In preparation or review

Vieira, M. V., Zinder, D., and S. Cobey. 2017. Selection and neutral mutations drive pervasive mutability losses in long-lived B cell lineages. bioRxiv. doi:10.1101/163741

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

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.

Cobey, 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., Helsey, S. E., and Y. H. Grad. 2017. Despite egg-adaptive mutations, the 2012-13 H3N2 influenza vaccine induced comparable antibody titers to the intended strain. bioRxiv. doi:0.1101/158550 [html · pdf]

Published or in press

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 (in press). doi:10.1101/128967 [html · pdf · code]

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

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

Cobey, S. and E. Baskerville. 2016. Limits to causal inference with state-space reconstruction for infectious disease. PLOS One doi:10.1371/journal.pone.0169050. [html · 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 doi:10.1111/j.1863-2378.2011.01439 [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

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