Jeffrey D. Jensen - Publications

Affiliations: 
Arizona State University, Tempe, AZ, United States 
Area:
population genetics

130 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Soni V, Jensen JD. Temporal challenges in detecting balancing selection from population genomic data. G3 (Bethesda, Md.). PMID 38551137 DOI: 10.1093/g3journal/jkae069  0.395
2024 Soni V, Pfeifer SP, Jensen JD. The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects. Genome Biology and Evolution. PMID 38207127 DOI: 10.1093/gbe/evae004  0.455
2023 Soni V, Pfeifer SP, Jensen JD. The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects. Biorxiv : the Preprint Server For Biology. PMID 38014252 DOI: 10.1101/2023.11.11.566703  0.457
2023 Terbot JW, Cooper BS, Good JM, Jensen JD. A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2. Genome Biology and Evolution. PMID 37950882 DOI: 10.1093/gbe/evad204  0.346
2023 Terbot JW, Cooper BS, Good JM, Jensen JD. A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2. Biorxiv : the Preprint Server For Biology. PMID 37503016 DOI: 10.1101/2023.07.13.548462  0.346
2023 Soni V, Johri P, Jensen JD. Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models. Biorxiv : the Preprint Server For Biology. PMID 37398347 DOI: 10.1101/2023.06.15.545166  0.795
2023 Soni V, Johri P, Jensen JD. Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models. Evolution; International Journal of Organic Evolution. PMID 37395482 DOI: 10.1093/evolut/qpad120  0.795
2023 Johri P, Pfeifer SP, Jensen JD. Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history. Molecular Biology and Evolution. PMID 37128989 DOI: 10.1093/molbev/msad100  0.818
2023 Johri P, Pfeifer SP, Jensen JD. Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history. Biorxiv : the Preprint Server For Biology. PMID 37090533 DOI: 10.1101/2023.04.11.536488  0.821
2023 Charlesworth B, Jensen JD. Effects of Selection at Linked Sites on Patterns of Genetic Variability. Annual Review of Ecology, Evolution, and Systematics. 52: 177-197. PMID 37089401 DOI: 10.1146/annurev-ecolsys-010621-044528  0.611
2023 Howell AA, Terbot Ii JW, Soni V, Johri P, Jensen JD, Pfeifer SP. Developing an appropriate evolutionary baseline model for the study of human cytomegalovirus. Genome Biology and Evolution. PMID 37071785 DOI: 10.1093/gbe/evad059  0.758
2023 Terbot JW, Johri P, Liphardt SW, Soni V, Pfeifer SP, Cooper BS, Good JM, Jensen JD. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. Plos Pathogens. 19: e1011265. PMID 37018331 DOI: 10.1371/journal.ppat.1011265  0.764
2023 Freund F, Kerdoncuff E, Matuszewski S, Lapierre M, Hildebrandt M, Jensen JD, Ferretti L, Lambert A, Sackton TB, Achaz G. Interpreting the pervasive observation of U-shaped Site Frequency Spectra. Plos Genetics. 19: e1010677. PMID 36952570 DOI: 10.1371/journal.pgen.1010677  0.781
2023 Jensen JD. Population genetic concerns related to the interpretation of empirical outliers and the neglect of common evolutionary processes. Heredity. 130: 109-110. PMID 36829044 DOI: 10.1038/s41437-022-00575-5  0.335
2023 Ghafoor S, Santos J, Versoza CJ, Jensen JD, Pfeifer SP. The impact of sample size and population history on observed mutational spectra: a case study in human and chimpanzee populations. Genome Biology and Evolution. PMID 36790107 DOI: 10.1093/gbe/evad019  0.447
2022 Charlesworth B, Jensen JD. Population genetic considerations regarding evidence for biased mutation rates in Arabidopsis thaliana. Molecular Biology and Evolution. PMID 36572441 DOI: 10.1093/molbev/msac275  0.613
2022 Charlesworth B, Jensen JD. Some complexities in interpreting apparent effects of hitchhiking: A commentary on Gompert et al. (2022). Molecular Ecology. PMID 35778972 DOI: 10.1111/mec.16573  0.494
2022 Charlesworth B, Jensen JD. How can we resolve Lewontin's Paradox? Genome Biology and Evolution. PMID 35738021 DOI: 10.1093/gbe/evac096  0.589
2022 Johri P, Eyre-Walker A, Gutenkunst RN, Lohmueller KE, Jensen JD. On the prospect of achieving accurate joint estimation of selection with population history. Genome Biology and Evolution. PMID 35675379 DOI: 10.1093/gbe/evac088  0.845
2022 Johri P, Aquadro CF, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A, Keightley PD, Lynch M, McVean G, Payseur BA, Pfeifer SP, Stephan W, Jensen JD. Recommendations for improving statistical inference in population genomics. Plos Biology. 20: e3001669. PMID 35639797 DOI: 10.1371/journal.pbio.3001669  0.837
2022 Sabin S, Morales-Arce AY, Pfeifer SP, Jensen JD. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis. G3 (Bethesda, Md.). PMID 35253851 DOI: 10.1093/g3journal/jkac055  0.421
2022 Johri P, Stephan W, Jensen JD. Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers. Plos Genetics. 18: e1010022. PMID 35202407 DOI: 10.1371/journal.pgen.1010022  0.822
2022 Morales-Arce AY, Johri P, Jensen JD. Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies. Heredity. 128: 79-87. PMID 34987185 DOI: 10.1038/s41437-021-00493-y  0.779
2021 Johri P, Charlesworth B, Howell EK, Lynch M, Jensen JD. Revisiting the Notion of Deleterious Sweeps. Genetics. PMID 34125884 DOI: 10.1093/genetics/iyab094  0.837
2021 Johri P, Riall K, Becher H, Excoffier L, Charlesworth B, Jensen JD. The impact of purifying and background selection on the inference of population history: problems and prospects. Molecular Biology and Evolution. PMID 33591322 DOI: 10.1093/molbev/msab050  0.843
2021 Johri P, Riall K, Becher H, Excoffier L, Charlesworth B, Jensen JD. The impact of purifying and background selection on the inference of population history: problems and prospects. Biorxiv : the Preprint Server For Biology. PMID 33501439 DOI: 10.1101/2020.04.28.066365  0.843
2020 Morales-Arce AY, Sabin SJ, Stone AC, Jensen JD. The population genomics of within-host Mycobacterium tuberculosis. Heredity. PMID 33060846 DOI: 10.1038/s41437-020-00377-7  0.346
2020 Jensen JD, Stikeleather RA, Kowalik TF, Lynch M. Imposed mutational meltdown as an antiviral strategy. Evolution; International Journal of Organic Evolution. PMID 33047822 DOI: 10.1111/evo.14107  0.506
2020 Jones MR, Mills LS, Jensen JD, Good JM. The Origin and Spread of Locally Adaptive Seasonal Camouflage in Snowshoe Hares. The American Naturalist. 196: 316-332. PMID 32813993 DOI: 10.1086/710022  0.536
2020 Harris RB, Jensen JD. Considering genomic scans for selection as coalescent model choice. Genome Biology and Evolution. PMID 32396636 DOI: 10.1093/Gbe/Evaa093  0.485
2020 Jones MR, Mills LS, Jensen JD, Good JM. Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range. Evolution; International Journal of Organic Evolution. PMID 32282064 DOI: 10.1111/Evo.13976  0.499
2020 Jensen JD, Lynch M. Considering mutational meltdown as a potential SARS-CoV-2 treatment strategy. Heredity. PMID 32251365 DOI: 10.1038/S41437-020-0314-Z  0.515
2020 Morales-Arce AY, Harris RB, Stone AC, Jensen JD. Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution. Evolution; International Journal of Organic Evolution. PMID 32233086 DOI: 10.1111/Evo.13954  0.51
2020 Johri P, Charlesworth B, Jensen JD. Towards an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection. Genetics. PMID 32152045 DOI: 10.1534/Genetics.119.303002  0.846
2019 Jensen JD, Kowalik TF. A consideration of within-host human cytomegalovirus genetic variation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31874930 DOI: 10.1073/Pnas.1915295117  0.355
2019 Harris RB, Irwin K, Jones MR, Laurent S, Barrett RDH, Nachman MW, Good JM, Linnen CR, Jensen JD, Pfeifer SP. The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity. PMID 31399719 DOI: 10.1038/S41437-019-0257-4  0.847
2019 Barrett RDH, Laurent S, Mallarino R, Pfeifer SP, Xu CCY, Foll M, Wakamatsu K, Duke-Cohan JS, Jensen JD, Hoekstra HE. Linking a mutation to survival in wild mice. Science (New York, N.Y.). 363: 499-504. PMID 30705186 DOI: 10.1126/Science.Aav3824  0.822
2019 Sackman AM, Harris RB, Jensen JD. Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions. Genetics. PMID 30651284 DOI: 10.1534/Genetics.118.301684  0.543
2018 Harris RB, Sackman A, Jensen JD. On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses. Plos Genetics. 14: e1007859. PMID 30592709 DOI: 10.1371/Journal.Pgen.1007859  0.563
2018 Jensen JD, Payseur BA, Stephan W, Aquadro CF, Lynch M, Charlesworth D, Charlesworth B. The importance of the neutral theory in 1968 and 50 years on: a response to Kern & Hahn 2018. Evolution; International Journal of Organic Evolution. PMID 30460993 DOI: 10.1111/Evo.13650  0.774
2018 Prachanronarong KL, Canale AS, Liu P, Somasundaran M, Hou S, Poh YP, Han T, Zhu Q, Renzette N, Zeldovich KB, Kowalik TF, Kurt-Yilmaz N, Jensen JD, Bolon DNA, Marasco WA, et al. Mutations in influenza A virus neuraminidase and hemagglutinin confer resistance against a broadly neutralizing hemagglutinin stem antibody. Journal of Virology. PMID 30381484 DOI: 10.1128/Jvi.01639-18  0.802
2018 Kapopoulou A, Pfeifer SP, Jensen JD, Laurent S. The demographic history of African Drosophila melanogaster. Genome Biology and Evolution. PMID 30169784 DOI: 10.1093/Gbe/Evy185  0.787
2018 Fragata I, Matuszewski S, Schmitz MA, Bataillon T, Jensen JD, Bank C. The fitness landscape of the codon space across environments. Heredity. PMID 30127529 DOI: 10.1038/S41437-018-0125-7  0.817
2018 Jones MR, Mills LS, Alves PC, Callahan CM, Alves JM, Lafferty DJR, Jiggins FM, Jensen JD, Melo-Ferreira J, Good JM. Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares. Science (New York, N.Y.). 360: 1355-1358. PMID 29930138 DOI: 10.1126/Science.Aar5273  0.345
2018 Canale AS, Venev SV, Whitfield TW, Caffrey DR, Marasco WA, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Zeldovich KB, Wang JP, Bolon DNA. Synonymous mutations at the beginning of the influenza A virus hemagglutinin gene impact experimental fitness. Journal of Molecular Biology. PMID 29466705 DOI: 10.1016/J.Jmb.2018.02.009  0.438
2018 Sackman AM, Pfeifer SP, Kowalik TF, Jensen JD. On the Demographic and Selective Forces Shaping Patterns of Human Cytomegalovirus Variation within Hosts. Pathogens (Basel, Switzerland). 7. PMID 29382090 DOI: 10.3390/Pathogens7010016  0.355
2018 Pfeifer SP, Laurent S, Sousa VC, Linnen CR, Foll M, Excoffier L, Hoekstra HE, Jensen JD. The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow. Molecular Biology and Evolution. PMID 29346646 DOI: 10.1093/Molbev/Msy004  0.826
2017 Matuszewski S, Ormond L, Bank C, Jensen JD. Two sides of the same coin: A population genetics perspective on lethal mutagenesis and mutational meltdown. Virus Evolution. 3: vex004. PMID 29977604 DOI: 10.1093/Ve/Vex004  0.826
2017 Carratalà A, Shim H, Zhong Q, Bachmann V, Jensen JD, Kohn T. Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to resistance to disinfection and ribavirin. Virus Evolution. 3: vex035. PMID 29225923 DOI: 10.1093/Ve/Vex035  0.433
2017 Matuszewski S, Hildebrandt ME, Achaz G, Jensen JD. Coalescent Processes with Skewed Offspring Distributions and Non-equilibrium Demography. Genetics. PMID 29127263 DOI: 10.1534/Genetics.117.300499  0.82
2017 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, et al. 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. PMID 29078326 DOI: 10.1073/Pnas.1708268114  0.789
2017 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, et al. Loci associated with skin pigmentation identified in African populations. Science (New York, N.Y.). PMID 29025994 DOI: 10.1126/Science.Aan8433  0.447
2017 Ormond L, Liu P, Matuszewski S, Renzette N, Bank C, Zeldovich K, Bolon DN, Kowalik TF, Finberg RW, Jensen JD, Wang JP. The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution. Genome Biology and Evolution. 9: 1913-1924. PMID 28854600 DOI: 10.1093/Gbe/Evx138  0.825
2017 Zhong Q, Carratala A, Shim H, Bachmann V, Jensen JD, Kohn T. Resistance of echovirus 11 to ClO2 is associated with enhanced host receptor use, altered entry routes and high fitness. Environmental Science & Technology. PMID 28837336 DOI: 10.1021/Acs.Est.7B03288  0.349
2016 Irwin KK, Renzette N, Kowalik TF, Jensen JD. Antiviral drug resistance as an adaptive process. Virus Evolution. 2: vew014. PMID 28694997 DOI: 10.1093/Ve/Vew014  0.762
2016 Pokalyuk C, Renzette N, Irwin KK, Pfeifer SP, Gibson L, Britt WJ, Yamamoto AY, Mussi-Pinhata MM, Kowalik TF, Jensen JD. Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective. Molecular Ecology. PMID 27988973 DOI: 10.1111/Mec.13953  0.819
2016 Renzette N, Pfeifer SP, Matuszewski S, Kowalik TF, Jensen JD. On the analysis of intra-host and inter-host viral populations: human cytomegalovirus as a case study of pitfalls and expectations. Journal of Virology. PMID 27974561 DOI: 10.1128/Jvi.01976-16  0.827
2016 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. Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase. Journal of Chemical Theory and Computation. 12: 6098-6108. PMID 27951676 DOI: 10.1021/Acs.Jctc.6B00703  0.328
2016 Bank C, Matuszewski S, Hietpas RT, Jensen JD. On the (un)predictability of a large intragenic fitness landscape. Proceedings of the National Academy of Sciences of the United States of America. PMID 27864516 DOI: 10.1073/Pnas.1612676113  0.816
2016 Pfeifer SP, Jensen JD. The Impact of Linked Selection in Chimpanzees: A Comparative Study. Genome Biology and Evolution. 8: 3202-3208. PMID 27678122 DOI: 10.1093/Gbe/Evw240  0.496
2016 Irwin KK, Laurent S, Matuszewski S, Vuilleumier S, Ormond L, Shim H, Bank C, Jensen JD. On the importance of skewed offspring distributions and background selection in virus population genetics. Heredity. PMID 27649621 DOI: 10.1038/Hdy.2016.58  0.829
2016 Bank C, Renzette N, Liu P, Matuszewski S, Shim H, Foll M, Bolon DN, Zeldovich KB, Kowalik TF, Finberg RW, Wang JP, Jensen JD. An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy. Evolution; International Journal of Organic Evolution. PMID 27566611 DOI: 10.1111/Evo.13041  0.816
2016 Matuszewski S, Hildebrandt ME, Ghenu AH, Jensen JD, Bank C. A Statistical Guide to the Design of Deep Mutational Scanning Experiments. Genetics. PMID 27412710 DOI: 10.1534/Genetics.116.190462  0.811
2016 Ferrer-Admetlla A, Leuenberger C, Jensen JD, Wegmann D. An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data. Genetics. 203: 831-46. PMID 27038112 DOI: 10.1534/Genetics.115.184598  0.764
2016 Shim H, Laurent S, Matuszewski S, Foll M, Jensen JD. Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data. G3 (Bethesda, Md.). PMID 26869618 DOI: 10.1534/G3.115.023200  0.815
2016 Jensen JD, Foll M, Bernatchez L. The past, present and future of genomic scans for selection. Molecular Ecology. 25: 1-4. PMID 26745554 DOI: 10.1111/Mec.13493  0.647
2015 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 DN. A balance between inhibitor binding and substrate processing confers influenza drug resistance. Journal of Molecular Biology. PMID 26656922 DOI: 10.1016/J.Jmb.2015.11.027  0.801
2015 Kapopoulou A, Mathew L, Wong A, Trono D, Jensen JD. The evolution of gene expression and binding specificity of the largest transcription factor family in primates. Evolution; International Journal of Organic Evolution. PMID 26593440 DOI: 10.1111/Evo.12819  0.794
2015 Ormond L, Foll M, Ewing GB, Pfeifer SP, Jensen JD. Inferring the Age of a Fixed Beneficial Allele. Molecular Ecology. PMID 26576754 DOI: 10.1111/Mec.13478  0.83
2015 Alcala N, Jensen JD, Telenti A, Vuilleumier S. The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV. G3 (Bethesda, Md.). PMID 26546308 DOI: 10.1534/G3.115.024208  0.408
2015 Ewing GB, Jensen JD. The consequences of not accounting for background selection in demographic inference. Molecular Ecology. PMID 26394805 DOI: 10.1111/Mec.13390  0.447
2015 Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB. The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards. Molecular Ecology. PMID 26363411 DOI: 10.1111/Mec.13385  0.843
2015 Mathew LA, Jensen JD. Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demography. Frontiers in Genetics. 6: 268. PMID 26347771 DOI: 10.3389/Fgene.2015.00268  0.845
2015 Renzette N, Kowalik TF, Jensen JD. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity. Molecular Ecology. PMID 26211679 DOI: 10.1111/Mec.13331  0.794
2015 Renzette N, Pokalyuk C, Gibson L, Bhattacharjee B, Schleiss MR, Hamprecht K, Yamamoto AY, Mussi-Pinhata MM, Britt WJ, Jensen JD, Kowalik TF. Limits and patterns of cytomegalovirus genomic diversity in humans. Proceedings of the National Academy of Sciences of the United States of America. PMID 26150505 DOI: 10.1073/Pnas.1501880112  0.819
2015 Mahajan S, Crisci J, Wong A, Akbarian S, Foll M, Jensen JD. Quantifying polymorphism and divergence from epigenetic data: a framework for inferring the action of selection. Frontiers in Genetics. 6: 190. PMID 26074949 DOI: 10.3389/Fgene.2015.00190  0.782
2015 Montano V, Didelot X, Foll M, Linz B, Reinhardt R, Suerbaum S, Moodley Y, Jensen JD. Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori. Genetics. 200: 947-63. PMID 25995212 DOI: 10.1534/Genetics.115.176404  0.677
2015 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. Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment. Molecular Biology and Evolution. 32: 1519-32. PMID 25713211 DOI: 10.1093/Molbev/Msv044  0.808
2015 Bank C, Hietpas RT, Jensen JD, Bolon DN. A systematic survey of an intragenic epistatic landscape. Molecular Biology and Evolution. 32: 229-38. PMID 25371431 DOI: 10.1093/Molbev/Msu301  0.741
2015 Foll M, Shim H, Jensen JD. WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data. Molecular Ecology Resources. 15: 87-98. PMID 24834845 DOI: 10.1111/1755-0998.12280  0.709
2014 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, ... ... Jensen JD, et al. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology : Cb. 24: R1035-7. PMID 25455029 DOI: 10.1016/J.Cub.2014.09.078  0.523
2014 Bank C, Ewing GB, Ferrer-Admettla A, Foll M, Jensen JD. Thinking too positive? Revisiting current methods of population genetic selection inference. Trends in Genetics : Tig. 30: 540-6. PMID 25438719 DOI: 10.1016/J.Tig.2014.09.010  0.834
2014 Poh YP, Domingues VS, Hoekstra HE, Jensen JD. On the prospect of identifying adaptive loci in recently bottlenecked populations. Plos One. 9: e110579. PMID 25383711 DOI: 10.1371/Journal.Pone.0110579  0.845
2014 Jensen JD. On the unfounded enthusiasm for soft selective sweeps. Nature Communications. 5: 5281. PMID 25345443 DOI: 10.1038/Ncomms6281  0.411
2014 Renzette N, Gibson L, Jensen JD, Kowalik TF. Human cytomegalovirus intrahost evolution-a new avenue for understanding and controlling herpesvirus infections. Current Opinion in Virology. 8: 109-15. PMID 25154343 DOI: 10.1016/J.Coviro.2014.08.001  0.739
2014 Simkin AT, Bailey JA, Gao FB, Jensen JD. Inferring the evolutionary history of primate microRNA binding sites: overcoming motif counting biases. Molecular Biology and Evolution. 31: 1894-901. PMID 24723422 DOI: 10.1093/Molbev/Msu129  0.772
2014 Foll M, Poh YP, Renzette N, Ferrer-Admetlla A, Bank C, Shim H, Malaspinas AS, Ewing G, Liu P, Wegmann D, Caffrey DR, Zeldovich KB, Bolon DN, Wang JP, Kowalik TF, ... ... Jensen JD, et al. Influenza virus drug resistance: a time-sampled population genetics perspective. Plos Genetics. 10: e1004185. PMID 24586206 DOI: 10.1371/Journal.Pgen.1004185  0.83
2014 Ewing GB, Jensen JD. Distinguishing neutral from deleterious mutations in growing populations. Frontiers in Genetics. 5: 7. PMID 24550931 DOI: 10.3389/Fgene.2014.00007  0.834
2014 Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD. 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: 841-852. PMID 24398421 DOI: 10.1534/Genetics.113.156190  0.786
2014 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. Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. Journal of Virology. 88: 272-81. PMID 24155392 DOI: 10.1128/Jvi.01067-13  0.839
2013 Hietpas RT, Bank C, Jensen JD, Bolon DNA. Shifting fitness landscapes in response to altered environments Evolution. 67: 3512-3522. PMID 24299404 DOI: 10.1111/Evo.12207  0.739
2013 Crisci JL, Poh YP, Mahajan S, Jensen JD. The impact of equilibrium assumptions on tests of selection. Frontiers in Genetics. 4: 235. PMID 24273554 DOI: 10.3389/Fgene.2013.00235  0.835
2013 Renzette N, Gibson L, Bhattacharjee B, Fisher D, Schleiss MR, Jensen JD, Kowalik TF. Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection. Plos Genetics. 9: e1003735. PMID 24086142 DOI: 10.1371/Journal.Pgen.1003735  0.804
2013 Joost S, Vuilleumier S, Jensen JD, Schoville S, Leempoel K, Stucki S, Widmer I, Melodelima C, Rolland J, Manel S. Meeting review. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics. Molecular Ecology. 22: 3659-65. PMID 24003454 DOI: 10.1111/Mec.12352  0.487
2013 Simkin A, Wong A, Poh YP, Theurkauf WE, Jensen JD. Recurrent and recent selective sweeps in the piRNA pathway. Evolution; International Journal of Organic Evolution. 67: 1081-90. PMID 23550757 DOI: 10.1111/Evo.12011  0.817
2013 Linnen CR, Poh YP, Peterson BK, Barrett RD, Larson JG, Jensen JD, Hoekstra HE. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science (New York, N.Y.). 339: 1312-6. PMID 23493712 DOI: 10.1126/Science.1233213  0.811
2013 Singh ND, Jensen JD, Clark AG, Aquadro CF. Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics. 193: 215-28. PMID 23105013 DOI: 10.1534/Genetics.112.145318  0.824
2012 Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles JF, Dermitzakis ET, Stone EA, Jensen JD, Mackay TF, Deplancke B. Genomic variation and its impact on gene expression in Drosophila melanogaster. Plos Genetics. 8: e1003055. PMID 23189034 DOI: 10.1371/Journal.Pgen.1003055  0.412
2012 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, et al. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. Plos Biology. 10: e1001427. PMID 23185133 DOI: 10.1371/Journal.Pbio.1001427  0.794
2012 Domingues VS, Poh YP, Peterson BK, Pennings PS, Jensen JD, Hoekstra HE. Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution; International Journal of Organic Evolution. 66: 3209-23. PMID 23025610 DOI: 10.1111/J.1558-5646.2012.01669.X  0.844
2012 Pavlidis P, Jensen JD, Stephan W, Stamatakis A. A critical assessment of storytelling: gene ontology categories and the importance of validating genomic scans. Molecular Biology and Evolution. 29: 3237-48. PMID 22617950 DOI: 10.1093/Molbev/Mss136  0.655
2012 Crisci JL, Poh YP, Bean A, Simkin A, Jensen JD. Recent progress in polymorphism-based population genetic inference. The Journal of Heredity. 103: 287-96. PMID 22246406 DOI: 10.1093/Jhered/Esr128  0.816
2012 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, et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology. 30: 105-11. PMID 22158310 DOI: 10.1038/Nbt.2050  0.719
2011 Sinha P, Dincer A, Virgil D, Xu G, Poh YP, Jensen JD. On detecting selective sweeps using single genomes. Frontiers in Genetics. 2: 85. PMID 22303379 DOI: 10.3389/Fgene.2011.00085  0.83
2011 Crisci JL, Wong A, Good JM, Jensen JD. On characterizing adaptive events unique to modern humans. Genome Biology and Evolution. 3: 791-8. PMID 21803765 DOI: 10.1093/Gbe/Evr075  0.827
2011 Jensen JD, Bachtrog D. Characterizing the influence of effective population size on the rate of adaptation: Gillespie's Darwin domain. Genome Biology and Evolution. 3: 687-701. PMID 21705473 DOI: 10.1093/Gbe/Evr063  0.729
2011 Renzette N, Bhattacharjee B, Jensen JD, Gibson L, Kowalik TF. Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants. Plos Pathogens. 7: e1001344. PMID 21625576 DOI: 10.1371/Journal.Ppat.1001344  0.777
2011 Hietpas RT, Jensen JD, Bolon DNA. Experimental illumination of a fitness landscape Proceedings of the National Academy of Sciences of the United States of America. 108: 7896-7901. PMID 21464309 DOI: 10.1073/Pnas.1016024108  0.463
2011 Albert FW, Hodges E, Jensen JD, Besnier F, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Good JM, Green RE, Burbano HA, Plyusnina IZ, Trut L, Andersson L, Schöneberg T, et al. Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity. 107: 205-14. PMID 21304545 DOI: 10.1038/Hdy.2011.4  0.43
2010 Cutler DJ, Jensen JD. To pool, or not to pool? Genetics. 186: 41-3. PMID 20855575 DOI: 10.1534/Genetics.110.121012  0.369
2010 Jensen JD, Bachtrog D. Characterizing recurrent positive selection at fast-evolving genes in Drosophila miranda and Drosophila pseudoobscura. Genome Biology and Evolution. 2: 371-8. PMID 20624741 DOI: 10.1093/Gbe/Evq028  0.689
2010 Jensen JD, Rando OJ. 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: E109-10; author repl. PMID 20566840 DOI: 10.1073/Pnas.1004391107  0.453
2010 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, et al. A draft sequence of the Neandertal genome. Science (New York, N.Y.). 328: 710-22. PMID 20448178 DOI: 10.1126/Science.1188021  0.729
2010 Pavlidis P, Jensen JD, Stephan W. Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics. 185: 907-22. PMID 20407129 DOI: 10.1534/Genetics.110.116459  0.717
2010 Pool JE, Hellmann I, Jensen JD, Nielsen R. Population genetic inference from genomic sequence variation. Genome Research. 20: 291-300. PMID 20067940 DOI: 10.1101/Gr.079509.108  0.782
2009 Jensen JD. On reconciling single and recurrent hitchhiking models. Genome Biology and Evolution. 1: 320-4. PMID 20333201 DOI: 10.1093/Gbe/Evp031  0.489
2009 Linnen CR, Kingsley EP, Jensen JD, Hoekstra HE. On the origin and spread of an adaptive allele in deer mice. Science (New York, N.Y.). 325: 1095-8. PMID 19713521 DOI: 10.1126/Science.1175826  0.435
2009 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, ... ... Jensen J, et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (New York, N.Y.). 326: 433-6. PMID 19713493 DOI: 10.1126/Science.1176620  0.575
2009 Bachtrog D, Jensen JD, Zhang Z. Accelerated adaptive evolution on a newly formed X chromosome. Plos Biology. 7: e82. PMID 19402745 DOI: 10.1371/Journal.Pbio.1000082  0.618
2008 Jensen JD, Thornton KR, Andolfatto P. An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. Plos Genetics. 4: e1000198. PMID 18802463 DOI: 10.1371/Journal.Pgen.1000198  0.739
2008 Jensen JD, Thornton KR, Aquadro CF. Inferring selection in partially sequenced regions. Molecular Biology and Evolution. 25: 438-46. PMID 18165259 DOI: 10.1093/Molbev/Msm273  0.683
2007 Singh ND, Macpherson JM, Jensen JD, Petrov DA. Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. Bmc Evolutionary Biology. 7: 202. PMID 17961244 DOI: 10.1186/1471-2148-7-202  0.669
2007 Jensen JD, Wong A, Aquadro CF. Approaches for identifying targets of positive selection. Trends in Genetics : Tig. 23: 568-77. PMID 17959267 DOI: 10.1016/J.Tig.2007.08.009  0.756
2007 Jensen JD, Bauer DuMont VL, Ashmore AB, Gutierrez A, Aquadro CF. Patterns of sequence variability and divergence at the diminutive gene region of Drosophila melanogaster: complex patterns suggest an ancestral selective sweep. Genetics. 177: 1071-85. PMID 17720938 DOI: 10.1534/Genetics.106.069468  0.669
2007 Jensen JD, Thornton KR, Bustamante CD, Aquadro CF. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations. Genetics. 176: 2371-9. PMID 17565955 DOI: 10.1534/Genetics.106.069450  0.746
2007 Thornton KR, Jensen JD, Becquet C, Andolfatto P. Progress and prospects in mapping recent selection in the genome. Heredity. 98: 340-8. PMID 17473869 DOI: 10.1038/Sj.Hdy.6800967  0.738
2007 Thornton KR, Jensen JD. Controlling the false-positive rate in multilocus genome scans for selection. Genetics. 175: 737-50. PMID 17110489 DOI: 10.1534/Genetics.106.064642  0.516
2007 Wong A, Jensen JD, Pool JE, Aquadro CF. Phylogenetic incongruence in the Drosophila melanogaster species group. Molecular Phylogenetics and Evolution. 43: 1138-50. PMID 17071113 DOI: 10.1016/J.Ympev.2006.09.002  0.779
2006 Casa AM, Mitchell SE, Jensen JD, Hamblin MT, Paterson AH, Aquadro CF, Kresovich S. Evidence for a selective sweep on chromosome 1 of cultivated sorghum Crop Science. 46: S-27-S-40. DOI: 10.2135/Cropsci2006.0001Tpg  0.673
2005 Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics. 170: 1401-10. PMID 15911584 DOI: 10.1534/Genetics.104.038224  0.727
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