lab members indicated


Soni, V., and J.D. Jensen. 2024. Temporal challenges in detecting balancing selection from population genomic data. G3 14: jkae069. pdf

Soni, V., J. Terbot, and J.D. Jensen. 2024. Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data. Nat Comm 15: 3240. pdf

Soni, V., S.P. Pfeifer, and J.D. Jensen. 2024. The effect of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects. GBE 16: evae004. pdf

Versoza, C.(*), S. Weiss(*), R. Johal, B. La Rosa, J.D. Jensen, and S.P. Pfeifer. 2024. Novel insights into the landscape of crossover and non-crossover events in rhesus macaques (Macaca mulatta). GBE 16: evad223. pdf

Charlesworth, B., and J.D. Jensen. 2024. Population genetics. Encyclopedia of Biodiversity, 3rd edition. Vol. 7: 467-483.


Terbot, J., B.S. Cooper, J.M. Good, and J.D. Jensen. 2023. A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2. GBE 15: evad204. pdf

Moström, M., S. Yu, D. Tran, F. Saccoccio, C. Versoza, D. Malouli, S. Valencia, M. Gilbert, R. Blair, S. Hansen, P. Barry, K. Fruh, J.D. Jensen, S.P. Pfeifer, T. Kowalik, S. Permar, and A. Kaur. 2023. Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. PLOS Pathogens 19: e1011646. pdf

Soni, V., P. Johri, and J.D. Jensen. 2023. Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models. Evolution 77: 2113-2127. pdf

Johri, P., S.P. Pfeifer, and J.D. Jensen. 2023. Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history. MBE 40: msad100. pdf

Howell, A.A., J. Terbot, V. Soni, P. Johri, J.D. Jensen(#), and S.P. Pfeifer(#). 2023. Developing an appropriate evolutionary baseline model for the study of human cytomegalovirus. GBE 15: evad059. pdf

Terbot, J., P. Johri, S. Liphardt, V. Soni, S.P. Pfeifer, B.S. Cooper(#), J.M. Good(#), and J.D. Jensen(#). 2023. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLOS Pathogens 19: e1011265. pdf

Freund, F., E. Kerdoncuff, S. Matuszewski, M. Lapierre, M. Hildebrandt, J.D. Jensen, L. Ferretti, A. Lambert, T. Sackton, and G. Achaz. 2023. Interpreting the pervasive observation of U-shaped site frequency spectra. PLOS Genetics 19: e1010677. pdf

Ghafoor, S., J. Santos, C.J. Versoza, J.D. Jensen, and S.P. Pfeifer. 2023. The impact of sample size and population history on observed mutational spectra: a case study in human and chimpanzee populations. GBE 15: evad019. pdf

Charlesworth, B., and J.D. Jensen. 2023. Population genetic considerations regarding evidence for biased mutation rates in Arabidopsis thaliana. MBE 40: msac275. pdf

Jensen, J.D. 2023. Population genetic concerns related to the interpretation of empirical outliers and the neglect of common evolutionary processes. Heredity 130: 109-110. pdf


Charlesworth, B., and J.D. Jensen. 2022. Some complexities in interpreting apparent effects of hitchhiking: a commentary on Gompert et al. 2022. Mol Ecol 31: 4440-4443. pdf

Hager, E.R.(*), O.S. Harringmeyer(*), T.B. Wooldridge, S. Theingi, J.T. Gable, S. McFadden, B. Neugeboren, K.M. Turner, J.D. Jensen, and H.E. Hoekstra. 2022. A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes. Science 377: 399-405. pdf

Charlesworth, B., and J.D. Jensen. 2022. How can we resolve Lewontin’s Paradox? GBE 14(7): evac096. pdf

Johri, P., A. Eyre-Walker, R.N. Gutenkunst, K.E. Lohmueller, and J.D. Jensen. 2022. On the prospect of achieving accurate joint estimation of selection with population history. GBE (14)7: evac088. pdf

Johri, P., C.F. Aquadro, M. Beaumont, B. Charlesworth, L. Excoffier, A. Eyre-Walker, P.D. Keightley, M. Lynch, G. McVean, B.A. Payseur, S.P. Pfeifer, W. Stephan, and J.D. Jensen. 2022. Recommendations for improving statistical inference in population genomics. PLOS Biology 20(5): e3001669. pdf

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

Jiang, L., N. Samant, P. Liu, M. Somasundaran, J.D. Jensen, W. Marasco, C. Schiffer, R.W. Finberg, J.P. Wang, T.F. Kowalik, and D.N. Bolon. 2022. Identification of a permissive secondary mutation that restores the enzymatic activity of oseltamivir resistance mutation H275Y. J Virol 96: e0198221. pdf

Johri, P., W. Stephan, and J.D. Jensen. 2022. Soft selective sweeps: addressing new definitions, evaluating competing models, and interpreting empirical outliers. PLOS Genetics 18(2): e1010022. pdf

Morales-Arce, A.Y.(*), P. Johri(*), and J.D. Jensen. 2022. Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies. Heredity 128: 79-87. pdf


Johri, P.(*), B. Charlesworth(*), E.K. Howell, M. Lynch(#), and J.D. Jensen(#). 2021. Revisiting the notion of deleterious sweeps. Genetics 219: iyab094. pdf

Charlesworth, B., and J.D. Jensen. 2021. Effects of selection at linked sites on patterns of genetic variability. AREES 52: 177-197. pdf

Johri, P., K. Riall, H. Becher, L. Excoffier, B. Charlesworth, and J.D. Jensen. 2021. The impact of purifying and background selection on the inference of population history: problems and prospects. MBE 38: 2986-3003. pdf

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

Clemente, F., M. Unterlander, O. Dolgova, C. Amorim, F. Coroado-Santos, S. Neuenschwander, E. Ganiatsou, D. Cruz Davalos, L. Anchieri, F. Michaud, L. Winkelbach, J. Blocher, Y. Cardenas, B. Sousa da Mota, E. Kalliga, A. Souleles, I. Kontopoulos, G. Karamitrou-Mendessidi, O. Philaniotou, A. Sampson, D. Theodorou, M. Tsipopoulou, I. Akamatis, P. Halstead, K. Kotsakis, D. Urem-Kotsou, D. Panagiotopoulos, C. Ziota, S. Triantaphyllou, O. Delaneau, J.D. Jensen, J. Morena-Mayar, J. Burger, V. Sousa, O. Lao, A.-S. Malaspinas(#), and C. Papageorgopoulou(#). 2021. The genomic history of the Aegean palatial civilizationsCell 184: 2565-2586. pdf

Jensen, J.D. 2021. Studying population genetic processes in viruses: from drug-resistance evolution to patient infection dynamics. In: Bamford, D.H. and Zuckerman, M. (eds.) Encyclopedia of Virology, 4th edition, vol.5: 227-232. Oxford Academic Press. pdf

Morales-Arce, A.Y., S.J. Sabin, A.C. Stone, and J.D. Jensen. 2021. The population genomics of within-host Mycobacterium tuberculosis. Heredity 126: 1-9. pdf


Jensen, J.D., R.A. Stikeleather, T.F. Kowalik, and M. Lynch. 2020. Imposed mutational meltdown as an antiviral strategy. Evolution 74: 2549-59. pdf

Jones, M.R., L.S. Mills, J.D. Jensen, and J.M. Good. 2020. Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range. Evolution 74: 2033-45. pdf

Jones, M.R., L.S. Mills, J.D. Jensen, and J.M. Good. 2020. The origin and spread of locally adaptive seasonal camouflage in snowshoe hares. Am Nat. 196: 316-32pdf

Harris, R.B., and J.D. Jensen. 2020. Considering genomic scans for selection as coalescent model choice. GBE 12: 871-77. pdf

Morales-Arce, A.Y., R.B. Harris, A.C. Stone, and J.D. Jensen. 2020. Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution. Evolution 74: 992-1001. pdf

Johri, P., B. Charlesworth, and J.D. Jensen. 2020. Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection. Genetics 215: 173-92. pdf

Jensen, J.D., and M. Lynch. 2020. Considering mutational meltdown as a potential SARS-CoV-2 treatment strategy. Heredity 124: 619-20. pdf

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

Jensen, J.D., and T.F. Kowalik. 2020. A consideration of within-host human cytomegalovirus genetic variation. PNAS 117: 816-7. pdf


Sackman, A., R.B. Harris, and J.D. Jensen. 2019. Inferring demography and selection in organisms characterized by skewed offspring distributions. Genetics 211: 1019-28. pdf

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

Jensen, J.D., B.A. Payseur, W. Stephan, C.F. Aquadro, M. Lynch, D. Charlesworth, and B. Charlesworth. 2019. The importance of the Neutral Theory in 1968 and 50 years on: a response to Kern & Hahn 2018. Evolution 73: 111-4. pdf

Prachanronarong, K., A. Canale, P. Liu, M. Somasundaran, S. Hou, Y.-P. Poh, T. Han, Q. Zhu, N. Renzette, K. Zeldovich, T. Kowalik, N. Kurt-Yilmaz, J.D. Jensen, D. Bolon,  W. Marasco, R. Finberg, C. Schiffer, and J.P. Wang. 2019. Mutations in influenza A virus neuraminidase and hemagglutinin confer resistance against a broadly neutralizing hemagglutinin stem antibody. J Virol 93(2): e01639. pdf


Harris, R.B.(*), A. Sackman(*), and J.D. Jensen. 2018. On the unfounded enthusiasm for soft selective sweeps II: examining recent evidence from humans, flies, and viruses. PLOS Genetics 14(12): e1007859. pdf

Fragata, I.(*), S. Matuszewski(*), M.A. Schmitz, T. Bataillon, J.D. Jensen, and C. Bank. 2018. The fitness landscape of the codon space across environments. Heredity 121: 422-37.  pdf

Kapopoulou, A., S.P. Pfeifer, J.D. Jensen, and S. Laurent. 2018. The demographic history of African Drosophila melanogaster. GBE 10(9): 2338-42. pdf

Jones, M.R., L. Mills, P. Alves, C. Callahan, J. Alves, D. Lafferty, F. Jiggins, J.D. Jensen, J. Melo-Ferreira, and J.M. Good. 2018. Adaptive introgression underlies polymorphic seasonal camouflage in Snowshoe Hares. Science 360: 1355-58. pdf

Canale, A., S. Venev, T. Whitfield, D. Caffrey, W. Marasco, C. Schiffer, T. Kowalik, J.D. Jensen, R.Finberg, K. Zeldovich, J. Wang, and D. Bolon. 2018. Synonymous mutations at the beginning of the influenza A virus hemagglutinin gene impact experimental fitness. JMB 430: 1098-1115. pdf

Pfeifer, S.P.(*), 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 flow. MBE 35: 792-806. pdf

Sackman, A.M., S.P. Pfeifer, T. F. Kowalik, and J.D. Jensen. 2018. On the demographic and selective forces shaping patterns of human cytomegalovirus variation within hosts. Pathogens 7: 16. pdf

Matuszewski, S., M.E. Hildebrandt, G. Achaz, and J.D. Jensen. 2018. Coalescent processes with skewed offspring distributions and non-equilibrium demography. Genetics 208: 323-38. pdf


Avnir, Y., K. Prachanronarong, Z. Zhang, S. Hou, E. Peterson, J. Sui, H. Zayed, V. Kurella, A. McGuire, L. Stamatatos, B. Hilbert, M. Bohn, K. Zeldovich, T. Kowalik, J.D. Jensen, D. Bolon, R. Finberg, J. Wang, R. Jefferis, Q. Zhu, N. Yilmaz, C. Shiffer, and W. Marasco. 2017. Structural determination of the broadly reactive anti-IGHV1-69 anti-idiotypic antibody G6 and its idiotope. Cell Reports 21: 3243-55. pdf

Carratala, A., H. Shim, Q. Zhong, V. Bachmann, J.D. Jensen, and T. Kohn. 2017. Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to resistance to disinfection and ribavirin. Virus Evol 3: 1-11. pdf

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

Ma, L., J. Boucher, J. Paulsen, S. Matuszewski, C. Eide, J. Ou, G. Eickelberg, R. Press, L. Zhu, B. Druker, S. Branford, S. Wolfe, J.D. Jensen, C.A. Schiffer, M.R. Green, and D.N. Bolon. 2017. CRISPR-Cas9 mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy. PNAS 114: 11751-756. pdf

Zhong, Q., A. Carratala, H. Shim, V. Bachmann, J.D. Jensen, and T. Kohn. 2017. Resistance of echovirus 11 to ClO2 is associated with enhanced host receptor use, altered entry routes and high fitness. Environ Sci Technol 51: 10746-55. pdf

Ormond, L., P. Liu, S. Matuszewski, N. Renzette, C. Bank, K. Zeldovich, D. Bolon, T. Kowalik, R. Finberg, J.D. Jensen(#), and J. Wang(#). 2017. The combined effect of oseltamivir and favipiravir on influenza A virus evolution. GBE 9: 1913-24. pdf

Pokalyuk, C., N. Renzette, K.K. IrwinS.P. Pfeifer, L. Gibson, W.J. Britt, A.Y. Yamamoto, M.M. Mussi-Pinhata, T.F. Kowalik(#), and J.D. Jensen(#). 2017. Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective. Mol Ecol 26: 1980-90. pdf

Matuszewski, S., L. Ormond, C. Bank, and J.D. Jensen. 2017. Two sides of the same coin: a population genetics perspective on lethal mutagenesis and mutational meltdown. Virus Evol 3: 1-5. pdf

Renzette, N., 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. J Virol 91: e01976-16. pdf


Bank, C.(*), S. Matuszewski(*), R.T. Hietpas, and J.D. Jensen. 2016. On the (un)predictability of a large intragenic fitness landscape. PNAS 113: 14085-90. pdf

Prachanronarong, K., A. Ozen, K. Thayer, L. Yilmaz, K. Zeldovich, D.N. Bolon, T.F. Kowalik, J.D. Jensen, R.W. Finberg, J.P. Wang, N. Kurt-Yilmaz, and C. Schiffer. 2016. Molecular basis for differential patterns of drug resistance in Influenza N1 and N2 neuraminidase. JCTC 12: 6098-6108. pdf

Irwin, K.K., S. Laurent, S. Matuszewski, S. Vuilleumier, L. Ormond, H. Shim, C. Bank, and J.D. Jensen. 2016. On the importance of skewed offspring distributions and background selection in virus population genetics. Heredity 117: 393-99. pdf

Pfeifer, S.P., and J.D. Jensen. 2016. The impact of linked selection in chimpanzees: a comparative study. GBE 8: 3202-8. pdf

Bank, C., N. Renzette, P. Liu, S. MatuszewskiH. Shim, M. Foll, D.N. Bolon, K.B. Zeldovich, T.F. Kowalik, R.W. Finberg, J.P. Wang(#), and J.D. Jensen(#). 2016. An experimental evaluation of drug induced mutational meltdown as an antiviral treatment strategyEvolution 70: 2470-84. pdf

Matuszewski, S.(*), M.E. Hildebrandt(*), A.-H. Ghenu, J.D. Jensen, and C. Bank. 2016. A statistical guide to the design of deep mutational scanning experimentsGenetics 204: 77-87. pdf

Irwin, K.K., N. Renzette, T.F. Kowalik, and J.D. Jensen. 2016. Antiviral drug resistance as an adaptive process. Virus Evol 2: 1-10. pdf

Ferrer-Admetlla, A., C. Leuenberger, J.D. Jensen, and D. Wegmann. 2016. An approximate Markov model for the Wright-Fisher diffusion and its application to time series data. Genetics 203: 831-46. pdf

Shim, H., S. Laurent, S. Matuszewski, M. Foll, and J.D. Jensen. 2016. Detecting and quantifying changing selection intensities from time-sampled polymorphism data. G3 6: 893-904. pdf

Jiang, L., P. Liu, C. Bank, N. Renzette, K. Prachanronarong, L. Yilmaz, D.R. Caffrey, K.B. Zeldovich, C.A. Schiffer, T.F. Kowalik, J.D. Jensen, R.W. Finberg, J.P. Wang and D.N. Bolon. 2016. A balance between inhibitor binding and substrate processing confers influenza drug resistance. JMB 428: 538-53. pdf

Alcala, N., J.D. Jensen, A. Telenti, and S. Vuilleumier. 2016. The genomic signature of population reconnection following isolation: from theory to HIV. G3 6: 107-20. pdf

Kapopoulou, A., L. Mathew, A. Wong, D. Trono, and J.D. Jensen. 2016. The evolution of gene expression and binding specificity of the largest transcription factor family in primates. Evolution 70: 167-80. pdf

Jensen, J.D., M. Foll, and L. Bernatchez. 2016. Introduction: the past, present, and future of genomic scans for selection. Mol Ecol 25: 1-4. pdf

Ormond, L., M. Foll, G. Ewing, S. Pfeifer, and J.D. Jensen, 2016. Inferring the age of a fixed beneficial allele. Mol Ecol 25: 157-9. pdf

Ewing, G. and J.D. Jensen, 2016. The consequences of not accounting for background selection in demographic inference. Mol Ecol 25: 135-141. pdf

Laurent, S.(*), S. Pfeifer(*), M. Settles, S. Hunter, K. Hardwick, L. Ormond, V. Sousa, J.D. Jensen(#), and E.B. Rosenblum(#), 2016. The population genomics of rapid adaptation: disentangling signatures of selection and demography in White Sands lizards. Mol Ecol 25: 306-23. pdf

Renzette, N., T.F. Kowalik, and J.D. Jensen, 2016. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus diversity. Mol Ecol 25: 403-13. pdf


Mathew, L. and J.D. Jensen, 2015. Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demography. Front Genet. 6: 268. pdf

Renzette, N., C. Pokalyuk, L. Gibson, M.R. Schleiss, K. Hamprecht, M. Mussi Pinhata, A.Y. Yamamoto, W.J. Britt, J.D. Jensen(#), and T.F. Kowalik(#), 2015. Limits and patterns of cytomegalovirus genomic diversity in humans. PNAS 112: E4120-28. pdf

Montano, V., X. Didelot, M. Foll, B. Linz, Y. Moodley(#), and J.D. Jensen(#), 2015. Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori. Genetics 200: 947-63. pdf

Mahajan, S., J. Crisci, A. Wong, S. Akbarian, M. Foll(#), and J.D. Jensen(#), 2015. Quantifying polymorphism and divergence from epigenetic data: a framework for inferring the action of selection. Front Genet. 6: 190. pdf

Ewing, G., P. Reiff, and J.D. Jensen, 2015. PopPlanner: Visually constructing demographic models for simulation. Front Genet. 6: 150. pdf

Zeldovich, K.B., P. Liu, N. Renzette, M. Foll, S.T. Pham, S.V. Venev, D.N. Bolon, E.A. Kurt-Jones, G.R. Gallagher, J.D. Jensen, D.R. Caffrey, C.A. Schiffer, T.F. Kowalik, J.P. Wang, and R.W. Finberg, 2015. Positive selection drives preferred segment combinations during influenza virus reassortment. MBE 32: 1519-32. pdf

Bank, C., R.T. Hietpas, J.D. Jensen, and D.N. Bolon, 2015. A systematic survey of an intragenic epistatic landscape. MBE 32: 229-38. pdf

Foll, M.(*), H. Shim(*), and J.D. Jensen, 2015. A Wright-Fisher ABC-based approach for inferring per-site effective population sizes and selection coefficients from time-sampled data. Mol Ecol Res 15: 87-98. pdf


Malaspinas, A.-S., O. Lao, H. Schroeder, M. Rasmussen, M. Raghavan, I. Moltke, P.F. Campos, V.F. Goncalves, S. Rasmussen, F. Santana Sagredo, A. Albrechtsen, M.E. Allentoft, P.L.F. Johnson, M. Li, S. Reis, D.V. Bernardo, A.T. Duggan, M. Bastos, E. Hodges, G.J. Hannon, M. DeGiorgio, Y. Wang, J. Stenderup, S. Brunak, T. Sicheritz-Ponten, L. Orlando, T.D. Price, J.D. Jensen, R. Nielsen, J. Heinemeier, J. Olsen, C. Rodrigues-Carvalho, M. Mirazon Lahr, W. Neves, M. Kayser, T. Higham, M. Stoneking, S.D.J. Pena, and E. Willerslev, 2014. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudo of Brazil. Curr Biol 24: R1035-7. pdf

Bank, C., M. Foll, A. Ferrer-Admetlla, G. Ewing, and J.D. Jensen, 2014. Thinking too positive? Revisiting current methods in population genetic selection inference. Trends Genet 30: 540-6. pdf

Poh, Y.-P., V. Domingues, H.E. Hoekstra, and J.D. Jensen, 2014. On the prospect of identifying adaptive loci in recently bottlenecked populations. PLOS One 9(11): e110579. pdf

Jensen, J.D., 2014. On the unfounded enthusiasm for soft selective sweeps. Nat Comm 5: 5281. pdf

Renzette, N., L. Gibson J.D. Jensen, and T.F. Kowalik, 2014. Human cytomegalovirus intrahost evolution – a new avenue for understanding and controlling herpesvirus infections. Curr Opin Virol 8C: 109-115. pdf

 Simkin, A., J. Bailey, B. Theurkauf, F.-B. Gao, and J.D. Jensen, 2014. Inferring the evolutionary history of primate miRNA binding sites: overcoming motif counting biases. MBE 31: 1894-1901. pdf

Bank, C., R.T. Hietpas, A. Wong, D.N.A. Bolon(#), and J.D. Jensen(#), 2014. A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments. Genetics 196: 841-52. pdf

Foll, M.(*), Y.-P. Poh(*), N. Renzette, A. Ferrer-Admetlla, H. Shim, A.-S. Malaspinas, G. Ewing, C. Bank, P. Liu, D. Wegmann, D. R. Caffrey, K.B. Zeldovich, D.N.A. Bolon, J. Wang, T.F. Kowalik, C.A. Schiffer, R.W. Finberg, and J.D. Jensen, 2014. Influenza virus drug resistance: a time-sampled population genetics perspective. PLOS Genetics 10(2): e1004185. pdf

Ewing, G., and J.D. Jensen, 2014. Distinguishing neutral from deleterious mutations in growing populations. Front Genet. 5: 7. pdf

Renzette, N., D.R. Caffrey, K.B. Zeldovich, P. Liu, G.R. Gallagher, D. Aiello, A.J. Porter, E.A. Kurt-Jones, D.N. Bolon, Y.-P. Poh, J.D. Jensen, C.A. Schiffer, T.F. Kowalik, R.W. Finberg, and J.P. Wang, 2014. Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. J Virol 88: 272-81. pdf


Hietpas, R.T.(*), C. Bank(*), J.D. Jensen(#), and D.N. Bolon(#), 2013. Shifting fitness landscapes in response to altered environments. Evolution 67: 3512-22. pdf

Crisci, J., Y.-P. Poh, S. Mahajan, and J.D. Jensen, 2013. The impact of equilibrium assumptions on tests of selection. Front Genet. 4: 235. pdf

Renzette, N., L. Gibson, B. Bhattacharjee, D. Fisher, M.R. Schleiss, J.D. Jensen(#), and T. F. Kowalik(#), 2013. Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selectionPLOS Genetics 9(9): e1003735. pdf

 Joost, S., S. Vuilleumier, J.D. Jensen, S. Schoville, K. Leempoel, S. Stucki, C. Melo de Lima, J. Rolland, I. Widmer, and S. Manel, 2013. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics. Mol Ecol 22: 3659-3665. pdf

 Simkin, A., A. Wong, Y.-P. Poh, B. Theurkauf, and J.D. Jensen, 2013. Recurrent and recent selective sweeps in the piRNA pathway. Evolution 67: 1081-90. pdf

Linnen, C.R., Y.-P. Poh, B. Peterson, R. Barrett, J. Larson, J.D. Jensen, and H.E. Hoekstra, 2013. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 339: 1312-1316. pdf

Singh, N.D., J.D. Jensen, A. G. Clark, and C.F. Aquadro, 2013. Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics 193: 215-28. pdf


Massouras, A., S.M. Waszak, M. Albarca, K. hens, W. Westphal, J.F. Ayroles, E.T. Dermitzakis, E.A. Stone, J.D. Jensen, T.F.C. Mackay, and B. Deplancke, 2012. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLOS Genetics 8(11): e1003055. pdf

Shulha, H.(*), J. Crisci(*), D. Reshetov(*), J.S. Tushir, I. Cheung, R. Bharadwaj, H.J. Chou, I. Houston, C.J. Peter, A.C. Mitchell, W-D. Yao, R.H. Myers, J-F. Chen, T. Preuss, E. Rogaev, J.D. Jensen(#), Z. Weng(#), and S. Akbarian(#), 2012. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLOS Biology. 10(11): e1001427. pdf

Pavlidis, P., J.D. Jensen, W. Stephan, A. Stamatakis, 2012. A critical assessment of story-telling: GO categories and the importance of validating genomic scans. MBE 29: 3237-48. pdf

Domingues, V., Y.-P. Poh, B. Peterson, P. Pennings, J.D. Jensen, and H.E. Hoekstra, 2012. Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution 66: 3209-23. pdf

Crisci, J., and J.D. Jensen, 2012. Evolution of the human genome: adaptive changes. eLS, John Wiley & Sons, Ltd. pdf

Crisci, J., Y.-P. Poh, A. Bean, A. Simkin, and J.D. Jensen, 2012. Recent progress in polymorphism-based population genetic inference. J Hered 103: 287-96. pdf


Xu, X.(*), S. Ge(*), J.D. Jensen(*), R. Gutenkunst(*), J. Li(*), X. Li(*), L. Fang, L. Huang, K. Ye, W. He, G. Zhang, X. Zheng, F. Zhang, F. Hu, Y. Li, C. Yu, Y. Guo, D. Li, K. Kristiansen, X. Zhang, J. Wang, R. Nielsen, J. Wang, and W. Wang, 2011. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30: 105-11. pdf

Sinha, P., A. Dincer, D. Virgil, G. Xu, Y.-P. Poh, and J.D. Jensen, 2011. On detecting selective sweeps using single genomes. Front Genet. 2: 85-90. pdf

Crisci, J., A. Wong, J. Good, and J.D. Jensen, 2011. On characterizing adaptive events unique to modern humans. GBE 3: 791-798. pdf

Albert, F.W., E. Hodges, J.D. Jensen, F. Besnier, Z. Xuan, M. Rooks, A. Bhattacharjee, L. Brizuela, J.M. Good, R. E. Green, H. Burbano, I.Z. Plyusnina, L. Trut, L. Andersson, T. Schoneberg, O. Carlborg, G.J. Hannon, and S. Paabo, 2011. Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity 107: 205-14. pdf

Jensen, J.D. and D. Bachtrog, 2011. Characterizing the influence of effective population size on the rate of adaptation: Gillespie’s Darwin Domain. GBE 3: 687-701. pdf

Renzette, N., B. Bhattarcharjee, J.D. Jensen, L. Gibson, and T.F. Kowalik, 2011. Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants. PLOS Pathogens 7(5): e1001344. pdf

Hietpas, R.T., J.D. Jensen, and D.N.A. Bolon, 2011. Experimental illumination of a fitness landscape. PNAS 108: 7896-901. pdf


Cutler, D.J. and J.D. Jensen, 2010. To pool, or not to pool. Genetics 186: 41-3. pdf

Pavlidis, P., J.D. Jensen, and W. Stephan, 2010. Searching for footprints of positive selection in whole-genome SNP data from non-equilibrium populations. Genetics 185: 907-22. pdf

Jensen, J.D., and O.J. Rando, 2010. Recent evidence for pervasive adaptation targeting gene expression attributable to population size change. PNAS 107: E109-110. pdf

Green, R.E., J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M. H-Y. Fritz, N. Hansen, E.Y. Durand, A.-S. Malaspinas, J.D. Jensen, T. Marques-Bonet, C. Alkan, M. Meyer, K. Prufer, H.A. Burbano, J.M. Good, R. Schultz, A. Aximu-Petri, A. Butthof, B. Hober, B. Hoffner, M. Siegemund, A. Weihmann, C. Nusbaum, E.S. Lander, C. Russ, N. Novod, J. Affourtit, M. Egholm, P. Rudan, D. Brajkovic, Z. Kucan, I. Gusic, V.B. Doronichev, L.V. Golovanova, C. Lalueza-Fox, M. de la Rasilla, J. Fortea, A. Rosas, R. Schmitz, P. Johnson, E.E. Eichler, D. Flash, E. Birney, J.C. Mullikin, M. Slatkin, R. Nielsen, J. Kelso, M. Lachmann, D. Reich, and S. Paabo, 2010. A draft sequence of the Neandertal genome. Science 328: 710-722. pdf

Jensen, J.D. and D. Bachtrog, 2010. Characterizing recurrent positive selection at fast evolving genes in Drosophila miranda and Drosophila pseudoobscura. GBE 2: 371-8. pdf

Pool, J. E., I. Hellmann, J.D. Jensen, and R. Nielsen. 2010, Population genetic inference from genomic sequence variation. Genome Res 20: 291-300. pdf


Jensen, J.D., 2009. On reconciling single and recurrent hitchhiking models. GBE 1: 320-4. pdf

Xia, Q., Y. Guo, Z. Zheng, D. Li, Z. Xuan, Z. Li, F. Dai, Y. Li, D. Cheng, R. Li, T. Cheng, T. Jiang, C. Becquet, X. Xu, C. Liu, X. Zha, W. Fan, Y. Lin, Y. Shen, L. Jiang, J.D. Jensen, I. Hellmann, S. Tang, P. Zhao, H. Xu, C. Yu, G. Zhang, J. Li, J. Cao, S. Liu, N. He, Y. Zhou, H. Liu, J. Zhao, C. Ye, C. Du, G. Pan, A. Zhao, H. Shao, W. Zeng, P. Wu, C. Li, M. Pan, J. Li, X. Yin, D. Li, J. Wang, H. Zheng, W. Wang, X. Zhang, S. Li, H. Yang, C. Lu, R. Nielsen, Z. Zhou, J. Wang, Z. Xiang, and J. Wang, 2009. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326: 433-6. pdf

Linnen, C.R., E. P. Kingsley, J.D. Jensen, and H.E. Hoekstra, 2009. On the origin and spread of an adaptive allele in deer mice. Science 325: 1095-1098. pdf

Bachtrog, D., J.D. Jensen, and Z. Zhang, 2009. Accelerated adaptive evolution on a newly formed X chromosome. PLOS Biology 7(4): e1000082. pdf


Jensen, J.D., K.R. Thornton, and P. Andolfatto, 2008. An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLOS Genetics 4(9): e1000198. pdf

Jensen, J.D., K.R. Thornton, and C.F. Aquadro, 2008. Inferring selection in partially sequenced regions. MBE 25: 438-46. pdf

Singh, N.D., J.M. Macpherson, J.D. Jensen, and D.A. Petrov, 2007. Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. BMC Evol Biol 7: 202-210. pdf

Jensen, J.D., K.R. Thornton, C.D. Bustamante, and C.F. Aquadro, 2007. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in non-equilibrium populations. Genetics 176: 2371-2379. pdf

Jensen, J.D., V. Bauer DuMont, A.B. Ashmore, A. Gutierrez and C.F. Aquadro, 2007. Patterns of sequence variability and divergence at the diminutive gene region of Drosophila melanogaster: complex patterns suggest an ancestral selective sweep. Genetics 177: 832-840. pdf

Jensen, J.D., A. Wong, and C.F. Aquadro, 2007. Approaches for identifying targets of positive selection. Trends Genet 23: 484-491. pdf

Thornton, K.R. and J.D. Jensen, 2007. Controlling the false positive rate in multi-locus genome scans for selection. Genetics 175: 737-750. pdf

Wong, A.W., J.D. Jensen, J.E. Pool and C.F. Aquadro, 2007. Phylogenetic incongruence in the Drosophila melanogaster species group. MPE 43: 1138-50. pdf

Thornton, K.R., J.D. Jensen, C. Bequet and P. Andolfatto, 2007. Progress and prospects in mapping recent selection in the genome. Heredity 98: 340-8. pdf

Casa, A.M., S.E. Mitchell, J.D. Jensen, M.T. Hamblin, A.H. Paterson, C.F. Aquadro, and S. Kresovich, 2006. Evidence for a selective sweep on chromosome 1 of cultivated sorghum. Crop Sci 46: S15-S26. pdf

 Jensen, J.D., Y. Kim, V. Bauer DuMont, C.F. Aquadro, and C.D. Bustamante, 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410. pdf