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Jeffrey Jensen

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Papers

Jensen JD, Kowalik TF. (2020). A consideration of within-host human cytomegalovirus genetic variation. Proceedings of the National Academy of Sciences of the United States of America, 117(2)

Sackman AM, Harris RB, Jensen JD. (2019). Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions. Genetics, 211(3)

Harris RB, Irwin K, Jones MR, Laurent S, Barrett RDH, Nachman MW, Good JM, Linnen CR, Jensen JD, Pfeifer SP. (2020). The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity, 124(1)

Barrett RDH, Laurent S, Mallarino R, Pfeifer SP, Xu CCY, Foll M, Wakamatsu K, Duke-Cohan JS, Jensen JD, Hoekstra HE. (2019). Linking a mutation to survival in wild mice. Science (New York, N.Y.), 363(6426)

Fragata I, Matuszewski S, Schmitz MA, Bataillon T, Jensen JD, Bank C. (2018). The fitness landscape of the codon space across environments. Heredity, 121(5)

Canale AS, Venev SV, Whitfield TW, Caffrey DR, Marasco WA, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Zeldovich KB, Wang JP, Bolon DNA. (2018). Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness. Journal of molecular biology, 430(8)

Jones MR, Mills LS, Alves PC, Callahan CM, Alves JM, Lafferty DJR, Jiggins FM, Jensen JD, Melo-Ferreira J, Good JM. (2018). Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares. Science (New York, N.Y.), 360(6395)

Pfeifer SP, Laurent S, Sousa VC, Linnen CR, Foll M, Excoffier L, Hoekstra HE, Jensen JD. (2018). The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow. Molecular biology and evolution, 35(4)

Kapopoulou A, Pfeifer SP, Jensen JD, Laurent S. (2018). The Demographic History of African Drosophila melanogaster. Genome biology and evolution, 10(9)

Harris RB, Sackman A, Jensen JD. (2018). On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses. PLoS genetics, 14(12)

Ma L, Boucher JI, Paulsen J, Matuszewski S, Eide CA, Ou J, Eickelberg G, Press RD, Zhu LJ, Druker BJ, Branford S, Wolfe SA, Jensen JD, Schiffer CA, Green MR, Bolon DN. (2017). CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy. Proceedings of the National Academy of Sciences of the United States of America, 114(44)

Zhong Q, Carratalà A, Shim H, Bachmann V, Jensen JD, Kohn T. (2017). Is Associated with Enhanced Host Receptor Use, Altered Entry Routes, and High Fitness. Environmental science & technology, 51(18)

Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Haut J, , Rothschild H, Zon L, Zhou Y, Kovacs MA, Xu M, Zhang T, Bishop K, Sinclair J, Rivas C, Elliot E, Choi J, Li SA, Hicks B, Burgess S, Abnet C, Watkins-Chow DE, Oceana E, Song YS, Eskin E, Brown KM, Marks MS, Loftus SK, Pavan WJ, Yeager M, Chanock S, Tishkoff SA. (2017). Loci associated with skin pigmentation identified in African populations. Science (New York, N.Y.), 358(6365)

Avnir Y, Prachanronarong KL, Zhang Z, Hou S, Peterson EC, Sui J, Zayed H, Kurella VB, McGuire AT, Stamatatos L, Hilbert BJ, Bohn MF, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Goodall M, Jefferis R, Zhu Q, Kurt Yilmaz N, Schiffer CA, Marasco WA. (2017). Structural Determination of the Broadly Reactive Anti-IGHV1-69 Anti-idiotypic Antibody G6 and Its Idiotope. Cell reports, 21(11)

Matuszewski S, Hildebrandt ME, Achaz G, Jensen JD. (2018). Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography. Genetics, 208(1)

Ormond L, Liu P, Matuszewski S, Renzette N, Bank C, Zeldovich K, Bolon DN, Kowalik TF, Finberg RW, Jensen JD, Wang JP. (2017). The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution. Genome biology and evolution, 9(7)

Carratalà A, Shim H, Zhong Q, Bachmann V, Jensen JD, Kohn T. (2017). Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to resistance to disinfection and ribavirin. Virus evolution, 3(2)

Pfeifer SP, Jensen JD. (2016). The Impact of Linked Selection in Chimpanzees: A Comparative Study. Genome biology and evolution, 8(10)

Bank C, Matuszewski S, Hietpas RT, Jensen JD. (2016). On the (un)predictability of a large intragenic fitness landscape. Proceedings of the National Academy of Sciences of the United States of America, 113(49)

Pokalyuk C, Renzette N, Irwin KK, Pfeifer SP, Gibson L, Britt WJ, Yamamoto AY, Mussi-Pinhata MM, Kowalik TF, Jensen JD. (2017). Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective. Molecular ecology, 26(7)

Renzette N, Pfeifer SP, Matuszewski S, Kowalik TF, Jensen JD. (2017). On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations. Journal of virology, 91(5)

Matuszewski S, Hildebrandt ME, Ghenu AH, Jensen JD, Bank C. (2016). A Statistical Guide to the Design of Deep Mutational Scanning Experiments. Genetics, 204(1)

Prachanronarong KL, Özen A, Thayer KM, Yilmaz LS, Zeldovich KB, Bolon DN, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Kurt-Yilmaz N, Schiffer CA. (2016). Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase. Journal of chemical theory and computation, 12(12)

Shim H, Laurent S, Matuszewski S, Foll M, Jensen JD. (2016). Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data. G3 (Bethesda, Md.), 6(4)

Irwin KK, Renzette N, Kowalik TF, Jensen JD. (2016). Antiviral drug resistance as an adaptive process. Virus evolution, 2(1)

Bank C, Renzette N, Liu P, Matuszewski S, Shim H, Foll M, Bolon DN, Zeldovich KB, Kowalik TF, Finberg RW, Wang JP, Jensen JD. (2016). An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy. Evolution; international journal of organic evolution, 70(11)

Mahajan S, Crisci J, Wong A, Akbarian S, Foll M, Jensen JD. (2015). Quantifying polymorphism and divergence from epigenetic data: a framework for inferring the action of selection. Frontiers in genetics, (6)

Renzette N, Kowalik TF, Jensen JD. (2016). On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity. Molecular ecology, 25(1)

Kapopoulou A, Mathew L, Wong A, Trono D, Jensen JD. (2016). The evolution of gene expression and binding specificity of the largest transcription factor family in primates. Evolution; international journal of organic evolution, 70(1)

Zeldovich KB, Liu P, Renzette N, Foll M, Pham ST, Venev SV, Gallagher GR, Bolon DN, Kurt-Jones EA, Jensen JD, Caffrey DR, Schiffer CA, Kowalik TF, Wang JP, Finberg RW. (2015). Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment. Molecular biology and evolution, 32(6)

Ewing GB, Jensen JD. (2016). The consequences of not accounting for background selection in demographic inference. Molecular ecology, 25(1)

Montano V, Didelot X, Foll M, Linz B, Reinhardt R, Suerbaum S, Moodley Y, Jensen JD. (2015). Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori. Genetics, 200(3)

Ewing GB, Reiff PA, Jensen JD. (2015). PopPlanner: visually constructing demographic models for simulation. Frontiers in genetics, (6)

Ormond L, Foll M, Ewing GB, Pfeifer SP, Jensen JD. (2016). Inferring the age of a fixed beneficial allele. Molecular ecology, 25(1)

Mathew LA, Jensen JD. (2015). Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demography. Frontiers in genetics, (6)

Jiang L, Liu P, Bank C, Renzette N, Prachanronarong K, Yilmaz LS, Caffrey DR, Zeldovich KB, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Bolon DNA. (2016). A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance. Journal of molecular biology, 428(3)

Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB. (2016). The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards. Molecular ecology, 25(1)

Renzette N, Pokalyuk C, Gibson L, Bhattacharjee B, Schleiss MR, Hamprecht K, Yamamoto AY, Mussi-Pinhata MM, Britt WJ, Jensen JD, Kowalik TF. (2015). Limits and patterns of cytomegalovirus genomic diversity in humans. Proceedings of the National Academy of Sciences of the United States of America, 112(30)

Alcala N, Jensen JD, Telenti A, Vuilleumier S. (2015). The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV. G3 (Bethesda, Md.), 6(1)

Jensen JD. (2014). On the unfounded enthusiasm for soft selective sweeps. Nature communications, (5)

Renzette N, Gibson L, Jensen JD, Kowalik TF. (2014). Human cytomegalovirus intrahost evolution-a new avenue for understanding and controlling herpesvirus infections. Current opinion in virology, (8)

Foll M, Shim H, Jensen JD. (2015). WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data. Molecular ecology resources, 15(1)

Simkin AT, Bailey JA, Gao FB, Jensen JD. (2014). Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases. Molecular biology and evolution, 31(7)

Poh YP, Domingues VS, Hoekstra HE, Jensen JD. (2014). On the prospect of identifying adaptive loci in recently bottlenecked populations. PloS one, 9(11)

Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD. (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(3)

Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PL, Li M, Reis S, Bernardo DV, DeGiorgio M, Duggan AT, Bastos M, Wang Y, Stenderup J, Moreno-Mayar JV, Brunak S, Sicheritz-Ponten T, Hodges E, Hannon GJ, Orlando L, Price TD, Jensen JD, Nielsen R, Heinemeier J, Olsen J, Rodrigues-Carvalho C, Lahr MM, Neves WA, Kayser M, Higham T, Stoneking M, Pena SD, Willerslev E. (2014). Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current biology : CB, 24(21)

Bank C, Ewing GB, Ferrer-Admettla A, Foll M, Jensen JD. (2014). Thinking too positive? Revisiting current methods of population genetic selection inference. Trends in genetics : TIG, 30(12)

Renzette N, Gibson L, Bhattacharjee B, Fisher D, Schleiss MR, Jensen JD, Kowalik TF. (2013). Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. PLoS genetics, 9(9)

Renzette N, Caffrey DR, Zeldovich KB, Liu P, Gallagher GR, Aiello D, Porter AJ, Kurt-Jones EA, Bolon DN, Poh YP, Jensen JD, Schiffer CA, Kowalik TF, Finberg RW, Wang JP. (2014). Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. Journal of virology, 88(1)

Linnen CR, Poh YP, Peterson BK, Barrett RD, Larson JG, Jensen JD, Hoekstra HE. (2013). Adaptive evolution of multiple traits through multiple mutations at a single gene. Science (New York, N.Y.), 339(6125)

Crisci JL, Poh YP, Mahajan S, Jensen JD. (2013). The impact of equilibrium assumptions on tests of selection. Frontiers in genetics, (4)

Hietpas RT, Bank C, Jensen JD, Bolon DNA. (2013). Shifting fitness landscapes in response to altered environments. Evolution; international journal of organic evolution, 67(12)

Simkin A, Wong A, Poh YP, Theurkauf WE, Jensen JD. (2013). Recurrent and recent selective sweeps in the piRNA pathway. Evolution; international journal of organic evolution, 67(4)

Joost S, Vuilleumier S, Jensen JD, Schoville S, Leempoel K, Stucki S, Widmer I, Melodelima C, Rolland J, Manel S. (2013). Meeting review. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics. Molecular ecology, 22(14)

Singh ND, Jensen JD, Clark AG, Aquadro CF. (2013). Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics, 193(1)

Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, Jensen JD, Weng Z, Akbarian S. (2012). Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS biology, 10(11)

Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles JF, Dermitzakis ET, Stone EA, Jensen JD, Mackay TF, Deplancke B. (2012). Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS genetics, 8(11)

Crisci JL, Wong A, Good JM, Jensen JD. (2011). On characterizing adaptive events unique to modern humans. Genome biology and evolution, (3)

Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W. (2011). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature biotechnology, 30(1)

Hietpas RT, Jensen JD, Bolon DN. (2011). Experimental illumination of a fitness landscape. Proceedings of the National Academy of Sciences of the United States of America, 108(19)

Renzette N, Bhattacharjee B, Jensen JD, Gibson L, Kowalik TF. (2011). Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants. PLoS pathogens, 7(5)

Jensen JD, Rando OJ. (2010). Recent evidence for pervasive adaptation targeting gene expression attributable to population size change. Proceedings of the National Academy of Sciences of the United States of America, 107(27)

Pavlidis P, Jensen JD, Stephan W. (2010). Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics, 185(3)

Pool JE, Hellmann I, Jensen JD, Nielsen R. (2010). Population genetic inference from genomic sequence variation. Genome research, 20(3)

Jensen JD, Bachtrog D. (2010). Characterizing recurrent positive selection at fast-evolving genes in Drosophila miranda and Drosophila pseudoobscura. Genome biology and evolution, (2)

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. (2010). A draft sequence of the Neandertal genome. Science (New York, N.Y.), 328(5979)

Cutler DJ, Jensen JD. (2010). To pool, or not to pool?. Genetics, 186(1)

Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, Cheng T, Jiang T, Becquet C, Xu X, Liu C, Zha X, Fan W, Lin Y, Shen Y, Jiang L, Jensen J, Hellmann I, Tang S, Zhao P, Xu H, Yu C, Zhang G, Li J, Cao J, Liu S, He N, Zhou Y, Liu H, Zhao J, Ye C, Du Z, Pan G, Zhao A, Shao H, Zeng W, Wu P, Li C, Pan M, Li J, Yin X, Li D, Wang J, Zheng H, Wang W, Zhang X, Li S, Yang H, Lu C, Nielsen R, Zhou Z, Wang J, Xiang Z, Wang J. (2009). Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (New York, N.Y.), 326(5951)

Linnen CR, Kingsley EP, Jensen JD, Hoekstra HE. (2009). On the origin and spread of an adaptive allele in deer mice. Science (New York, N.Y.), 325(5944)

Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, Cheng T, Jiang T, Becquet C, Xu X, Liu C, Zha X, Fan W, Lin Y, Shen Y, Jiang L, Jensen J, Hellmann I, Tang S, Zhao P, Xu H, Yu C, Zhang G, Li J, Cao J, Liu S, He N, Zhou Y, Liu H, Zhao J, Ye C, Du Z, Pan G, Zhao A, Shao H, Zeng W, Wu P, Li C, Pan M, Li J, Yin X, Li D, Wang J, Zheng H, Wang W, Zhang X, Li S, Yang H, Lu C, Nielsen R, Zhou Z, Wang J, Xiang Z, Wang J. (2009). Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (New York, N.Y.), 326(5951)

Bachtrog D, Jensen JD, Zhang Z. (2009). Accelerated adaptive evolution on a newly formed X chromosome. PLoS biology, 7(4)

Jensen JD, Thornton KR, Andolfatto P. (2008). An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS genetics, 4(9)

Jensen JD, Bauer DuMont VL, Ashmore AB, Gutierrez A, Aquadro CF. (2007). Patterns of sequence variability and divergence at the diminutive gene region of Drosophila melanogaster: complex patterns suggest an ancestral selective sweep. Genetics, 177(2)

Jensen JD, Wong A, Aquadro CF. (2007). Approaches for identifying targets of positive selection. Trends in genetics : TIG, 23(11)

Singh ND, Macpherson JM, Jensen JD, Petrov DA. (2007). Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. BMC evolutionary biology, (7)

Jensen JD, Thornton KR, Bustamante CD, Aquadro CF. (2007). On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics, 176(4)

Wong A, Jensen JD, Pool JE, Aquadro CF. (2007). Phylogenetic incongruence in the Drosophila melanogaster species group. Molecular phylogenetics and evolution, 43(3)

Thornton KR, Jensen JD. (2007). Controlling the false-positive rate in multilocus genome scans for selection. Genetics, 175(2)

Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD. (2005). Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics, 170(3)

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