• 5968 Citations
  • 36 h-Index
20052024

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Article
2020

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

Toward an evolutionarily appropriate null model: Jointly inferring demography and purifying selection

Johri, P., Charlesworth, B. & Jensen, J. D., May 2020, In : Genetics. 215, 1, p. 173-192 20 p.

Research output: Contribution to journalArticle

Open Access
2019

Inferring demography and selection in organisms characterized by skewed offspring distributions

Sackman, A. M., Harris, R. B. & Jensen, J., Mar 1 2019, In : Genetics. 211, 3, p. 1019-1028 10 p.

Research output: Contribution to journalArticle

2 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

22 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
2018

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

40 Scopus citations

Coalescent processes with skewed offspring distributions and nonequilibrium demography

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

Research output: Contribution to journalArticle

6 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 1 2018, In : PLoS Genetics. 14, 12, e1007859.

Research output: Contribution to journalArticle

4 Scopus citations

Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness

Canale, A. S., Venev, S. V., Whitfield, T. W., Caffrey, D. R., Marasco, W. A., Schiffer, C. A., Kowalik, T. F., Jensen, J., Finberg, R. W., Zeldovich, K. B., Wang, J. P. & Bolon, D. N. A., Apr 13 2018, In : Journal of Molecular Biology. 430, 8, p. 1098-1115 18 p.

Research output: Contribution to journalArticle

2 Scopus citations

The evolutionary history of Nebraska deer mice: Local adaptation in the face of strong gene flow

Pfeifer, S., Laurent, S., Sousa, V. C., Linnen, C. R., Foll, M., Excoffier, L., Hoekstra, H. E. & Jensen, J., Apr 1 2018, In : Molecular biology and evolution. 35, 4, p. 792-806 15 p.

Research output: Contribution to journalArticle

18 Scopus citations

The fitness landscape of the codon space across environments

Fragata, I., Matuszewski, S., Schmitz, M. A., Bataillon, T., Jensen, J. & Bank, C., Jan 1 2018, (Accepted/In press) In : Heredity.

Research output: Contribution to journalArticle

6 Scopus citations
2017

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

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

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

82 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

11 Scopus citations

Resistance of Echovirus 11 to ClO2 Is Associated with Enhanced Host Receptor Use, Altered Entry Routes, and High Fitness

Zhong, Q., Carratalà, A., Shim, H., Bachmann, V., Jensen, J. & Kohn, T., Sep 19 2017, In : Environmental Science and Technology. 51, 18, p. 10746-10755 10 p.

Research output: Contribution to journalArticle

9 Scopus citations

Structural Determination of the Broadly Reactive Anti-IGHV1-69 Anti-idiotypic Antibody G6 and Its Idiotope

Avnir, Y., Prachanronarong, K. L., Zhang, Z., Hou, S., Peterson, E. C., Sui, J., Zayed, H., Kurella, V. B., McGuire, A. T., Stamatatos, L., Hilbert, B. J., Bohn, M. F., Kowalik, T. F., Jensen, J., Finberg, R. W., Wang, J. P., Goodall, M., Jefferis, R., Zhu, Q., Kurt Yilmaz, N. & 2 others, Schiffer, C. A. & Marasco, W. A., Dec 12 2017, In : Cell Reports. 21, 11, p. 3243-3255 13 p.

Research output: Contribution to journalArticle

7 Scopus citations

The combined effect of oseltamivir and favipiravir on influenza a virus evolution

Ormond, L., Liu, P., Matuszewski, S., Renzette, N., Bank, C., Zeldovich, K., Bolon, D. N., Kowalik, T. F., Finberg, R. W., Jensen, J. & Wang, J. P., Jul 1 2017, In : Genome biology and evolution. 9, 7, p. 1913-1924 12 p.

Research output: Contribution to journalArticle

5 Scopus citations
2016

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

17 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

12 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

10 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

A statistical guide to the design of deep mutational scanning experiments

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

Research output: Contribution to journalArticle

12 Scopus citations

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

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

Research output: Contribution to journalArticle

7 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

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

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

39 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

The consequences of not accounting for background selection in demographic inference

Ewing, G. B. & Jensen, J., Jan 1 2016, In : Molecular Ecology. 25, 1, p. 135-141 7 p.

Research output: Contribution to journalArticle

50 Scopus citations

The evolution of gene expression and binding specificity of the largest transcription factor family in primates

Kapopoulou, A., Mathew, L., Wong, A., Trono, D. & Jensen, J., Jan 1 2016, In : Evolution. 70, 1, p. 167-180 14 p.

Research output: Contribution to journalArticle

4 Scopus citations

The genomic signature of population reconnection following isolation: From theory to HIV

Alcala, N., Jensen, J. D., Telenti, A. & Vuilleumier, S., Jan 1 2016, In : G3: Genes, Genomes, Genetics. 6, 1, p. 107-120 14 p.

Research output: Contribution to journalArticle

7 Scopus citations

The impact of linked selection in chimpanzees: A comparative study

Pfeifer, S. & Jensen, J., 2016, In : Genome Biology and Evolution. 8, 10, p. 3202-3208 7 p.

Research output: Contribution to journalArticle

4 Scopus citations

The population genomics of rapid adaptation: Disentangling signatures of selection and demography in white sands lizards

Laurent, S., Pfeifer, S., Settles, M. L., Hunter, S. S., Hardwick, K. M., Ormond, L., Sousa, V. C., Jensen, J. & Rosenblum, E. B., Jan 1 2016, In : Molecular Ecology. 25, 1, p. 306-323 18 p.

Research output: Contribution to journalArticle

26 Scopus citations

The SIB Swiss Institute of bioinformatics' resources: Focus on curated databases

Bultet, L. A., Aguilar-Rodríguez, J., Ahrens, C. H., Ahrné, E. L., Ai, N., Aimo, L., Akalin, A., Aleksiev, T., Alocci, D., Altenhoff, A., Alves, I., Ambrosini, G., Pedone, P. A., Angelino, P., Anisimova, M., Appel, R., Argoud-Puy, G., Arnold, K., Arpat, B., Artimo, P. & 658 others, Ascencao, K., Auchincloss, A., Axelsen, K., Gerritsen, V. B., Bairoch, A., Bansal, P., Baratin, D., Barbato, A., Barbié, V., Barras, D., Barreiro, M., Barret, S., Bastian, F., Neto, T. B., Baudis, M., Beaudoing, E., Beckmann, J. S., Bekkar, A. K., Ben Hamida Cammoun, L., Benmohammed, S., Bernard, M., Bertelli, C., Bertoni, M., Bienert, S., Bignucolo, O., Bilbao, A., Bilican, A., Blank, D., Blatter, M. C., Blum, L., Bocquet, J., Boeckmann, B., Bolleman, J. T., Bordoli, L., Bosshard, L., Bouchet, G., Bougueleret, L., Boutet, E., Bovigny, C., Bratulic, S., Breuza, L., Bridge, A. J., Britan, A., Brito, F., Frazão, J. B., Bruggmann, R., Bucher, P., Burdet, F., Burger, L., Cabello, E. M., Gomez, R. M. C., Calderon, S., Cannarozzi, G., Carl, S., Casas, C. C., Catherinet, S., Périer, R. C., Charpilloz, C., Chaskar, P. D., Chen, W., Pepe, A. C., Chopard, B., Chu, H. Y., Civic, N., Claassen, M., Clottu, S., Colombo, M., Cosandier, I., Coudert, E., Crespo, I., Creus, M., Cuche, B., Cuendet, M. A., Cusin, I., Daga, N., Daina, A., Dauvillier, J. Ô., David, F., Davydov, I., De Sa Ricca Manadelo Ferreira, M., De Beer, T., De Castro, E., De Santana, C., Delafontaine, J., Delorenzi, M., Delucinge-Vivier, C., Demirel, Ö., Derham, R., Dermitzakis, E. M., Dib, L., Diene, S., Dilek, N., Dilmi, J., Domagalski, M. J., Dorier, J., Dornevil, D., Dousse, A., Dreos, R., Duchen, P., Roggli, P. D., Duperret, I. D., Durinx, C., Duvaud, S., Engler, R., Erkek, S., López, P. E., Estreicher, A., Excoffier, L., Fabbretti, R., Falcone, J. L., Falquet, L., Famiglietti, M. L., Ferreira, A. M., Feuermann, M., Filliettaz, M., Flegel, V., Foucal, A., Franceschini, A., Fucile, G., Gaidatzis, D., Garcia, V., Gasteiger, E., Gateau, A., Gatti, L., Gaudet, P., Gaudinat, A., Gehant, S., Gfeller, D., Gharib, W. H., Ghraichy, M., Gidoin, C., Gil, M., Gleizes, A., Gobeill, J., Gonnet, G., Gos, A., Gotz, L., Gouy, A., Grbic, D., Groux, R., Gruaz-Gumowski, N., Grun, D., Gschwind, A., Guex, N., Gupta, S., Gétaz, M., Haake, D., Haas, J., Hatzimanikatis, V., Heckel, G., Gardiol, D. F. H., Hinard, V., Hinz, U., Homicsko, K., Horlacher, O., Hosseini, S. R., Hotz, H. R., Hulo, C., Hundsrucker, C., Ibberson, M., Ilmjärv, S., Ioannidis, V., Ioannidis, P., Iseli, C., Ivanek, R., Iwaszkiewicz, J., Jacquet, P., Jacquot, M., Jagannathan, V., Jan, M., Jensen, J., Johansson, M. U., Johner, N., Jungo, F., Junier, T., Kahraman, A., Katsantoni, M., Keller, G., Kerhornou, A., Khalid, F., Klingbiel, D., Komljenovic, A., Kriventseva, E., Kryuchkova, N., Kumar, S., Kutalik, Z., Kuznetsov, D., Kuzyakiv, R., Lane, L., Lara, V., Ledesma, L., Leleu, M., Lemercier, P., Lew, D., Lieberherr, D., Liechti, R., Lisacek, F., Lischer, H., Litsios, G., Liu, J., Lombardot, T., Macé, A., Maffioletti, S., Mahi, M. A., Maiolo, M., Majjigapu, S. R., Malmström, L., Mangold, V., Marek, D., Mariethoz, J., Marin, R., Martin, O., Martin, X., Martín-Campos, T., Mary, C., Masclaux, F., Masson, P., Meier, C., Messina, A., Lenoir, M. M., Meyer, X., Michel, P. A., Michielin, O., Milanese, A., Missiaglia, E., Perez, J. M., Caria, V. M., Moret, P., Moretti, S., Morgat, A., Mottaz, A., Mottin, L., Mouscaz, Y., Mueller, M., Murri, R., Mylonas, R., Neuenschwander, S., Nikitin, F., Niknejad, A., Nouspikel, N., Nso, L. N., Okoniewski, M., Omasits, U., Paccaud, B., Pachkov, M., Paesano, S. G., Pagni, M., Palagi, P. M., Pasche, E., Payne, J. L., Pedruzzi, I., Peischl, S., Peitsch, M., Perlini, S., Pilbout, S., Podvinec, M., Pohlmann, R., Polizzi, D., Potter, D., Poux, S., Pozzato, M., Pradervand, S., Praz, V., Pruess, M., Pujadas, E., Racle, J., Raschi, M., Ratib, O., Rausell, A., De Laval, V. R., Redaschi, N., Rempfer, C., Ren, G., Vahdati, R. A. R., Rib, L., Grognuz, O. R., Altimiras, E. R., Rivoire, C., Robin, T., Robinson-Rechavi, M., Rodrigues, J., Roechert, B., Roelli, P., Romano, V., Rossier, G., Roth, A., Rougemont, J., Roux, J., Royo, H., Ruch, P., Ruinelli, M., Sater, M. R. A., Röhrig, U. F., Rüeger, S., Salamin, N., Sankar, M., Sarkar, N., Saxenhofer, M., Schaeffer, M., Schaerli, Y., Schaper, E., Schmid, A., Schmid, E., Schmid, C., Schmid, M., Schmidt, S., Schmocker, D., Schneider, M., Schuepbach, T., Schwede, T., Schütz, F., Sengstag, T., Serrano, M., Sethi, A., Shahmirzadi, O., Sigrist, C., Silvestro, D., Neto, F. A. S., Simillion, C., Simonovic, M., Skunca, N., Sluzek, K., Soneson, C., Sprouffske, K., Stadler, M., Staehli, S., Stevenson, B., Stockinger, H., Straszewski, J., Stricker, T., Studer, G., Stutz, A., Suffiotti, M., Sundaram, S., Szklarczyk, D., Övenyi, P. S., Tegenfeldt, F., Teixeira, D., Tellenbach, S., Smith, A. A. T., Tognolli, M., Topolsky, I., Van Du Tran, T., Tsantoulis, P., Tzika, A. C., Agote, A. U., Van Nimwegen, E., Von Mering, C., Varadarajan, A., Veranneman, M., Verbregue, L., Veuthey, A. L., Vishnyakova, D., Vyas, R., Wagner, A., Walther, D., Wan, H. W., Wang, M., Waterhouse, R., Waterhouse, A., Wicki, A., Wigger, L., Wirapati, P., Witschi, U., Wyder, S., Wyler, K., Wüthrich, D., Xenarios, I., Yamada, K., Yan, Z., Yasrebi, H., Zahn, M., Zangger, N., Zdobnov, E., Zerzion, D., Zoete, V., Zoller, S., Abriata, L., Aebischer, T., Akhmedov, M., Filho, A. A. M., Andreozzi, S., Appel, N., Armand, F., Arribas, A., Asgari, S., Ataman, M., Audagnotto, M., Aydin, D., Bady, P., Bank, C., Barac, D., Bargeton, B., Barido-Sottani, J., Barillari, C., Bartha, I., Bean, A., Becker, J., Beerenwinkel, N., Bellement, G., Benedetti, F., Bergmann, S., Berneche, S., Bevers, R., Biasse, D., Bichsel, M., Bieler, J., Piccini, A. P. B., Do Amaral, M. B., Bolliger, C., Boskova, V., Brown, A., Bryois, J., Buil, A., Cannavo, R., Cardner, M., Carelli, F. N., Carmona, S., Cascione, L., Chakrabarti, A., Chaturvedi, N., Choobdar, S., Clivaz, C., Constantinescu, S., Corre, T., Quezada, D. C. C., Croce, R., Cuendet, A., Cui, J., Dainese, R., Dal Peraro, M., Dallavilla, T., De Oliveira, L., Delaleu, N., Delaneau, O., Deplancke, B., Dharmarajan, L., Diekmann, M., Dimitrakopoulos, C., Dimitriades-Schmutz, B., Dimitrova, Y., Dirmeier, S., Dobay, M. P., Dougoud, M., Duc, J., Dumont, G., Du Plessis, L., Dörr, D., Elfstroem, K., Elmer, F. J., Ewing, G. B., Fanaswala, I., Fellay, J., Feller, C., Fengos, G., Ferrer, A., Fiaux, S., Field, C., Finci, I., Fofonjka, A., Fonti, G., Fried, P., Frochaux, M., Fuentes, J., Galbusera, L., Galimberti, M., Garcia-Albornoz, M., Garcia-Escudero, R., Garieri, M., Georgieva, L., Ghiurcuta, C. G., Ghosh, S., Gnann, A., Gnuegge, R., Golumbeanu, M., Gomez, H., Goudet, J. Ô., Gruber, A. J., Gruhl, F., Guethe, S., Guillot, E., Guimarães, J., Gumienny, R. W., Gunawan, R., Gustafson, K., Gypas, F., Hadadi, N., Hameri, T., Hammer, C., Heer, F., Heller, D. M., Hersch, M., Hofmann, A. L., Howald, C., Hutter, S., Iber, D., Irwin, K., Jahn, K., Jedlinski, D., Jethava, V., Jorjani, H., Julou, T., Kaessmann, H., Kalantzi, A., Kanitz, A., Kapopoulou, A., Karamasioti, E., Karimaddini, Z., Keller, I., Kiparissides, A., Kohler, M., Kousathanas, A., Kuipers, J., Kupczyk, P., Kwee, I., Kühnert, D., Lakshmanan, L. N., Lamparter, D., Lang, B., Laurent, S., Laurent, S., Leigh, D., Lin, Y., Lindsay, H., Link, V., Linnik, J., Liphardt, T., Liu, Y., Loetscher, A., Luomi, A. O., Lykov, K., Machlab, D., Magnus, C., Maillard-Wermelinger, A., Malafeev, A., Malaspinas, A. S., Parera, R. M., Manesso, E., Manukyan, L., Mapelli, S. N., Marbach, D., Lopez, M. J. M., Wynn, M. M., Martin, G., Martins, A. F., Matthes, K., Mazza, C., McDaid, A., Mermet, J. Ô., Michos, O., Milinkovitch, M. C., Misios, A., Miskovic, L., Mitov, V., Mitra, A., Mittal, N., Montazeri, H., Moret, B., Naef, F., Nair, N., Nicolas, D. L., Nicolet, S., Noh, H., Nowicka, M., Oeyaas, O., Omidi, S., Ongen, H., Ormond, L., Ottoz, D., Panousis, N., Gao, N. P., Modarres, H. P., Pečerska, J., Vieira, J. P., Pivkin, I., Planet, E., Céspedes, S. P., Pradhan, R., Prados, J., Racko, D., Radigois, M. F., Rasmussen, D., Riba, A., Rinn, B., Rivoal, M., Robinson, M., Rossi, S., Rudolf, F., Rueedi, R., Ruscheweyh, H. J., Rybinski, M., Rzepiela, A. J., Sakoparnig, T., San Román Rincón, M. M., Savoglidis, G., Scepanovic, P., Schaad, O., Schleiss, R., Schmich, F., Schmidt, R., Schulthess, S., Schwalie, P. C., Seifert, D., Seijo, M., Shao, M., Shim, H., Singer, J., Sobel, J., Soh, K. C., Flitman, R. S., Soto, S., Sousa, V., Stadler, T., Stasiak, A., Stefani, A., Steger, Y., Stelling, J., Stopka, A., Stévant, I., Sunnaker, M., Syed, A. P., Tamo, G., Tanaka, S., Theiler, G., Thorball, C. A. W., Thurnherr, T., Ccenhua, M. R. T., Tidin, O., Tokic, M., Riera, M. T., Tomasini, M., Tymoshenko, S., Ud-Dean, M., Urchueguia, A., Quintero, N. V., Vinckenbosch, L., Viñuela, A., Vollmer, J., Voordijk, S., Wang, J., Wang, Z., Warnefors, M., Weber, L. M., Wegmann, D., Whitehead, E., Wicky, A., Widmer, L., Ye, M., Yerly, F., Yeung, J., Yordanov, P., Zavolan, M., Zehnder, T., Zhang, C., Zhou, X., Zisaki, A., Zoller, B. & Zollinger, A., Jan 1 2016, In : Nucleic acids research. 44, D1, p. D27-D37

Research output: Contribution to journalArticle

19 Scopus citations
2015

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

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

Research output: Contribution to journalArticle

4 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

56 Scopus citations

PopPlanner: Visually constructing demographic models for simulation

Ewing, G. B., Reiff, P. A. & Jensen, J. D., Jan 1 2015, In : Frontiers in Genetics. 6, MAR, 150.

Research output: Contribution to journalArticle

8 Scopus citations

Positive selection drives preferred segment combinations during influenza virus reassortment

Zeldovich, K. B., Liu, P., Renzette, N., Foll, M., Pham, S. T., Venev, S. V., Gallagher, G. R., Bolon, D. N., Kurt-Jones, E. A., Jensen, J. D., Caffrey, D. R., Schiffer, C. A., Kowalik, T. F., Wang, J. P. & Finberg, R. W., Jun 1 2015, In : Molecular biology and evolution. 32, 6, p. 1519-1532 14 p.

Research output: Contribution to journalArticle

10 Scopus citations

Quantifying polymorphism and divergence from epigenetic data: A framework for inferring the action of selection

Mahajan, S., Crisci, J., Wong, A., Akbarian, S., Foll, M. & Jensen, J. D., Jan 1 2015, In : Frontiers in Genetics. 6, MAY, 190.

Research output: Contribution to journalArticle

44 Scopus citations

Worldwide population structure, long-term demography, and local adaptation of Helicobacter pylori

Montano, V., Didelot, X., Foll, M., Linz, B., Reinhardt, R., Suerbaum, S., Moodley, Y. & Jensen, J. D., Jul 1 2015, In : Genetics. 200, 3, p. 947-963 17 p.

Research output: Contribution to journalArticle

32 Scopus citations
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

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

45 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

26 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

63 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

23 Scopus citations
2013

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

174 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

Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection

Renzette, N., Gibson, L., Bhattacharjee, B., Fisher, D., Schleiss, M. R., Jensen, J. D. & Kowalik, T. F., Sep 1 2013, In : PLoS genetics. 9, 9, e1003735.

Research output: Contribution to journalArticle

67 Scopus citations

Recurrent and recent selective sweeps in the piRNA pathway

Simkin, A., Wong, A., Poh, Y. P., Theurkauf, W. E. & Jensen, J. D., Apr 1 2013, In : Evolution. 67, 4, p. 1081-1090 10 p.

Research output: Contribution to journalArticle

27 Scopus citations