lab members indicated
2024
Soni, V., and J.D. Jensen. 2024. Temporal challenges in detecting balancing selection from population genomic data. G3, in press.
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.
2023
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
2022
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
2021
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 civilizations. Cell 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
2020
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: 316-32. pdf
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
2019
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
2018
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
2017
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. Irwin, S.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
2016
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. Matuszewski, H. 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 strategy. Evolution 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 experiments. Genetics 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
2015
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
2014
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
2013
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 selection. PLOS 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
2012
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
2011
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
2010
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
2009
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
2005-2008
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