* authors contributed equally, # co-corresponding authors

A. Sackman, S.P. Pfeifer, T.F. Kowalik, and J.D. Jensen. 2018. On the demographic and selective forces shaping patterns of human cytomegalovirus variation within hostsPathogens, 7(1):16.

S.P. Pfeifer*, S. Laurent*, V.C. Sousa*, C.R. Linnen*, M. Foll, L. Excoffier#, H.E. Hoekstra#, and J.D. Jensen#. 2018. The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flowMBE, in press. DOI: 10.1093/molbev/msy004.

S.P. Pfeifer. 2017. Direct estimate of the spontaneous germ line mutation rate in African green monkeys. Evolution. 71(12):2858-2870.

E. Dexter, J. Goudet, S. Bollens, J. Cordell, H.J. Soh, G. Rollwagen-Bollens, S.P. Pfeifer, S. Vuilleumier. 2017. A genetic reconstruction of the invasion of the calanoid copepod Pseudodiaptomus inopinus across the North American Pacific Coast. Biological Invasions, 1-19.

N.G. Crawford, D.E. Kelley, M.E.B. Hansen, M.H. Beltrame, S. Fan, S.L. Bowman, E. Jewett, A. Ranciaro, S. Thompson, Y. Lo, S.P. Pfeifer, J.D. Jensen, M.C. Campbell, W. Beggs, F. Hormozdiari, S.W. Mpoloka, G.G. Mokone, T. Nyambo, D.W. Meskel, G. Belay, J. Haut, H. Rothschild, L. Zon, Y. Zhou, M.A. Kovacs, M. Xu, T. Zhang, K. Bishop, J. Sinclair, C. Rivas, E. Elliot, J. Choi, S.A. Li, B. Hicks, S. Burgess, C. Abnet, D.E. Watkins-Chow, E. Oceana, Y.S. Song, E. Eskin, K.M. Brown, M.S. Marks, S.K. Loftus, W.J. Pavan, M. Yeager, S. Chancock, S. Tishkoff. 2017. Loci associated with skin pigmentation identified in African populations. Science. 358 (6365).

S.P. Pfeifer. 2017. The demographic and adaptive history of the African green monkey. Molecular Biology and Evolution. 34 (5): 1055-1065.

C. Pokalyuk, N. Renzette, S.P. Pfeifer, L. Gibson, W.J. Britt, Y. Aparecida, Y. Yamamoto, M.M. Mussi-Pinhata, T.F. Kowalik#, and J.D. Jensen#. 2017. Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspectiveMolecular Ecology. 26 (7), 1980-1990.

E.P. Kingsley*, K.M. Kozak*, S.P. Pfeifer, D. Yang, H.E. Hoekstra. 2017. The ultimate and proximate mechanisms driving the evolution of long tails in forest deer mice. Evolution. 71 (2), 261-273.

N. Renzette, S.P. Pfeifer, S. Matuszewski, T.F. Kowalik, and J.D. Jensen. 2017. On the analysis of intra-host and inter-host viral populations: human cytomegalovirus as a case study of pitfalls and expectations. Journal of Virology. 91 (5), e01976-16.

S.P. Pfeifer. 2017. From Next-Generation Resequencing Reads to a High Quality Variant Data Set. Heredity 118 (2):111-124.

S.P. Pfeifer, J.D. Jensen. 2016. The Impact of Linked Selection in Chimpanzees: A Comparative Study. Genome Biology and Evolution 8 (10), 3202-3208.

L. Ormond, M. Foll, G.B. Ewing, S.P. Pfeifer, J.D. Jensen. 2016. Inferring the age of a fixed beneficial allele. Molecular Ecology 25 (1), 157-169.

S. Laurent*, S.P. Pfeifer*, M.L. Settles, S.S. Hunter, K.M. Hardwick, L. Ormond, V.C. Sousa, J.D. Jensen#, E.B. Rosenblum#. 2016. The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizardsMolecular Ecology 25 (1), 306-323.

E. Giannoulatou, G. McVean, I.B. Taylor, S.J. McGowan, G.J. Maher, Z. Iqbal, S.P. Pfeifer, I. Turner, E.M.M. Burkitt Wright, J. Shorto, A. Itani, K. Turner, L. Gregory, D. Buck, E. Rajpert-De Meyts, L.H.J. Looijenga, B. Kerr, A.O.M. Wilkie, A. Goriely. 2013. Contributions of intrinsic mutation rate and selfish selection to levels of de novo HRAS mutations in the paternal germlineProceedings of the National Academy of Sciences 110 (50), 20152-20157.

E.M. Leffler*, Z. Gao*, S.P. Pfeifer*, L. Ségurel*, A. Auton, O. Venn, R. Bowden, R. Bontrop, J.D. Wall, G. Sella, P. Donnelly, G. McVean#, M. Przeworski#. 2013. Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339 (6127), 1578-1582.

A. Auton*, A. Fledel-Alon*, S.P. Pfeifer*, O. Venn*, L. Ségurel, T. Street, E.M. Leffler, R. Bowden, I. Aneas, J. Broxholme, P. Humburg, Z. Iqbal, G. Lunter, J. Maller, R.D. Hernandez, C. Melton, A. Venkat, M.A. Nobrega, R. Bontrop, S. Myers, P. Donnelly, M. Przeworski#, G. McVean#. 2012. A fine-scale chimpanzee genetic map from population sequencing. Science 336 (6078), 193-198.

A. Goriely, R.M.S. Hansen, I.B. Taylor, I.A. Olesen, G.K. Jacobsen, S.J. McGowan, S.P. Pfeifer, G.A.T. McVean, E. Rajpert-De Meyts, A.O.M. Wilkie. 2009. Activating mutations in FGFR3 and HRAS reveal a shared genetic origin for congenital disorders and testicular tumors. Nature Genetics 41 (11), 1247-1252.