lab members indicated, * authors contributed equally, # co-corresponding authors
2024
M. Milhaven, A. Garg, C.J. Versoza, S.P. Pfeifer. Quantifying the effects of computational filter criteria on the accurate identification of de novo mutations at varying levels of sequencing coverage. In revision.
C.J. Versoza and S.P. Pfeifer. 2024. A hybrid genome assembly of the endangered aye-aye (Daubentonia madagascariensis). G3 (Bethesda): jkae185. Epub ahead of print.
S.P. Pfeifer, A. Baxter, L.E. Savidge, F.J. Sedlazeck, K.L. Bales. 2024. De novo reference assembly for the coppery titi monkey (Plecturocebus cupreus) – an emerging non-human primate model for behavioral research. Genome Biol. Evol. 16(5): evae108. pdf
C.J. Versoza*, S. Weiss*, R. Johal, B. La Rosa, J.D. Jensen, S.P. Pfeifer. 2024. Novel insights into the landscape of crossover and non-crossover events in rhesus macaques (Macaca mulatta). Genome Biol. Evol., 16(1): evad223. pdf
2023
M. Moström, S. Yu, D. Tran, F. Saccoccio, C.J. Versoza, D. Malouli, S. Valencia, M. Gilbert, R. Blair, S. Hansen, P. Barry, K. Früh, J.D. Jensen, S.P. Pfeifer, T. Kowalik, S. Permar, A. Kaur. 2023. Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. PLoS Pathogens, 19(10): e1011646. pdf
P. Johri, S.P. Pfeifer, J.D. Jensen. 2023. Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history. Mol. Biol. Evol., 40(5): msad100. pdf
S. Ghafoor*, C.J. Versoza*, J. Santos*, J.D. Jensen, S.P. Pfeifer. 2023. The impact of sample size and population history on observed mutational spectra. Genome Biol. Evol., 15(3): evad019. pdf
2022
K. Walker, D. Kalra, R. Lowdon, G. Chen, D. Molik, D.C. Soto, F. Dabbaghie, A.A. Khleifat, M. Mahmoud, L.F. Paulin, M. Sohail Raza, S.P. Pfeifer, D. Paiva Agustinho, E. Aliyev, P. Avdeyev, E.R. Barrozo, S. Behera, K. Billingsley, L. Chuin Chong, D. Choubey, W. De Coster, Y. Fu, A.R. Gener, T. Hefferon, D. Morgan Henke, W. Höps, A. Illarionova, M.D. Jochum, M. Jose, R.K. Kesharwani, S. Rohit Raj Kolora, J. Kubica, P. Lakra, D. Lattimer, C.-S. Liew, B.-W. Lo, C. Lo, A. Lötter, S. Majidian, S.Kumar Mendem, R. Mondal, H. Ohmiya, N. Parvin, C. Peralta, C.-L. Poon, R. Prabhakaran, M. Saitou, A. Sammi, P. Sanio, N. Sapoval, N. Syed, T. Treangen, G. Wang, T. Xu, J. Yang, S. Zhang, W. Zhou, F.J. Sedlazeck, B. Busby. 2022. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000 Res., 11: 530. pdf
P. Johri, C.F. Aquadro, M. Beaumont, B. Charlesworth, L. Excoffier, A. Eyre-Walker, P. Keightley, M. Lynch, G. McVean, B.A. Payseur, S.P. Pfeifer, W. Stephan, J.D. Jensen. 2022. Recommendations for improving statistical inference in population genomics. PLoS Biology, 20(5): e3001669. pdf
L.A. Bergeron, S. Besenbacher, T.N. Turner, C.J. Versoza, R.J. Wang, A.L. Price, E. Armstrong, M. Riera, J. Carlson, H. Chen, M.W. Hahn, K. Harris, A.S.L.N.M. Kleppe, E.H. López-Nandam, P. Moorjani, S.P. Pfeifer, G.P. Tiley, A.D. Yoder, G. Zhang, M.H. Schierup. 2022. The mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates. eLife, 11: e73577. pdf
2021
S.P. Pfeifer. 2021. Studying mutation rate evolution in primates – the effects of computational pipeline and parameter choices. GigaScience, 10(10): giab069. pdf
2020
S.P. Pfeifer. 2020. Spontaneous mutation rates. In The Molecular Evolutionary Clock. Theory and Practice. Springer Nature.
S.P. Pfeifer. 2020. A fine-scale genetic map for vervet monkeys. Mol. Biol. Evol., 37(7): 1855-1865. pdf
M. Apata and S.P. Pfeifer. 2020. Recent population genomic insights in to the genetic basis of arsenic tolerance in humans: the difficulties of identifying positively selected loci in strongly bottlenecked populations. Heredity, 124(2): 253-262. pdf
2019 and earlier
L.A.P. Tran and S.P. Pfeifer. 2018. Germline mutation rates in Old World monkeys. eLS, John Wiley & Sons, Ltd: Chichester. doi: 10.1002/9780470015902.a0028242. pdf
S.P. Pfeifer. 2017. Direct estimate of the spontaneous germ line mutation rate in African green monkeys. Evolution, 71(12): 2858-2870. pdf
S.P. Pfeifer. 2017. The demographic and adaptive history of the African green monkey. Mol. Biol. Evol., 34(5): 1055-1065. pdf
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). pdf
S.P. Pfeifer, J.D. Jensen. 2016. The impact of linked selection in chimpanzees: a comparative study. Genome Biol. Evol., 8(10): 3202-3208. pdf
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 germline. Proc. Natl. Acad. Sci. U.S.A., 110(50): 20152-20157. pdf
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. pdf
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. pdf
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. Nat. Genet., 41(11): 1247-1252. pdf