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Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment

Zeldovich, Konstantin B. ; Liu, Ping ; Renzette, Nicholas ; Foll, Matthieu ; Pham, Serena T. ; Venev, Sergey V. ; Gallagher, Glen R. ; Bolon, Daniel N. ; Kurt-Jones, Evelyn A. ; Jensen, Jeffrey D. ; Caffrey, Daniel R. ; Schiffer, Celia A. ; Kowalik, Timothy F. ; Wang, Jennifer P. ; Finberg, Robert W.

In: Molecular Biology and Evolution, 2015, vol. 32, no. 6, p. 1519-1532

Influenza virus drug resistance: A time-sampled population genetics perspective

Foll, Matthieu ; Poh, Yu-Ping ; Renzette, Nicholas ; Ferrer-Admetlla, Anna ; Bank, Claudia ; Shim, Hyunjin ; Malaspinas, Anna-Sapfo ; Ewing, Gregory ; Liu, Ping ; Wegmann, Daniel ; Caffrey, Daniel R. ; Zeldovich, Konstantin B. ; Bolon, Daniel N. ; Wang, Jennifer P. ; Kowalik, Timothy F. ; Schiffer, Celia A. ; Finberg, Robert W. ; Jensen, Jeffrey D.

In: PLoS Genet, 2014, vol. 10, no. 2, p. e1004185

The challenge of distinguishing genetic drift from selection remains a central focus of population genetics. Time-sampled data may provide a powerful tool for distinguishing these processes, and we here propose approximate Bayesian, maximum likelihood, and analytical methods for the inference of demography and selection from time course data. Utilizing these novel statistical and computational...