| Year |
Citation |
Score |
| 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 |
0.8 |
|
| 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 |
0.8 |
|
| 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 |
0.822 |
|
| 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 |
0.825 |
|
| 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 |
0.764 |
|
| 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 |
0.769 |
|
| 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 |
0.495 |
|
| 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 |
0.847 |
|
| 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 |
0.825 |
|
| 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 |
0.784 |
|
| 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 |
0.347 |
|
| 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 |
0.486 |
|
| 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 |
0.516 |
|
| 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 |
0.849 |
|
| 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 |
0.848 |
|
| 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 |
0.564 |
|
| 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 |
0.789 |
|
| 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 |
0.648 |
|
| 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 |
0.448 |
|
| 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 |
0.82 |
|
| 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 |
0.783 |
|
| 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 |
0.678 |
|
| 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 |
0.742 |
|
| 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 |
0.71 |
|
| 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 |
0.835 |
|
| 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 |
0.787 |
|
| 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 |
0.74 |
|
| 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 |
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| 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 |
0.818 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.795 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.72 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.73 |
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| 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 |
0.718 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.517 |
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| 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 |
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| 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 |
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| 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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