• 6149 Citations
  • 36 h-Index
20052020

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Article

A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance

Jiang, L., Liu, P., Bank, C., Renzette, N., Prachanronarong, K., Yilmaz, L. S., Caffrey, D. R., Zeldovich, K. B., Schiffer, C. A., Kowalik, T. F., Jensen, J., Finberg, R. W., Wang, J. P. & Bolon, D. N. A., Feb 13 2016, In : Journal of Molecular Biology. 428, 3, p. 538-553 16 p.

Research output: Contribution to journalArticle

18 Scopus citations

A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: Uncovering the potential for adaptive walks in challenging environments

Bank, C., Hietpas, R. T., Wong, A., Bolon, D. N. & Jensen, J. D., Mar 2014, In : Genetics. 196, 3, p. 841-852 12 p.

Research output: Contribution to journalArticle

51 Scopus citations

Accelerated adaptive evolution on a newly formed × chromosome

Bachtrog, D., Jensen, J. D. & Zhang, Z., Apr 2009, In : PLoS biology. 7, 4, p. 712-719 8 p.

Research output: Contribution to journalArticle

36 Scopus citations

A critical assessment of storytelling: Gene ontology categories and the importance of validating genomic scans

Pavlidis, P., Jensen, J. D., Stephan, W. & Stamatakis, A., Oct 1 2012, In : Molecular biology and evolution. 29, 10, p. 3237-3248 12 p.

Research output: Contribution to journalArticle

121 Scopus citations

Adaptive evolution of multiple traits through multiple mutations at a single gene

Linnen, C. R., Poh, Y. P., Peterson, B. K., Barrett, R. D. H., Larson, J. G., Jensen, J. D. & Hoekstra, H. E., Mar 15 2013, In : Science. 339, 6125, p. 1312-1316 5 p.

Research output: Contribution to journalArticle

178 Scopus citations

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

Jones, M. R., Scott Mills, L., Alves, P. C., Callahan, C. M., Alves, J. M., Lafferty, D. J. R., Jiggins, F. M., Jensen, J., Melo-Ferreira, J. & Good, J. M., Jun 22 2018, In : Science. 360, 6395, p. 1355-1358 4 p.

Research output: Contribution to journalArticle

46 Scopus citations

A draft sequence of the neandertal genome

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H. Y., Hansen, N. F., Durand, E. Y., Malaspinas, A. S., Jensen, J. D., Marques-Bonet, T., Alkan, C., Prüfer, K., Meyer, M., Burbano, H. A., Good, J. M. & 36 others, Schultz, R., Aximu-Petri, A., Butthof, A., Höber, B., Höffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E. S., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Ž., Gušic, I., Doronichev, V. B., Golovanova, L. V., Lalueza-Fox, C., De La Rasilla, M., Fortea, J., Rosas, A., Schmitz, R. W., Johnson, P. L. F., Eichler, E. E., Falush, D., Birney, E., Mullikin, J. C., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D. & Pääbo, S., May 7 2010, In : Science. 328, 5979, p. 710-722 13 p.

Research output: Contribution to journalArticle

1902 Scopus citations

An approximate bayesian estimator suggests strong, recurrent selective sweeps in drosophila

Jensen, J. D., Thornton, K. R. & Andolfatto, P., Sep 1 2008, In : PLoS genetics. 4, 9, e1000198.

Research output: Contribution to journalArticle

67 Scopus citations

An approximate markov model for the wright–fisher diffusion and its application to time series data

Ferrer-Admetlla, A., Leuenberger, C., Jensen, J. D. & Wegmann, D., Jun 2016, In : Genetics. 203, 2, p. 831-846 16 p.

Research output: Contribution to journalArticle

13 Scopus citations

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy

Bank, C., Renzette, N., Liu, P., Matuszewski, S., Shim, H., Foll, M., Bolon, D. N. A., Zeldovich, K. B., Kowalik, T. F., Finberg, R. W., Wang, J. P. & Jensen, J., Nov 1 2016, In : Evolution. 70, 11, p. 2470-2484 15 p.

Research output: Contribution to journalArticle

11 Scopus citations

Antiviral drug resistance as an adaptive process

Irwin, K. K., Renzette, N., Kowalik, T. F. & Jensen, J. D., Jan 1 2016, In : Virus Evolution. 2, 1, vew014.

Research output: Contribution to journalArticle

Open Access
24 Scopus citations

A statistical guide to the design of deep mutational scanning experiments

Matuszewski, S., Hildebrandt, M. E., Ghenu, A. H., Jensen, J. D. & Bank, C., Sep 2016, In : Genetics. 204, 1, p. 77-87 11 p.

Research output: Contribution to journalArticle

12 Scopus citations

Characterizing human cytomegalovirus reinfection in congenitally infected infants: An evolutionary perspective

Pokalyuk, C., Renzette, N., Irwin, K. K., Pfeifer, S., Gibson, L., Britt, W. J., Yamamoto, A. Y., Mussi-Pinhata, M. M., Kowalik, T. F. & Jensen, J., 2017, (Accepted/In press) In : Molecular Ecology.

Research output: Contribution to journalArticle

15 Scopus citations

Characterizing recurrent positive selection at fast-evolving genes in Drosophila miranda and Drosophila pseudoobscura

Jensen, J. D. & Bachtrog, D., Oct 29 2010, In : Genome biology and evolution. 2, 1, p. 371-378 8 p.

Research output: Contribution to journalArticle

12 Scopus citations

Characterizing the influence of effective population size on the rate of adaptation: Gillespie's Darwin domain

Jensen, J. D. & Bachtrog, D., Dec 1 2011, In : Genome biology and evolution. 3, 1, p. 687-701 15 p.

Research output: Contribution to journalArticle

33 Scopus citations

Coalescent processes with skewed offspring distributions and nonequilibrium demography

Matuszewski, S., Hildebrandt, M. E., Achaz, G. & Jensen, J., Jan 2018, In : Genetics. 208, 1, p. 323-338 16 p.

Research output: Contribution to journalArticle

6 Scopus citations

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

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. & 38 others, 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., Oct 16 2009, In : Science. 326, 5951, p. 433-436 4 p.

Research output: Contribution to journalArticle

238 Scopus citations

Controlling the false-positive rate in multilocus genome scans for selection

Thornton, K. R. & Jensen, J. D., Feb 1 2007, In : Genetics. 175, 2, p. 737-750 14 p.

Research output: Contribution to journalArticle

111 Scopus citations

Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range

Jones, M. R., Mills, L. S., Jensen, J. D. & Good, J. M., Jan 1 2020, (Accepted/In press) In : Evolution.

Research output: Contribution to journalArticle

1 Scopus citations

CRISPR-Cas9–mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy

Ma, L., Boucher, J. I., Paulsen, J., Matuszewski, S., Eide, C. A., Ou, J., Eickelberg, G., Press, R. D., Zhu, L. J., Druker, B. J., Branford, S., Wolfe, S. A., Jensen, J., Schiffer, C. A., Green, M. R. & Bolon, D. N., Oct 31 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 44, p. 11751-11756 6 p.

Research output: Contribution to journalArticle

15 Scopus citations

Detecting and quantifying changing selection intensities from time-sampled polymorphism data

Shim, H., Laurent, S., Matuszewski, S., Foll, M. & Jensen, J. D., Jan 1 2016, In : G3: Genes, Genomes, Genetics. 6, 4, p. 893-904 12 p.

Research output: Contribution to journalArticle

9 Scopus citations

Distinguishing between selective sweeps and demography using DNA polymorphism data

Jensen, J. D., Kim, Y., DuMont, V. B., Aquadro, C. F. & Bustamante, C. D., Jul 1 2005, In : Genetics. 170, 3, p. 1401-1410 10 p.

Research output: Contribution to journalArticle

160 Scopus citations

Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demography

Mathew, L. A. & Jensen, J. D., Jan 1 2015, In : Frontiers in Genetics. 6, Aug, 268.

Research output: Contribution to journalArticle

4 Scopus citations

Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution

Morales-Arce, A. Y., Harris, R. B., Stone, A. C. & Jensen, J. D., May 1 2020, In : Evolution. 74, 5, p. 992-1001 10 p.

Research output: Contribution to journalArticle

Evidence for a selective sweep on chromosome 1 of cultivated sorghum

Casa, A. M., Mitchell, S. E., Jensen, J. D., Hamblin, M. T., Paterson, A. H., Aquadro, C. F. & Kresovich, S., Dec 1 2006, In : Crop Science. 46, SUPPL. 1, p. S-27-S-40

Research output: Contribution to journalArticle

13 Scopus citations

Evidence of adaptation from ancestral variation in young populations of beach mice

Domingues, V. S., Poh, Y. P., Peterson, B. K., Pennings, P. S., Jensen, J. & Hoekstra, H. E., 2012, In : Evolution. 66, 10, p. 3209-3223 15 p.

Research output: Contribution to journalArticle

46 Scopus citations

Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro

Renzette, N., Caffrey, D. R., Zeldovich, K. B., Liu, P., Gallagher, G. R., Aiello, D., Porter, A. J., Kurt-Jones, E. A., Bolon, D. N., Poh, Y. P., Jensen, J. D., Schiffer, C. A., Kowalik, T. F., Finberg, R. W. & Wang, J. P., Jan 1 2014, In : Journal of virology. 88, 1, p. 272-281 10 p.

Research output: Contribution to journalArticle

27 Scopus citations

Experimental illumination of a fitness landscape

Hietpas, R. T., Jensen, J. D. & Bolon, D. N. A., May 10 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 19, p. 7896-7901 6 p.

Research output: Contribution to journalArticle

153 Scopus citations

Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants

Renzette, N., Bhattacharjee, B., Jensen, J. D., Gibson, L. & Kowalik, T. F., May 1 2011, In : PLoS Pathogens. 7, 5, e1001344.

Research output: Contribution to journalArticle

121 Scopus citations

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Massouras, A., Waszak, S. M., Albarca-Aguilera, M., Hens, K., Holcombe, W., Ayroles, J. F., Dermitzakis, E. T., Stone, E. A., Jensen, J. D., Mackay, T. F. C. & Deplancke, B., Nov 1 2012, In : PLoS genetics. 8, 11, e1003055.

Research output: Contribution to journalArticle

72 Scopus citations

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

Shulha, H. P., Crisci, J. L., Reshetov, D., Tushir, J. S., Cheung, I., Bharadwaj, R., Chou, H. J., Houston, I. B., Peter, C. J., Mitchell, A. C., Yao, W. D., Myers, R. H., Chen, J. F., Preuss, T. M., Rogaev, E. I., Jensen, J. D., Weng, Z. & Akbarian, S., Nov 1 2012, In : PLoS biology. 10, 11, e1001427.

Research output: Contribution to journalArticle

82 Scopus citations

Inferences of demography and selection in an african population of drosophila melanogaster

Singh, N. D., Jensen, J. D., Clark, A. G. & Aquadro, C. F., Jan 1 2013, In : Genetics. 193, 1, p. 215-228 14 p.

Research output: Contribution to journalArticle

18 Scopus citations

Inferring demography and selection in organisms characterized by skewed offspring distributions

Sackman, A. M., Harris, R. B. & Jensen, J., Mar 2019, In : Genetics. 211, 3, p. 1019-1028 10 p.

Research output: Contribution to journalArticle

2 Scopus citations

Inferring selection in partially sequenced regions

Jensen, J. D., Thornton, K. R. & Aquadro, C. F., Feb 1 2008, In : Molecular biology and evolution. 25, 2, p. 438-446 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

Inferring the age of a fixed beneficial allele

Ormond, L., Foll, M., Ewing, G. B., Pfeifer, S. & Jensen, J., Jan 1 2016, In : Molecular Ecology. 25, 1, p. 157-169 13 p.

Research output: Contribution to journalArticle

11 Scopus citations

Inferring the evolutionary history of primate microRNA binding sites: Overcoming motif counting biases

Simkin, A. T., Bailey, J. A., Gao, F. B. & Jensen, J. D., Jul 2014, In : Molecular biology and evolution. 31, 7, p. 1894-1901 8 p.

Research output: Contribution to journalArticle

2 Scopus citations

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

Foll, M., Poh, Y. P., Renzette, N., Ferrer-Admetlla, A., Bank, C., Shim, H., Malaspinas, A. S., Ewing, G., Liu, P., Wegmann, D., Caffrey, D. R., Zeldovich, K. B., Bolon, D. N., Wang, J. P., Kowalik, T. F., Schiffer, C. A., Finberg, R. W. & Jensen, J. D., Feb 1 2014, In : PLoS genetics. 10, 2, e1004185.

Research output: Contribution to journalArticle

65 Scopus citations

Limits and patterns of cytomegalovirus genomic diversity in humans

Renzette, N., Pokalyuk, C., Gibson, L., Bhattacharjee, B., Schleiss, M. R., Hamprecht, K., Yamamoto, A. Y., Mussi-Pinhata, M. M., Britt, W. J., Jensen, J. D. & Kowalik, T. F., Jul 28 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 30, p. E4120-E4128

Research output: Contribution to journalArticle

60 Scopus citations

Linking a mutation to survival in wild mice

Barrett, R. D. H., Laurent, S., Mallarino, R., Pfeifer, S., Xu, C. C. Y., Foll, M., Wakamatsu, K., Duke-Cohan, J. S., Jensen, J. & Hoekstra, H. E., Feb 1 2019, In : Science. 363, 6426, p. 499-504 6 p.

Research output: Contribution to journalArticle

28 Scopus citations

Loci associated with skin pigmentation identified in African populations

NISC Comparative Sequencing Program, Nov 17 2017, In : Science. 358, 6365, eaan8433.

Research output: Contribution to journalArticle

87 Scopus citations

Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase

Prachanronarong, K. L., Özen, A., Thayer, K. M., Yilmaz, L. S., Zeldovich, K. B., Bolon, D. N., Kowalik, T. F., Jensen, J., Finberg, R. W., Wang, J. P., Kurt-Yilmaz, N. & Schiffer, C. A., Dec 13 2016, In : Journal of Chemical Theory and Computation. 12, 12, p. 6098-6108 11 p.

Research output: Contribution to journalArticle

9 Scopus citations

Mutations in influenza A virus neuraminidase and hemagglutinin confer resistance against a broadly neutralizing hemagglutinin stem antibody

Prachanronarong, K. L., Canale, A. S., Liu, P., Somasundaran, M., Hou, S., Poh, Y. P., Han, T., Zhu, Q., Renzette, N., Zeldovich, K. B., Kowalik, T. F., Kurt-Yilmaz, N., Jensen, J., Bolon, D. N. A., Marasco, W. A., Finberg, R. W., Schiffer, C. A. & Wang, J. P., Jan 1 2019, In : Journal of virology. 93, 2, e01639-18.

Research output: Contribution to journalArticle

4 Scopus citations

On detecting selective sweeps using single genomes

Sinha, P., Dincer, A., Virgil, D., Xu, G., Poh, Y. P. & Jensen, J. D., Dec 1 2011, In : Frontiers in Genetics. 2, DEC, Article 85.

Research output: Contribution to journalArticle

2 Scopus citations

On the (un)predictability of a large intragenic fitness landscape

Bank, C., Matuszewski, S., Hietpas, R. T. & Jensen, J., Dec 6 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 49, p. 14085-14090 6 p.

Research output: Contribution to journalArticle

40 Scopus citations

On the analysis of intrahost and interhost viral populations: Human cytomegalovirus as a case study of pitfalls and expectations

Renzette, N., Pfeifer, S., Matuszewski, S., Kowalik, T. F. & Jensen, J., Jan 1 2017, In : Journal of virology. 91, 5, e01976-16.

Research output: Contribution to journalArticle

14 Scopus citations

On the origin and spread of an adaptive allele in deer mice

Linnen, C. R., Kingsley, E. P., Jensen, J. D. & Hoekstra, H. E., Sep 7 2009, In : Science. 325, 5944, p. 1095-1098 4 p.

Research output: Contribution to journalArticle

159 Scopus citations

On the prospect of identifying adaptive loci in recently bottlenecked populations

Poh, Y. P., Domingues, V. S., Hoekstra, H. E. & Jensen, J. D., Nov 10 2014, In : PloS one. 9, 11, e110579.

Research output: Contribution to journalArticle

24 Scopus citations

On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity

Renzette, N., Kowalik, T. F. & Jensen, J., Jan 1 2016, In : Molecular Ecology. 25, 1, p. 403-413 11 p.

Research output: Contribution to journalArticle

19 Scopus citations

On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses

Harris, R. B., Sackman, A. & Jensen, J., Dec 2018, In : PLoS genetics. 14, 12, e1007859.

Research output: Contribution to journalArticle

6 Scopus citations

On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations

Jensen, J. D., Thornton, K. R., Bustamante, C. D. & Aquadro, C. F., Aug 1 2007, In : Genetics. 176, 4, p. 2371-2379 9 p.

Research output: Contribution to journalArticle

62 Scopus citations