Graham Coop

Graham Coop

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Graham Coop

Graham Coop

Publications by authors named "Graham Coop"

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63Publications

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Donnelly (1983) and the limits of genetic genealogy.

Theor Popul Biol 2019 Aug 17. Epub 2019 Aug 17.

Center for Population Biology & Department of Evolution and Ecology, University of California, Davis, United States of America.

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http://dx.doi.org/10.1016/j.tpb.2019.08.002DOI Listing
August 2019

Population genomics perspectives on convergent adaptation.

Philos Trans R Soc Lond B Biol Sci 2019 Jul 3;374(1777):20180236. Epub 2019 Jun 3.

1 Center for Population Biology, University of California , Davis, CA 95616 , USA.

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http://dx.doi.org/10.1098/rstb.2018.0236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6560269PMC
July 2019

Detecting Adaptive Differentiation in Structured Populations with Genomic Data and Common Gardens.

Genetics 2019 03 24;211(3):989-1004. Epub 2019 Jan 24.

Department of Evolution and Ecology, University of California, Davis, California 95616.

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http://dx.doi.org/10.1534/genetics.118.301786DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404252PMC
March 2019

Allele frequency dynamics in a pedigreed natural population.

Proc Natl Acad Sci U S A 2019 02 31;116(6):2158-2164. Epub 2018 Dec 31.

Center for Population Biology, University of California, Davis, CA 95616.

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http://dx.doi.org/10.1073/pnas.1813852116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369762PMC
February 2019

Reconstructing the History of Polygenic Scores Using Coalescent Trees.

Genetics 2019 01 2;211(1):235-262. Epub 2018 Nov 2.

Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California 95616

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http://dx.doi.org/10.1534/genetics.118.301687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325695PMC
January 2019

Inferring Continuous and Discrete Population Genetic Structure Across Space.

Genetics 2018 09 19;210(1):33-52. Epub 2018 Jul 19.

Institute of Ecology and Evolution, Departments of Mathematics and Biology, University of Oregon, Eugene, Oregon 97403.

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http://dx.doi.org/10.1534/genetics.118.301333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116973PMC
September 2018

Estimating Time to the Common Ancestor for a Beneficial Allele.

Mol Biol Evol 2018 04;35(4):1003-1017

Department of Ecology and Evolution, University of Chicago, Chicago, IL.

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http://dx.doi.org/10.1093/molbev/msy006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5888984PMC
April 2018

Distinguishing Among Modes of Convergent Adaptation Using Population Genomic Data.

Genetics 2017 12 18;207(4):1591-1619. Epub 2017 Oct 18.

Center for Population Biology, University of California, Davis, California 95616

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http://dx.doi.org/10.1534/genetics.117.300417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714468PMC
December 2017

Deconstructing isolation-by-distance: The genomic consequences of limited dispersal.

PLoS Genet 2017 Aug 3;13(8):e1006911. Epub 2017 Aug 3.

Cornell Laboratory of Ornithology, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5542401PMC
August 2017

Population-genomic inference of the strength and timing of selection against gene flow.

Proc Natl Acad Sci U S A 2017 07 20;114(27):7061-7066. Epub 2017 Jun 20.

Department of Evolution and Ecology, University of California, Davis, CA 95616.

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http://dx.doi.org/10.1073/pnas.1616755114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502586PMC
July 2017

Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.

Genetics 2017 03 20;205(3):1335-1351. Epub 2017 Jan 20.

Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria

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http://dx.doi.org/10.1534/genetics.116.196220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340342PMC
March 2017

The Strength of Selection against Neanderthal Introgression.

PLoS Genet 2016 Nov 8;12(11):e1006340. Epub 2016 Nov 8.

Center for Population Biology, University of California, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100956PMC
November 2016

A Genealogical Look at Shared Ancestry on the X Chromosome.

Genetics 2016 09 29;204(1):57-75. Epub 2016 Jun 29.

Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California 95616.

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http://dx.doi.org/10.1534/genetics.116.190041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012405PMC
September 2016

A Genomic Map of the Effects of Linked Selection in Drosophila.

PLoS Genet 2016 08 18;12(8):e1006130. Epub 2016 Aug 18.

Department of Biological Sciences, Columbia University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990265PMC
August 2016

A Spatial Framework for Understanding Population Structure and Admixture.

PLoS Genet 2016 Jan 15;12(1):e1005703. Epub 2016 Jan 15.

Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714911PMC
January 2016

Convergent Evolution During Local Adaptation to Patchy Landscapes.

PLoS Genet 2015 Nov 16;11(11):e1005630. Epub 2015 Nov 16.

Evolution and Ecology, University of California, Davis, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646681PMC
November 2015

A Coalescent Model for a Sweep of a Unique Standing Variant.

Genetics 2015 Oct 25;201(2):707-25. Epub 2015 Aug 25.

Center for Population Biology, University of California, Davis, California 95616 Department of Evolution and Ecology, University of California, Davis, California 95616

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http://dx.doi.org/10.1534/genetics.115.178962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596678PMC
October 2015

The Role of Standing Variation in Geographic Convergent Adaptation.

Am Nat 2015 Oct 8;186 Suppl 1:S5-23. Epub 2015 Sep 8.

Computational Biology and Bioinformatics, University of Southern California, Los Angeles, California 90089.

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http://biorxiv.org/content/biorxiv/early/2015/04/22/009803.f
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http://www.jstor.org/stable/info/10.1086/682948
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http://dx.doi.org/10.1086/682948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827716PMC
October 2015

The Spatial Mixing of Genomes in Secondary Contact Zones.

Genetics 2015 Sep 22;201(1):243-61. Epub 2015 Jul 22.

Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95616.

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http://dx.doi.org/10.1534/genetics.115.179838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4566267PMC
September 2015

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation.

Evolution 2015 Jun 9;69(6):1406-1422. Epub 2015 Jun 9.

Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California.

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http://dx.doi.org/10.1111/evo.12674DOI Listing
June 2015

Sperm should evolve to make female meiosis fair.

Evolution 2015 Apr 23;69(4):1004-14. Epub 2015 Mar 23.

Department of Plant Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota 55108.

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http://dx.doi.org/10.1111/evo.12621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5539998PMC
April 2015

A population genetic signal of polygenic adaptation.

PLoS Genet 2014 Aug 7;10(8):e1004412. Epub 2014 Aug 7.

Center for Population Biology, University of California, Davis, Davis, California, United States of America; Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125079PMC
August 2014

Speciation and introgression between Mimulus nasutus and Mimulus guttatus.

PLoS Genet 2014 Jun 26;10(6):e1004410. Epub 2014 Jun 26.

Department of Genetics, University of Georgia, Athens, Georgia, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072524PMC
June 2014

Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella.

PLoS Genet 2013 12;9(9):e1003754. Epub 2013 Sep 12.

Department of Evolution and Ecology & Center for Population Biology, University of California - Davis, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772084PMC
March 2014

The geography of recent genetic ancestry across Europe.

PLoS Biol 2013 7;11(5):e1001555. Epub 2013 May 7.

Department of Evolution and Ecology & Center for Population Biology, University of California, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1001555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646727PMC
January 2014

Disentangling the effects of geographic and ecological isolation on genetic differentiation.

Evolution 2013 Nov 24;67(11):3258-73. Epub 2013 Jul 24.

Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, California, 95616.

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http://dx.doi.org/10.1111/evo.12193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808528PMC
November 2013

Robust identification of local adaptation from allele frequencies.

Genetics 2013 Sep 2;195(1):205-20. Epub 2013 Jul 2.

Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.

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http://dx.doi.org/10.1534/genetics.113.152462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3761302PMC
September 2013

Patterns of neutral diversity under general models of selective sweeps.

Genetics 2012 Sep 19;192(1):205-24. Epub 2012 Jun 19.

Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1534/genetics.112.141861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430537PMC
September 2012

Is your phylogeny informative? Measuring the power of comparative methods.

Evolution 2012 Jul 19;66(7):2240-51. Epub 2012 Feb 19.

Center for Population Biology, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2011.01574.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448289PMC
July 2012

Scrambling eggs: meiotic drive and the evolution of female recombination rates.

Genetics 2012 Feb 5;190(2):709-23. Epub 2011 Dec 5.

Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California 95616, USA.

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http://www.genetics.org/lookup/doi/10.1534/genetics.111.1367
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http://dx.doi.org/10.1534/genetics.111.136721DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276612PMC
February 2012

Variation in human recombination rates and its genetic determinants.

PLoS One 2011 17;6(6):e20321. Epub 2011 Jun 17.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020321PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117798PMC
November 2011

Parallel adaptation: one or many waves of advance of an advantageous allele?

Genetics 2010 Oct 26;186(2):647-68. Epub 2010 Jul 26.

Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1534/genetics.110.119594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954473PMC
October 2010

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae).

Mol Ecol 2010 Sep 13;19(17):3789-805. Epub 2010 Aug 13.

Section of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2010.04698.xDOI Listing
September 2010

Using environmental correlations to identify loci underlying local adaptation.

Genetics 2010 Aug 1;185(4):1411-23. Epub 2010 Jun 1.

Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, Calfornia 95616, USA.

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http://dx.doi.org/10.1534/genetics.110.114819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2927766PMC
August 2010

The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation.

Curr Biol 2010 Feb;20(4):R208-15

Department of Human Genetics, The University of Chicago, Room 507, 929 E. 58th St, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/j.cub.2009.11.055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994553PMC
February 2010

Expression quantitative trait loci detected in cell lines are often present in primary tissues.

Hum Mol Genet 2009 Nov 11;18(22):4296-303. Epub 2009 Aug 11.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/hmg/ddp382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766291PMC
November 2009

Broad-scale recombination patterns underlying proper disjunction in humans.

PLoS Genet 2009 Sep 18;5(9):e1000658. Epub 2009 Sep 18.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734982PMC
September 2009

No effect of recombination on the efficacy of natural selection in primates.

Genome Res 2008 Apr 16;18(4):544-54. Epub 2008 Jan 16.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.071548.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279242PMC
April 2008

High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans.

Science 2008 Mar 31;319(5868):1395-8. Epub 2008 Jan 31.

Department of Human Genetics, University of Chicago, 920 East 58th Street, Cummings Life Science Center, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1126/science.1151851DOI Listing
March 2008

Adaptations to climate in candidate genes for common metabolic disorders.

PLoS Genet 2008 Feb;4(2):e32

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0040032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242814PMC
February 2008

Adaptive drool in the gene pool.

Nat Genet 2007 Oct;39(10):1188-90

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http://dx.doi.org/10.1038/ng1007-1188DOI Listing
October 2007

Live hot, die young: transmission distortion in recombination hotspots.

PLoS Genet 2007 Mar 12;3(3):e35. Epub 2007 Jan 12.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.0030035
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http://dx.doi.org/10.1371/journal.pgen.0030035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1817654PMC
March 2007

An evolutionary view of human recombination.

Nat Rev Genet 2007 Jan 5;8(1):23-34. Epub 2006 Dec 5.

Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1038/nrg1947DOI Listing
January 2007

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome.

Nat Genet 2006 Nov 22;38(11):1251-60. Epub 2006 Oct 22.

Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1038/ng1911DOI Listing
November 2006

Sequencing and analysis of Neanderthal genomic DNA.

Science 2006 Nov;314(5802):1113-8

U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1126/science.1131412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583069PMC
November 2006

How reliable are empirical genomic scans for selective sweeps?

Genome Res 2006 Jun 10;16(6):702-12. Epub 2006 May 10.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.5105206
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http://dx.doi.org/10.1101/gr.5105206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473181PMC
June 2006

Spread of an inactive form of caspase-12 in humans is due to recent positive selection.

Am J Hum Genet 2006 Apr 21;78(4):659-70. Epub 2006 Feb 21.

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1086/503116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424700PMC
April 2006

Can a genome change its (hot)spots?

Authors:
Graham Coop

Trends Ecol Evol 2005 Dec 21;20(12):643-5. Epub 2005 Oct 21.

Department of Human Genetics, University of Chicago, 920 E 58th Street, CLSC 505, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/j.tree.2005.10.006DOI Listing
December 2005

The signature of positive selection on standing genetic variation.

Evolution 2005 Nov;59(11):2312-23

Department of Human Genetics, University of Chicago, Illinois 60637, USA.

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November 2005

The rise and fall of the chemoattractant receptor GPR33.

J Biol Chem 2005 Sep 29;280(35):31068-75. Epub 2005 Jun 29.

Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M503586200
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http://dx.doi.org/10.1074/jbc.M503586200DOI Listing
September 2005

SelSim: a program to simulate population genetic data with natural selection and recombination.

Bioinformatics 2004 Dec 22;20(18):3673-5. Epub 2004 Jul 22.

Department of Statistics, 1 South Parks Road, Oxford OX1 3TG, UK.

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http://dx.doi.org/10.1093/bioinformatics/bth417DOI Listing
December 2004

Darwinian selection on a selfing locus.

Science 2004 Dec;306(5704):2081-4

Department of Genetics, North Carolina State University, Box 7614, Raleigh, NC 27695, USA.

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http://dx.doi.org/10.1126/science.1103776DOI Listing
December 2004

Ancestral inference on gene trees under selection.

Theor Popul Biol 2004 Nov;66(3):219-32

Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S004058090400082
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http://dx.doi.org/10.1016/j.tpb.2004.06.006DOI Listing
November 2004