In preparation or review

Ranjeva, S., Subramanian, R., Fang, V. J., Leung, G. M., Ip, D. K. M., Perera, R. A. P. M., Peiris, J. S. M., Cowling, B. J. and S. Cobey. 2018. Age-specific differences in the dynamics of protective immunity to influenza. bioRxiv. doi: [html · pdf · code]

Wen, F. T., Malani, A., and S. Cobey. 2017. Vaccination and the evolution of seasonal influenza. bioRxiv. doi:10.1101/162545 [html]

Published or in press

Lewnard, J. A. and S. Cobey. 2018. Immune History and Influenza Vaccine Effectiveness. Vaccines 6(2), 28. [html · pdf]

Vieira, M. V., Zinder, D., and S. Cobey. 2018. Selection and neutral mutations drive pervasive mutability losses in long-lived B cell lineages. Molecular Biology and Evolution 35(5):1135-1146. doi:10.1093/molbev/mst012. [html · pdf]

Cobey, S., Gouma, S., Parkhouse, K., Chambers, B.S., Ertl, H.C., Schmader, K. E., Halpin, R.A., Lin, X., Stockwell, T. B., Das, S. R., Landon, E., Tesic, V., Youngster, I., Pinsky, B., Wentworth, D.E., Hensley, S. E., and Y. H. Grad. 2018. Poor immunogenicity, not vaccine strain egg adaptation, may explain the low H3N2 influenza vaccine effectiveness in 2012-2013. Clinical Infectious Diseases doi:10.1093/cid/ciy097. [html · pdf]

Zost, S.J., Parkhouse, K., Gumina, M.E., Kim, K., Treanor, J.J., Sant, A.J., Cobey, S., and S. Hensley. 2017. Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies to egg-adapted vaccine strains. PNAS 114(47):12578-12583 [html · pdf · code]

Ranjeva, S., Baskerville, E. B., Dukic, V., Lacanzo, E., Villa, L., Giuliano, A.R., Dwyer, G. and S. Cobey. 2017. Recurring infection with ecologically distinct human papillomavirus (HPV) types explains high prevalence and diversity. PNAS 114(51):13573-13578 [html · pdf · code]

Cobey, S., Baskerville, E. B. , Colijn, C., Hanage, W., Fraser, C., and M. Lipsitch. 2017. Host population structure and treatment frequency maintain balancing selection on drug resistance. Journal of The Royal Society Interface 14(33):20170295 [html · pdf · code]

Baskerville, E. and S. Cobey. 2017. Does influenza drive absolute humidity? PNAS 114(12):E2270-E2271 [html · pdf · code]

Cobey, S. and S. Hensley. 2017. Immune history and influenza virus susceptibility. Current Opinion in Virology 22:105-111 [html · pdf]

Cobey, S. and E. Baskerville. 2016. Limits to causal inference with state-space reconstruction for infectious disease. PLoS One 11(12):e0169050 [html · pdf · code ]

Wen, F., Bedford, T., and S. Cobey. 2016. Explaining the geographical origins of seasonal influenza A (H3N2). Proceedings of the Royal Society B 283(1838) [html · pdf · code]

Pessia, A., Grad, Y., Cobey, S., Puranen, J.S., and J. Corander. 2015. K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets. Microbial Genomics 1(1) [html · pdf]

Cobey, S., Wilson, P. and F. Matsen. 2015. The evolution within us. Philosophical Transactions of the Royal Society B 370(1676):20140235 [html · pdf]

Childs, L., Baskerville, E. and S. Cobey. 2015. Tradeoffs in antibody repertoires to complex antigens. Philosophical Transactions of the Royal Society B 370(1676): 20140245 [html · pdf · code]

Perron, G., Inglis, R., Pennings, P. and S. Cobey. 2015. Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health. Evolutionary Applications 8(13):211-222 [html · pdf]

Cobey, S. 2014. Pathogen evolution and the immunological niche. Annals of the New York Academy of Sciences 1320:1-15 [html · pdf]

Cobey, S. and M. Lipsitch. 2013. Pathogen diversity and hidden regimes of apparent competition. American Naturalist 181(1):12-24 [html · pdf]

Flanagan, M., Parrish, C., Cobey, S., Glass, G., Bush, R. and T. Leighton. 2011. Anticipating the species jump: Surveillance for emerging viral threats. Zoonoses and Public Health 59(3):155-163 [html · pdf]

Bedford, T., Cobey, S., and M. Pascual. 2011. Strength and tempo of selection revealed in viral gene genealogies. BMC Evolutionary Biology 11:220 [html · pdf]

Goldstein, E., Cobey, S., Takahashi, S., Miller, J.C. and M. Lipsitch. 2011. Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method. PLoS Medicine 8(7):e1001051 [html · pdf]

Cobey, S. and M. Pascual. 2010. Consequences of host heterogeneity, epitope immunodominance, and immune breadth for strain competition. Journal of Theoretical Biology 270(1):80-87 [html · pdf]

Cobey, S., Pascual, M. and U. Dieckmann. 2010. Ecological factors driving the long-term evolution of influenza’s host range. Proceedings of the Royal Society B 277(1695):2803-2810 [html · pdf]

Bedford, T., Cobey, S., Beerli, P. and M. Pascual. 2010. Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS Pathogens 6(5):e1000918 [html · pdf]

Cobey, S. and K. Koelle. 2008. Capturing escape in infectious disease dynamics. Trends in Ecology and Evolution 23(10):572-577 [html · pdf]

Koelle*, K., Cobey*, S., Grenfell, B. and M. Pascual. 2006. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 314:1898-1903 (*equal contribution) [html · pdf]

Not peer-reviewed

Cobey, S. 2017. Sick if you do, sick if you don’t. 1(11):1602 [html]

WHO Writing Group, Ampofo, W., Baylor, N., Cobey, S., Cox, N., Daves, S., Edwards, S., Ferguson, N., Grohmann, G., Hay, A., Katz, J., Kullabutr, K., Lambert, L., Levandowski, R., Mishra, A., Monto, A., Siqueira, M., Tashiro, M., Waddell, A., Wairagkar, N., Wood, J., Zambon, M., Zhang, W. 2012. Improving influenza vaccine virus selection: Report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010. Influenza and Other Respiratory Diseases 6(2):142-152 [html · pdf]

Cobey, S. 2005. “Sea lampreys in the Great Lakes.” In Ecological Networks. J.A. Dunne and M.P. Pascual, eds. (Oxford University Press). [html]