Publications

lab members indicated

2017

Pfeifer, S.P.(*), S. Laurent(*), V.C. Sousa(*), C.R. Linnen(*), M. Foll, L. Excoffier(#), H.E. Hoekstra(#), and J.D. Jensen(#). The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow. In revision, PLoS Genetics. biorxiv

Matuszewski, M., M.E. Hildebrandt, G. Achaz, and J.D. Jensen. 2017. Coalescent processes with skewed offspring distributions and non-equilibrium demography. Accepted, Geneticsbiorxiv

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 tolerance to disinfection and mutagenic resistance to ribavirin. In press, Virus Evol.

Ma, L., J. Boucher, J. Paulsen, S. Matuszewski, 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. In press, PNAS.

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. In press, Science.

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): 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(5): 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. J Chem Theory Comput 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 viral 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, 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): 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(4): 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. J Mol Biol 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): 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(1): 157-9. pdf

Ewing, G. and J.D. Jensen, 2016. The consequences of not accounting for background selection in demographic inference. Mol Ecol 25(1): 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(1): 306-23. pdf

Renzette, N., T.F. Kowalik, and J.D. Jensen, 2016. The relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus diversity. Mol Ecol 25(1): 403-13. pdf

2015

Mathew, L. and J.D. Jensen, 2015. Evaluating the ability of the 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(21): 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(12): 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: a case study in beach mice. 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. On 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(14): 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(1): 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(10): 3237-48. pdf

Domingues, V., Y.-P. Poh, B. Peterson, P. Pennings, J.D. Jensen, and H.E. Hoekstra, 2012. Targeted resequencing reveals a single recent origin of a beneficial pigment allele in cryptic 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 recent adaptive events 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. The existence of the human cytomegalovirus quasispecies as revealed by high throughput sequencing. PLOS Pathogens 7(5): e1001344. pdf

Hietpas, R.T., J.D. Jensen, and D.N.A. Bolon, 2011. Experimental dissection 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. GBE 2: 371-8. pdf

Pool, J. E., I. Hellmann, J.D. Jensen, and R. Nielsen. 2010, Population genomics and next-generation sequencing technology. 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 (5951): 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 Peromyscus mice. Science 325 (5944): 1095-1098. pdf

Bachtrog, D., J.D. Jensen, and Z. Zhang, 2009. Pervasive 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. 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 variability and divergence at the diminutive gene region of Drosophila melanogaster. Genetics 177: 832-840. pdf

Jensen, J.D., A. Wong, and C.F. Aquadro, 2007. On statistical and functional 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. Phylogenetics of the Drosophila melanogaster species group – evidence for ancestral lineage sorting and recombination. 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