006
|Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies elicited by egg-adapted vaccine strains|
SJ Zost, K Parkhouse, ME Gumina, K Kim, SD Perez, PC Wilson, ...
Proceedings of the National Academy of Sciences 114 (47), 12578-12583, 2017
|Global migration dynamics underlie evolution and persistence of human influenza A (H3N2)|
T Bedford, S Cobey, P Beerli, M Pascual
PLoS Pathog 6 (5), e1000918, 2010
|Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes|
S Cobey, M Lipsitch
Science 335 (6074), 1376-1380, 2012
|Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method|
E Goldstein, S Cobey, S Takahashi, JC Miller, M Lipsitch
PLoS Med 8 (7), e1001051, 2011
|Immune history and influenza virus susceptibility|
S Cobey, SE Hensley
Current opinion in virology 22, 105-111, 2017
|Immune history and influenza vaccine effectiveness|
JA Lewnard, S Cobey
Vaccines 6 (2), 28, 2018
|Modeling infectious disease dynamics|
Science 368 (6492), 713-714, 2020
|Improving influenza vaccine virus selectionReport of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14–16 June 2010|
WHO Writing Group, WK Ampofo, N Baylor, S Cobey, NJ Cox, S Daves, ...
Influenza and other respiratory viruses 6 (2), 142-152, 2012
|Strength and tempo of selection revealed in viral gene genealogies|
T Bedford, S Cobey, M Pascual
BMC evolutionary biology 11 (1), 1-16, 2011
|Practical considerations for measuring the effective reproductive number, Rt|
KM Gostic, L McGough, EB Baskerville, S Abbott, K Joshi, C Tedijanto, ...
PLoS computational biology 16 (12), e1008409, 2020
|Science forum: Viral factors in influenza pandemic risk assessment|
M Lipsitch, W Barclay, R Raman, CJ Russell, JA Belser, S Cobey, ...
Elife 5, e18491, 2016
|Influenza virus vaccination elicits poorly adapted B cell responses in elderly individuals|
C Henry, NY Zheng, M Huang, A Cabanov, KT Rojas, K Kaur, SF Andrews, ...
Cell host & microbe 25 (3), 357-366. e6, 2019
|Pathogen diversity and hidden regimes of apparent competition|
S Cobey, M Lipsitch
The American Naturalist 181 (1), 12-24, 2013
|Trade-offs in antibody repertoires to complex antigens|
LM Childs, EB Baskerville, S Cobey
Philosophical Transactions of the Royal Society B: Biological Sciences 370 …, 2015
|Pathogen evolution and the immunological niche|
Annals of the New York Academy of Sciences 1320 (1), 1, 2014
|Age-specific differences in the dynamics of protective immunity to influenza|
S Ranjeva, R Subramanian, VJ Fang, GM Leung, DKM Ip, RAPM Perera, ...
Nature Communications 10 (1), 1-11, 2019
|Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health|
GG Perron, RF Inglis, PS Pennings, S Cobey
Evolutionary applications 8 (3), 211-222, 2015
|Limits to causal inference with state-space reconstruction for infectious disease|
S Cobey, EB Baskerville
PLOS One 11 (12), e0169050, 2016
|Poor immunogenicity, not vaccine strain egg adaptation, may explain the low H3N2 influenza vaccine effectiveness in 2012-13|
S Cobey, S Gouma, K Parkhouse, BS Chambers, HC Ertl, KE Schmader, ...
Clinical Infectious Diseases, 2018