Jeffrey D Jensen

Jeffrey D Jensen

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Jeffrey D Jensen

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Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions.

Genetics 2019 03 16;211(3):1019-1028. Epub 2019 Jan 16.

School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287.

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http://www.genetics.org/lookup/doi/10.1534/genetics.118.3016
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http://dx.doi.org/10.1534/genetics.118.301684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404255PMC
March 2019

Linking a mutation to survival in wild mice.

Science 2019 02 31;363(6426):499-504. Epub 2019 Jan 31.

Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA USA.

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http://dx.doi.org/10.1126/science.aav3824DOI Listing
February 2019

The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018.

Evolution 2019 Jan 27;73(1):111-114. Epub 2018 Nov 27.

Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1111/evo.13650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6496948PMC
January 2019

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

PLoS Genet 2018 12 28;14(12):e1007859. Epub 2018 Dec 28.

School of Life Sciences, Arizona State University, Tempe, AZ, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1007859
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http://dx.doi.org/10.1371/journal.pgen.1007859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336318PMC
December 2018

The fitness landscape of the codon space across environments.

Heredity (Edinb) 2018 11 20;121(5):422-437. Epub 2018 Aug 20.

Instituto Gulbenkian de Ciência, Oeiras, Portugal.

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http://dx.doi.org/10.1038/s41437-018-0125-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180090PMC
November 2018

The demographic history of African Drosophila melanogaster.

Genome Biol Evol 2018 Aug 29. Epub 2018 Aug 29.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland.

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http://dx.doi.org/10.1093/gbe/evy185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6363051PMC
August 2018

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

J Mol Biol 2018 04 18;430(8):1098-1115. Epub 2018 Feb 18.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2018.02.009DOI Listing
April 2018

Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.

Genetics 2018 01 10;208(1):323-338. Epub 2017 Nov 10.

School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

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http://dx.doi.org/10.1534/genetics.117.300499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753866PMC
January 2018

On the Demographic and Selective Forces Shaping Patterns of Human Cytomegalovirus Variation within Hosts.

Pathogens 2018 Jan 28;7(1). Epub 2018 Jan 28.

School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.

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http://dx.doi.org/10.3390/pathogens7010016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5874742PMC
January 2018

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

Environ Sci Technol 2017 Sep 8;51(18):10746-10755. Epub 2017 Sep 8.

Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/acs.est.7b03288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607461PMC
September 2017

Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to resistance to disinfection and ribavirin.

Virus Evol 2017 Jul 20;3(2):vex035. Epub 2017 Nov 20.

Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), CH-1015 Lausanne.

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http://dx.doi.org/10.1093/ve/vex035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714166PMC
July 2017

Characterizing human cytomegalovirus reinfection in congenitally infected infants: an evolutionary perspective.

Mol Ecol 2017 Apr 8;26(7):1980-1990. Epub 2017 Feb 8.

School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1111/mec.13953DOI Listing
April 2017

Two sides of the same coin: A population genetics perspective on lethal mutagenesis and mutational meltdown.

Virus Evol 2017 Jan 2;3(1):vex004. Epub 2017 Mar 2.

School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.

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http://dx.doi.org/10.1093/ve/vex004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007402PMC
January 2017

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

Proc Natl Acad Sci U S A 2016 12 18;113(49):14085-14090. Epub 2016 Nov 18.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;

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http://dx.doi.org/10.1073/pnas.1612676113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5150413PMC
December 2016

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

J Chem Theory Comput 2016 Dec 17;12(12):6098-6108. Epub 2016 Nov 17.

School of Life Sciences, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/acs.jctc.6b00703DOI Listing
December 2016

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

Evolution 2016 11 13;70(11):2470-2484. Epub 2016 Sep 13.

School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1111/evo.13041DOI Listing
November 2016

The Impact of Linked Selection in Chimpanzees: A Comparative Study.

Genome Biol Evol 2016 10 30;8(10):3202-3208. Epub 2016 Oct 30.

School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1093/gbe/evw240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174744PMC
October 2016

A Statistical Guide to the Design of Deep Mutational Scanning Experiments.

Genetics 2016 Sep 13;204(1):77-87. Epub 2016 Jul 13.

School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland Instituto Gulbenkian de Ciência, Oeiras, Portugal

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http://dx.doi.org/10.1534/genetics.116.190462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012406PMC
September 2016

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data.

Genetics 2016 06 2;203(2):831-46. Epub 2016 Apr 2.

Department of Biology, University, of Fribourg, 1700 Fribourg Switzerland Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland

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http://dx.doi.org/10.1534/genetics.115.184598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896197PMC
June 2016

Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data.

G3 (Bethesda) 2016 04 7;6(4):893-904. Epub 2016 Apr 7.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1534/g3.115.023200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825659PMC
April 2016

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

J Mol Biol 2016 Feb 4;428(3):538-553. Epub 2015 Dec 4.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.11.027DOI Listing
February 2016

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

Mol Ecol 2016 01 3;25(1):403-13. Epub 2015 Sep 3.

Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland.

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http://doi.wiley.com/10.1111/mec.13331
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http://dx.doi.org/10.1111/mec.13331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706826PMC
January 2016

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

Mol Ecol 2016 01 30;25(1):306-23. Epub 2015 Oct 30.

Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.

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http://dx.doi.org/10.1111/mec.13385DOI Listing
January 2016

The consequences of not accounting for background selection in demographic inference.

Mol Ecol 2016 01 30;25(1):135-41. Epub 2015 Oct 30.

Ecole Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, AAB 0 46, Station 15, CH 1015, Lausanne, Switzerland.

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http://dx.doi.org/10.1111/mec.13390DOI Listing
January 2016

Inferring the age of a fixed beneficial allele.

Mol Ecol 2016 01 24;25(1):157-69. Epub 2015 Dec 24.

School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland.

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http://doi.wiley.com/10.1111/mec.13478
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http://dx.doi.org/10.1111/mec.13478DOI Listing
January 2016

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

Evolution 2016 Jan 9;70(1):167-80. Epub 2015 Dec 9.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1111/evo.12819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894471PMC
January 2016

The past, present and future of genomic scans for selection.

Mol Ecol 2016 Jan;25(1):1-4

IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, Québec, Canada.

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http://dx.doi.org/10.1111/mec.13493DOI Listing
January 2016

Antiviral drug resistance as an adaptive process.

Virus Evol 2016 Jan 10;2(1):vew014. Epub 2016 Jun 10.

School of Life Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1093/ve/vew014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499642PMC
January 2016

The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV.

G3 (Bethesda) 2015 Nov 6;6(1):107-20. Epub 2015 Nov 6.

Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland Institute of Microbiology, University Hospital and University of Lausanne, Lausanne CH-1011, Switzerland.

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http://dx.doi.org/10.1534/g3.115.024208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704709PMC
November 2015

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

Front Genet 2015 17;6:268. Epub 2015 Aug 17.

School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland.

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http://journal.frontiersin.org/Article/10.3389/fgene.2015.00
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http://dx.doi.org/10.3389/fgene.2015.00268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538300PMC
September 2015

On the prospect of identifying adaptive loci in recently bottlenecked populations.

PLoS One 2014 10;9(11):e110579. Epub 2014 Nov 10.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States of America; School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110579PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226487PMC
July 2015

Limits and patterns of cytomegalovirus genomic diversity in humans.

Proc Natl Acad Sci U S A 2015 Jul 6;112(30):E4120-8. Epub 2015 Jul 6.

Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655; Immunology and Virology Program, University of Massachusetts Medical School, Worcester, MA 01655

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http://dx.doi.org/10.1073/pnas.1501880112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522815PMC
July 2015

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

Front Genet 2015 28;6:190. Epub 2015 May 28.

School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland ; Swiss Institute of Bioinformatics Lausanne, Switzerland.

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http://dx.doi.org/10.3389/fgene.2015.00190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446996PMC
June 2015

PopPlanner: visually constructing demographic models for simulation.

Front Genet 2015 23;6:150. Epub 2015 Apr 23.

School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland.

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http://dx.doi.org/10.3389/fgene.2015.00150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4407479PMC
May 2015

WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data.

Mol Ecol Resour 2015 Jan 11;15(1):87-98. Epub 2014 Jun 11.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, CH-1015, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1111/1755-0998.12280DOI Listing
January 2015

A systematic survey of an intragenic epistatic landscape.

Mol Biol Evol 2015 Jan 3;32(1):229-38. Epub 2014 Nov 3.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA.

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http://dx.doi.org/10.1093/molbev/msu301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271534PMC
January 2015

Thinking too positive? Revisiting current methods of population genetic selection inference.

Trends Genet 2014 Dec 19;30(12):540-6. Epub 2014 Nov 19.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland.

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http://www.cell.com/trends/genetics/pdf/S0168-9525(14)00158-
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http://linkinghub.elsevier.com/retrieve/pii/S016895251400158
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http://dx.doi.org/10.1016/j.tig.2014.09.010DOI Listing
December 2014

Human cytomegalovirus intrahost evolution-a new avenue for understanding and controlling herpesvirus infections.

Curr Opin Virol 2014 Oct 25;8:109-15. Epub 2014 Aug 25.

Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA; Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address:

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http://dx.doi.org/10.1016/j.coviro.2014.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4195796PMC
October 2014

On the unfounded enthusiasm for soft selective sweeps.

Authors:
Jeffrey D Jensen

Nat Commun 2014 Oct 27;5:5281. Epub 2014 Oct 27.

1] School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1007, Switzerland [2] Swiss Institute of Bioinformatics (SIB), Lausanne 1007, Switzerland.

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http://dx.doi.org/10.1038/ncomms6281DOI Listing
October 2014

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

Mol Biol Evol 2014 Jul 9;31(7):1894-901. Epub 2014 Apr 9.

Swiss Institute of Bioinformatics (SIB), Lausanne, SwitzerlandEcole Polytechnique Federale de Lausanne (EPFL), School of Life Sciences, Lausanne, Switzerland.

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http://dx.doi.org/10.1093/molbev/msu129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069616PMC
July 2014

Rapid intrahost evolution of human cytomegalovirus is shaped by demography and positive selection.

PLoS Genet 2013 26;9(9):e1003735. Epub 2013 Sep 26.

Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784496PMC
March 2014

Distinguishing neutral from deleterious mutations in growing populations.

Front Genet 2014 31;5. Epub 2014 Jan 31.

School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne Switzerland, Swiss Institute of Bioinformatics Lausanne, Switzerland.

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http://dx.doi.org/10.3389/fgene.2014.00007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907712PMC
February 2014

Influenza virus drug resistance: a time-sampled population genetics perspective.

PLoS Genet 2014 Feb 27;10(2):e1004185. Epub 2014 Feb 27.

School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland ; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.pgen.1004185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937227PMC
February 2014

Shifting fitness landscapes in response to altered environments.

Evolution 2013 Dec 2;67(12):3512-22. Epub 2013 Aug 2.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1111/evo.12207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855258PMC
December 2013

The impact of equilibrium assumptions on tests of selection.

Front Genet 2013 11;4:235. Epub 2013 Nov 11.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School Worcester, MA, USA ; Swiss Institute of Bioinformatics Lausanne, Switzerland.

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http://dx.doi.org/10.3389/fgene.2013.00235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822286PMC
November 2013

Genomic variation and its impact on gene expression in Drosophila melanogaster.

PLoS Genet 2012 15;8(11):e1003055. Epub 2012 Nov 15.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.pgen.1003055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499359PMC
May 2013

Recurrent and recent selective sweeps in the piRNA pathway.

Evolution 2013 Apr 17;67(4):1081-90. Epub 2013 Jan 17.

Program in Bioinformatics & Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

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http://dx.doi.org/10.1111/evo.12011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992950PMC
April 2013

Inferences of demography and selection in an African population of Drosophila melanogaster.

Genetics 2013 Jan 26;193(1):215-28. Epub 2012 Oct 26.

Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA.

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http://dx.doi.org/10.1534/genetics.112.145318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527247PMC
January 2013

On detecting selective sweeps using single genomes.

Front Genet 2011 1;2:85. Epub 2011 Dec 1.

School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland.

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http://dx.doi.org/10.3389/fgene.2011.00085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268637PMC
October 2012

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

Mol Biol Evol 2012 Oct 21;29(10):3237-48. Epub 2012 May 21.

The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany.

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http://jensenlab.epfl.ch/files/content/sites/jensen-lab/file
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/mss136
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http://dx.doi.org/10.1093/molbev/mss136DOI Listing
October 2012

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

Evolution 2012 Oct 4;66(10):3209-23. Epub 2012 May 4.

Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2012.01669.xDOI Listing
October 2012

Recent progress in polymorphism-based population genetic inference.

J Hered 2012 Mar-Apr;103(2):287-96. Epub 2012 Jan 12.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.

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http://dx.doi.org/10.1093/jhered/esr128DOI Listing
June 2012

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

Genome Biol Evol 2011 24;3:687-701. Epub 2011 Jun 24.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1093/gbe/evr063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157839PMC
December 2011

On characterizing adaptive events unique to modern humans.

Genome Biol Evol 2011 29;3:791-8. Epub 2011 Jul 29.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, USA.

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http://jensenlab.epfl.ch/files/content/sites/jensen-lab/file
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http://gbe.oxfordjournals.org/content/3/791.full.pdf
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http://gbe.oxfordjournals.org/cgi/doi/10.1093/gbe/evr075
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http://dx.doi.org/10.1093/gbe/evr075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163466PMC
December 2011

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.

Nat Biotechnol 2011 Dec 11;30(1):105-11. Epub 2011 Dec 11.

CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China.

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http://dx.doi.org/10.1038/nbt.2050DOI Listing
December 2011

Experimental illumination of a fitness landscape.

Proc Natl Acad Sci U S A 2011 May 4;108(19):7896-901. Epub 2011 Apr 4.

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1016024108
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http://dx.doi.org/10.1073/pnas.1016024108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093508PMC
May 2011

Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants.

PLoS Pathog 2011 May 19;7(5):e1001344. Epub 2011 May 19.

Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098220PMC
May 2011

To pool, or not to pool?

Genetics 2010 Sep;186(1):41-3

Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30222, USA.

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http://dx.doi.org/10.1534/genetics.110.121012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940305PMC
September 2010

Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations.

Genetics 2010 Jul 20;185(3):907-22. Epub 2010 Apr 20.

Department of Biology II, Ludwig-Maximilians-University Munich, 82152 Planegg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907208PMC
July 2010

Population genetic inference from genomic sequence variation.

Genome Res 2010 Mar 12;20(3):291-300. Epub 2010 Jan 12.

Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.079509.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840988PMC
March 2010

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

Science 2009 Aug;325(5944):1095-8

Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1126/science.1175826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736094PMC
August 2009

Accelerated adaptive evolution on a newly formed X chromosome.

PLoS Biol 2009 Apr;7(4):e82

Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1371/journal.pbio.1000082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672600PMC
April 2009

An approximate bayesian estimator suggests strong, recurrent selective sweeps in Drosophila.

PLoS Genet 2008 Sep 19;4(9):e1000198. Epub 2008 Sep 19.

Section of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2529407PMC
September 2008

Inferring selection in partially sequenced regions.

Mol Biol Evol 2008 Feb 28;25(2):438-46. Epub 2007 Dec 28.

Department of Molecular Biology and Genetics, Cornell University, USA.

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http://dx.doi.org/10.1093/molbev/msm273DOI Listing
February 2008

Approaches for identifying targets of positive selection.

Trends Genet 2007 Nov 23;23(11):568-77. Epub 2007 Oct 23.

Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.tig.2007.08.009DOI Listing
November 2007

Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster.

BMC Evol Biol 2007 Oct 25;7:202. Epub 2007 Oct 25.

Department of Biological Sciences, Stanford University, Stanford, CA 94305 USA.

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http://dx.doi.org/10.1186/1471-2148-7-202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2164965PMC
October 2007

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

Genetics 2007 Aug 11;176(4):2371-9. Epub 2007 Jun 11.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.

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August 2007

Phylogenetic incongruence in the Drosophila melanogaster species group.

Mol Phylogenet Evol 2007 Jun 9;43(3):1138-50. Epub 2006 Sep 9.

Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1016/j.ympev.2006.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2041876PMC
June 2007

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

Genetics 2007 Feb 16;175(2):737-50. Epub 2006 Nov 16.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1534/genetics.106.064642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800626PMC
February 2007

Distinguishing between selective sweeps and demography using DNA polymorphism data.

Genetics 2005 Jul 23;170(3):1401-10. Epub 2005 May 23.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.104.038224
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1451184PMC
July 2005