Search Results - "Jeffrey D. Jensen"

Recommendations for improving statistical inference in population genomics by Johri, Parul, Aquadro, Charles F, Beaumont, Mark, Charlesworth, Brian, Excoffier, Laurent, Eyre-Walker, Adam, Keightley, Peter D, Lynch, Michael, McVean, Gil, Payseur, Bret A, Pfeifer, Susanne P, Stephan, Wolfgang, Jensen, Jeffrey D

“…The field of population genomics has grown rapidly in response to the recent advent of affordable, large-scale sequencing technologies. As opposed to the…”
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Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers by Johri, Parul, Stephan, Wolfgang, Jensen, Jeffrey D

“…The ability to accurately identify and quantify genetic signatures associated with soft selective sweeps based on patterns of nucleotide variation has remained…”
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WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data by Foll, Matthieu, Shim, Hyunjin, Jensen, Jeffrey D.

“…With novel developments in sequencing technologies, time‐sampled data are becoming more available and accessible. Naturally, there have been efforts in…”
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On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses by Harris, Rebecca B, Sackman, Andrew, Jensen, Jeffrey D

“…Since the initial description of the genomic patterns expected under models of positive selection acting on standing genetic variation and on multiple…”
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Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares by Jones, Matthew R, Mills, L Scott, Alves, Paulo Célio, Callahan, Colin M, Alves, Joel M, Lafferty, Diana J R, Jiggins, Francis M, Jensen, Jeffrey D, Melo-Ferreira, José, Good, Jeffrey M

“…Snowshoe hares ( ) maintain seasonal camouflage by molting to a white winter coat, but some hares remain brown during the winter in regions with low snow…”
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Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples by Terbot, 2nd, John W, Johri, Parul, Liphardt, Schuyler W, Soni, Vivak, Pfeifer, Susanne P, Cooper, Brandon S, Good, Jeffrey M, Jensen, Jeffrey D

“…Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a…”
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An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data by Ferrer-Admetlla, Anna, Leuenberger, Christoph, Jensen, Jeffrey D, Wegmann, Daniel

“…The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since…”
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Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes by Xu, Xun, Liu, Xin, Ge, Song, Jensen, Jeffrey D, Hu, Fengyi, Li, Xin, Dong, Yang, Gutenkunst, Ryan N, Fang, Lin, Huang, Lei, Li, Jingxiang, He, Weiming, Zhang, Guojie, Zheng, Xiaoming, Zhang, Fumin, Li, Yingrui, Yu, Chang, Kristiansen, Karsten, Zhang, Xiuqing, Wang, Jian, Wright, Mark, McCouch, Susan, Nielsen, Rasmus, Wang, Jun, Wang, Wen

“…A catalog of genetic variation in a crop species facilitates marker-assisted breeding, gene mapping and analysis of elite traits. Xu et al . resequenced 40…”
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Interpreting the pervasive observation of U-shaped Site Frequency Spectra by Freund, Fabian, Kerdoncuff, Elise, Matuszewski, Sebastian, Lapierre, Marguerite, Hildebrandt, Marcel, Jensen, Jeffrey D, Ferretti, Luca, Lambert, Amaury, Sackton, Timothy B, Achaz, Guillaume

“…The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45…”
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Experimental illumination of a fitness landscape by Hietpas, Ryan T, Jensen, Jeffrey D, Bolon, Daniel N.A

“…The genes of all organisms have been shaped by selective pressures. The relationship between gene sequence and fitness has tremendous implications for…”
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Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection by Renzette, Nicholas, Gibson, Laura, Bhattacharjee, Bornali, Fisher, Donna, Schleiss, Mark R, Jensen, Jeffrey D, Kowalik, Timothy F

“…Populations of human cytomegalovirus (HCMV), a large DNA virus, are highly polymorphic in patient samples, which may allow for rapid evolution within human…”
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Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions by Sackman, Andrew M, Harris, Rebecca B, Jensen, Jeffrey D

“…The recent increase in time-series population genomic data from experimental, natural, and ancient populations has been accompanied by a promising growth in…”
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Population genetic inference from genomic sequence variation by Pool, John E, Hellmann, Ines, Jensen, Jeffrey D, Nielsen, Rasmus

“…Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the…”
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Thinking too positive? Revisiting current methods of population genetic selection inference by Bank, Claudia, Ewing, Gregory B, Ferrer-Admettla, Anna, Foll, Matthieu, Jensen, Jeffrey D

“…Highlights • Novel technologies provide us with data of vast dimensions in terms of amount, resolution, and design. • To improve selection inference from…”
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Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene by Linnen, Catherine R., Poh, Yu-Ping, Peterson, Brant K., Barrett, Rowan D. H., Larson, Joanna G., Jensen, Jeffrey D., Hoekstra, Hopi E.

“…The identification of precise mutations is required for a complete understanding of the underlying molecular and evolutionary mechanisms driving adaptive…”
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Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data by Soni, Vivak, Terbot, John W., Jensen, Jeffrey D.

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The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow by Pfeifer, Susanne P, Laurent, Stefan, Sousa, Vitor C, Linnen, Catherine R, Foll, Matthieu, Excoffier, Laurent, Hoekstra, Hopi E, Jensen, Jeffrey D

“…Abstract The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective…”
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Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants by Renzette, Nicholas, Bhattacharjee, Bornali, Jensen, Jeffrey D, Gibson, Laura, Kowalik, Timothy F

“…Research has shown that RNA virus populations are highly variable, most likely due to low fidelity replication of RNA genomes. It is generally assumed that…”
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Limits and patterns of cytomegalovirus genomic diversity in humans by Renzette, Nicholas, Cornelia Pokalyuk, Laura Gibson, Bornali Bhattacharjee, Mark R. Schleiss, Klaus Hamprecht, Aparecida Y. Yamamoto, Marisa M. Mussi-Pinhata, William J. Britt, Jeffrey D. Jensen, Timothy F. Kowalik

“…Human cytomegalovirus (HCMV) is the leading cause of birth defects associated with infections and a leading cause of transplantation failure. This study…”
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Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori by Montano, Valeria, Didelot, Xavier, Foll, Matthieu, Linz, Bodo, Reinhardt, Richard, Suerbaum, Sebastian, Moodley, Yoshan, Jensen, Jeffrey D

“…Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its…”
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