Publications

lab members indicated, * authors contributed equally, # co-corresponding authors,
associated popular press 

R.D.H. Barrett*, S. Laurent*, R. Mallarino*, S.P. Pfeifer, C.C. Xu, M. Foll, K. Wakamatsu, J. Duke-Cohan, J.D. Jensen, and H.E. Hoekstra. 2018. The fitness consequences of genetic variation in wild populations of mice. In review.

L.A.P. TranS.P. Pfeifer. 2018. Germline mutation rates in Old World monkeyseLS, John Wiley & Sons, Ltd: Chichester. doi: 10.1002/9780470015902.a0028242

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. 35(4):792-806.

A. Kapopoulou, S.P. Pfeifer, J.D. Jensen, S. Laurent. 2018. The demographic history of African Drosophila melanogasterGBE. 10(9):2338-2342.

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. 2017. Direct estimate of the spontaneous germ line mutation rate in African green monkeys. Evolution. 71(12):2858-2870.
Human mutation rate a legacy from our past, Science (April 2018)

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

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

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).
New gene variants reveal the evolution of human skin color, Science (October 2017)

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.

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.

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.

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, 20 (6): 1577-1595.

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.

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.

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.

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.
Humans and chimps share genetic strategy in battle against pathogens, Science Daily, Science Life (February 2013)

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.
Scientists map hotspots for genetic exchange in chimpanzees, Science Daily (March 2012)

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.