Publications

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

M. Mostrom, 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, and A. Kaur. Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. In review.

P. Johri, S.P. Pfeifer, J.D. Jensen. Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history. In review.

A.A. Howell, J. Terbot, V. Soni, P. Johri, J.D. Jensen, S.P. Pfeifer. Developing an appropriate evolutionary baseline model for the study of human cytomegalovirus. In review.

J. Terbot, P. Johri, S. Liphardt, V. Soni, S.P. Pfeifer, B.S. Cooper, J.M. Good, J.D. Jensen. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. In review.

S. Ghafoor*, C.J. Versoza*, J. Santos*, J.D. Jensen, S.P. Pfeifer. The impact of sample size and population history on observed mutational spectra. Accepted pending revision, GBE.

M. Milhaven, C.J. Versoza, A. Garg, L. Cai, S. Cherian, K. Johnson, K. Salas Perez, M. Blanco, J. Lobatos, C. Mitra, M. Strasser, S.P. Pfeifer. 2023. Bacteriophages of cluster EA: phylogenomic relationships and host range predictions. Microorganisms. 11: 170. pdf

M. Milhaven, L. Cai, S. Cherian, K. Johnson, K. Salas Perez, M. Blanco, A. Garg, J. Lobatos, C. Mitra, M. Strasser, R. Harms, S.P. Pfeifer. 2023. Complete genome sequence of the Microbacterium bacteriophage Chako. Microbiol. Resour. Announc. pdf 

M. Milhaven and S.P. Pfeifer. 2022. Performance comparison of six popular short-read simulators. Heredity, online ahead of print. pdf

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 organismsF1000 Res., 11: 530. pdf

A.A. Howell*, C.J. Versoza*, G. Cerna, T. Johnston, S. Kakde, K. Karuku, M. Kowal, J. Monahan, J. Murray, T. Nguyen, A. Sanchez Carreon, A. Streiff, B. Su, F. Youkhana, S. Munig, Z. Patel, M. So, M. Sy, S. Weiss, S.P. Pfeifer. 2022. Phylogenomic analyses and host range prediction of cluster P mycobacteriophages. G3 (Bethesda), 12(11): e0054022. pdf 

C.J. Versoza*, A.A. Howell*, T. Aftab, M. Blanco, A. Brar, E. Chaffee, N. Howell, W. Leach, J. Lobatos, M. Luca, M. Maddineni, R. Mirji, C. Mitra, M. Strasser, S. Munig, Z. Patel, M. So, M. Sy, S. Weiss, S.P. Pfeifer. 2022. Comparative genomics of closely-related Gordonia terrae cluster DR bacteriophages. Viruses, 14(8): 1647. pdf 

C.J. Versoza*, A.A. Howell*, T. Aftab, M. Blanco, A. Brar, E. Chaffee, N. Howell, W. Leach, J. Lobatos, M. Luca, M. Maddineni, R. Mirji, C. Mitra, M. Strasser, S. Munig, Z. Patel, M. So, M. Sy, S. Weiss, C.D. Herren, M. Smith Caldas, S.P. Pfeifer. 2022. Complete genome sequence of the Gordonia bacteriophage BiggityBass. Microbiol. Resour. Announc. 11(9): e00469-22. pdf

A.A. Howell*, C.J. Versoza*, G. Cerna, T. Johnston, S. Kakde, K. Karuku, M. Kowal, J. Monahan, J. Murray, T. Nguyen, A. Sanchez Carreon, E. Song, A. Streiff, B. Su, F. Youkhana, S. Munig, Z. Patel, M. So, M. Sy, S. Weiss, Y. Zhou, S.P. Pfeifer. 2022. Complete genome sequence of the cluster P mycobacteriophage Phegasus. Microbiol. Resour. Announc. 11(9): e00540-22. 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 

S. Sabin, A.Y. Morales-Arce, S.P. Pfeifer, J.D. Jensen. 2022. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canetti and Mycobacterium tuberculosis. G3 (Bethesda), 12(5): jkac055. 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 rateseLife, 11: e73577. pdf 

C.J. Versoza and S.P. Pfeifer. 2022. Computational prediction of bacteriophage host ranges. Microorganisms, 10(1): 149. pdf 

S.P. Pfeifer. 2021. Studying mutation rate evolution in primates – the effects of computational pipeline and parameter choices. GigaScience, 10(10): giab069. pdf 

C.J. Versoza*, J.A. Rivera*, E.B. Rosenblum, C. Vital García, D.K. Hews, S.P. Pfeifer. 2021. The recombination landscapes of spiny lizards (genus Sceloporus). G3 (Bethesda), 12(2): jkab402. pdf 

A. Crane*, C.J. Versoza*, T. Hua, R. Kapoor, L. Lloyd, R. Mehta, J. Menolascino, A. Morais, S. Munig, Z. Patel, D. Sackett, B. Schmit, M. Sy, S.P. Pfeifer. 2021. Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages. G3 (Bethesda), 11(11): jkab291. pdf

H-Y. Wang, S.M. Valencia, S.P. Pfeifer, J.D. Jensen, T.F. Kowalik, S.R. Permar. 2021. Common polymorphisms in the glycoproteins of human cytomegalovirus and associated strain-specific immunity. Viruses, 13(6): 1106. pdf

M. Milhaven, E. Hastings, D. Brister, L. Cevallos, S. Chilukuri, A. Diyya, A. Garg, R. Hernandez, D. Kelly, K. Lazo, J. Le, G. Maag, P.D. Marfatia, R. Mehta, A. Nejad, J. Porche, A. Queiroz, D. Sackett, P. Santos Molina, T. Slade, M. So, K. Thakur, A. Urquidez Negrete, S. Wackett, S. Weiss, L. McCarthy,  K. Wheaton, A.D. Rudner, J.P. McCutcheon, S.P. Pfeifer. 2021. Complete genome sequence of the Microbacterium bacteriophage Erla. Microbiol. Resour. Announc., 10(3): e01354-20. pdf

S.P. Pfeifer. 2020. Spontaneous mutation rates. In The Molecular Evolutionary Clock. Theory and Practice. Springer Nature.

A. Crane, J. Abaidoo, G. Beltran, D. Fry, C. Furey, N. Green, R. Johal, B. La Rosa, C. Lopez Jimenez, L. Luong, G. Maag, J. Porche, L. Reyes, A. Robinson, S. Sabbara, L. Soto Herrera, A. Urquidez Negrete, P. Wilson, K. Geiler-Samerotte, S.P. Pfeifer. 2020. The complete genome sequence of the Staphylococcus bacteriophage Metroid. G3 (Bethesda), 10(9): 2975-2979. pdf

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

R.B. Harris, K. Irwin, M.R. Jones, S. Laurent, R.D.H. Barrett, M.W. Nachman, J.M. Good, C.R. Linnen, J.D. Jensen, S.P. Pfeifer. 2020. The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity, 124(1): 1-14. pdf

R.D.H. Barrett*, S. Laurent*, R. Mallarino*, S.P. Pfeifer, C.C. Xu, M. Foll, K. Wakamatsu, J. Duke-Cohan, J.D. Jensen, H.E. Hoekstra. 2019. Linking genetic variation to survival in wild mice. Science, 363(6426): 499-504. pdf

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

S.P. Pfeifer*, S. Laurent*, V.C. Sousa*, C.R. Linnen*, M. Foll, L. Excoffier#, H.E. Hoekstra#, J.D. Jensen#. 2018. The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flowMol. Biol. Evol., 35(4): 792-806. pdf

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

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

S.P. Pfeifer. 2017. From next-generation resequencing reads to a high quality variant data set. Heredity, 118(2): 111-124. 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

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. pdf

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

N. Renzette, S.P. Pfeifer, S. Matuszewski, T.F. Kowalik, 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. J. Virol., 91(5): e01976-16. pdf

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. Biol. Invasions, 20(6): 1577-1595. 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

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 lizards. Mol. Ecol., 25(1): 306-323. pdf

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

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