Publications by authors named "Jeffrey D Wall"

62Publications

A comparison of humans and baboons suggests germline mutation rates do not track cell divisions.

PLoS Biol 2020 08 17;18(8):e3000838. Epub 2020 Aug 17.

Department of Systems Biology, Columbia University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.3000838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7467331PMC
August 2020

Identification of African-Specific Admixture between Modern and Archaic Humans.

Am J Hum Genet 2019 12;105(6):1254-1261

Departments of Molecular Biology and Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080, USA; Division of Bioinformatics, MedGenome, Inc., Foster City, CA 94404, USA.

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http://dx.doi.org/10.1016/j.ajhg.2019.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904834PMC
December 2019

Evaluating the quality of the 1000 genomes project data.

BMC Genomics 2019 Aug 16;20(1):620. Epub 2019 Aug 16.

Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.

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http://dx.doi.org/10.1186/s12864-019-5957-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696682PMC
August 2019

Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony.

Genome Res 2019 05 29;29(5):848-856. Epub 2019 Mar 29.

Institute for Human Genetics, University of California, San Francisco, California 94143, USA.

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http://dx.doi.org/10.1101/gr.247122.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499309PMC
May 2019

Whole-Genome Analysis of Introgression Between the Spotted Owl and Barred Owl ( and , Respectively; Aves: Strigidae) in Western North America.

G3 (Bethesda) 2018 12 10;8(12):3945-3952. Epub 2018 Dec 10.

Institute for Human Genetics, University of California San Francisco, San Francisco, California,

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http://dx.doi.org/10.1534/g3.118.200754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288836PMC
December 2018

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing.

Authors:
Jeffrey D Wall

Am J Hum Genet 2017 May;100(5):766-772

Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420348PMC
May 2017

Archaic admixture in human history.

Curr Opin Genet Dev 2016 Dec 20;41:93-97. Epub 2016 Sep 20.

Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, United States; Department of Integrative Biology, University of California, Berkeley, Valley Life Sciences Building, Berkeley, CA 94720, United States.

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https://linkinghub.elsevier.com/retrieve/pii/S0959437X163009
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http://dx.doi.org/10.1016/j.gde.2016.07.002DOI Listing
December 2016

A genomic history of Aboriginal Australia.

Nature 2016 Oct 21;538(7624):207-214. Epub 2016 Sep 21.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

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http://dx.doi.org/10.1038/nature18299DOI Listing
October 2016

Genomic analyses inform on migration events during the peopling of Eurasia.

Authors:
Luca Pagani Daniel John Lawson Evelyn Jagoda Alexander Mörseburg Anders Eriksson Mario Mitt Florian Clemente Georgi Hudjashov Michael DeGiorgio Lauri Saag Jeffrey D Wall Alexia Cardona Reedik Mägi Melissa A Wilson Sayres Sarah Kaewert Charlotte Inchley Christiana L Scheib Mari Järve Monika Karmin Guy S Jacobs Tiago Antao Florin Mircea Iliescu Alena Kushniarevich Qasim Ayub Chris Tyler-Smith Yali Xue Bayazit Yunusbayev Kristiina Tambets Chandana Basu Mallick Lehti Saag Elvira Pocheshkhova George Andriadze Craig Muller Michael C Westaway David M Lambert Grigor Zoraqi Shahlo Turdikulova Dilbar Dalimova Zhaxylyk Sabitov Gazi Nurun Nahar Sultana Joseph Lachance Sarah Tishkoff Kuvat Momynaliev Jainagul Isakova Larisa D Damba Marina Gubina Pagbajabyn Nymadawa Irina Evseeva Lubov Atramentova Olga Utevska François-Xavier Ricaut Nicolas Brucato Herawati Sudoyo Thierry Letellier Murray P Cox Nikolay A Barashkov Vedrana Skaro Lejla Mulahasanovic Dragan Primorac Hovhannes Sahakyan Maru Mormina Christina A Eichstaedt Daria V Lichman Syafiq Abdullah Gyaneshwer Chaubey Joseph T S Wee Evelin Mihailov Alexandra Karunas Sergei Litvinov Rita Khusainova Natalya Ekomasova Vita Akhmetova Irina Khidiyatova Damir Marjanović Levon Yepiskoposyan Doron M Behar Elena Balanovska Andres Metspalu Miroslava Derenko Boris Malyarchuk Mikhail Voevoda Sardana A Fedorova Ludmila P Osipova Marta Mirazón Lahr Pascale Gerbault Matthew Leavesley Andrea Bamberg Migliano Michael Petraglia Oleg Balanovsky Elza K Khusnutdinova Ene Metspalu Mark G Thomas Andrea Manica Rasmus Nielsen Richard Villems Eske Willerslev Toomas Kivisild Mait Metspalu

Nature 2016 Oct 21;538(7624):238-242. Epub 2016 Sep 21.

Estonian Biocentre, Tartu, Estonia.

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http://dx.doi.org/10.1038/nature19792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164938PMC
October 2016

Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.

G3 (Bethesda) 2016 08 9;6(8):2265-71. Epub 2016 Aug 9.

Institute for Human Genetics, University of California, San Francisco, California 94143 Department of Biological Sciences, Auburn University, Alabama 36849.

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http://g3journal.org/lookup/doi/10.1534/g3.116.029587
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http://dx.doi.org/10.1534/g3.116.029587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978882PMC
August 2016

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples.

Genetics 2016 06 20;203(2):699-714. Epub 2016 Apr 20.

Department of Evolutionary Anthropology, Duke University, Durham, North Carolina Department of Biology, Duke University, Durham, North Carolina Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya Duke University Population Research Institute, Duke University, Durham, North Carolina 27708

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http://dx.doi.org/10.1534/genetics.116.187492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896188PMC
June 2016

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.

Genome Res 2016 Mar 17;26(3):291-300. Epub 2016 Feb 17.

Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA;

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http://dx.doi.org/10.1101/gr.196634.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772012PMC
March 2016

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection.

Genome Res 2016 Mar 17;26(3):279-90. Epub 2016 Feb 17.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA.

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http://dx.doi.org/10.1101/gr.192971.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772011PMC
March 2016

The Time Scale of Recombination Rate Evolution in Great Apes.

Mol Biol Evol 2016 Apr 15;33(4):928-45. Epub 2015 Dec 15.

Institute for Human Genetics, University of California San Francisco Department of Epidemiology & Biostatistics, University of California San Francisco

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http://dx.doi.org/10.1093/molbev/msv331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870646PMC
April 2016

Estimating genotype error rates from high-coverage next-generation sequence data.

Genome Res 2014 Nov 10;24(11):1734-9. Epub 2014 Oct 10.

Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, California 94143, USA; Kaiser Permanente Northern California Division of Research, Oakland, California 94612, USA.

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http://dx.doi.org/10.1101/gr.168393.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216915PMC
November 2014

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

Great ape genomics.

Authors:
Jeffrey D Wall

ILAR J 2013 ;54(2):82-90

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http://dx.doi.org/10.1093/ilar/ilt048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814392PMC
July 2014

Great ape genetic diversity and population history.

Nature 2013 Jul 3;499(7459):471-5. Epub 2013 Jul 3.

Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.

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http://dx.doi.org/10.1038/nature12228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822165PMC
July 2013

Higher levels of neanderthal ancestry in East Asians than in Europeans.

Genetics 2013 May 14;194(1):199-209. Epub 2013 Feb 14.

Institute for Human Genetics, University of California, San Francisco, California 94143, USA.

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http://dx.doi.org/10.1534/genetics.112.148213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632468PMC
May 2013

Function and regulation of AUTS2, a gene implicated in autism and human evolution.

PLoS Genet 2013 17;9(1):e1003221. Epub 2013 Jan 17.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547868PMC
May 2013

Incomplete lineage sorting is common in extant gibbon genera.

PLoS One 2013 14;8(1):e53682. Epub 2013 Jan 14.

Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053682PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544895PMC
July 2013

Paleopopulation genetics.

Annu Rev Genet 2012 17;46:635-49. Epub 2012 Sep 17.

Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94134, USA.

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http://dx.doi.org/10.1146/annurev-genet-110711-155557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5102055PMC
April 2013

Genetic evidence for archaic admixture in Africa.

Proc Natl Acad Sci U S A 2011 Sep 6;108(37):15123-8. Epub 2011 Sep 6.

Arizona Research Laboratories, Division of Biotechnology, Department of Ecology and Evolutionary Biology, and Mathematics Department, University of Arizona, Tucson, AZ 85721, USA.

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http://dx.doi.org/10.1073/pnas.1109300108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174671PMC
September 2011

Patterns of genetic variation within and between Gibbon species.

Mol Biol Evol 2011 Aug 2;28(8):2211-8. Epub 2011 Mar 2.

Institute for Human Genetics, University of California San Francisco, CA, USA.

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http://dx.doi.org/10.1093/molbev/msr033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144381PMC
August 2011

Genetic variation in Native Americans, inferred from Latino SNP and resequencing data.

Mol Biol Evol 2011 Aug 2;28(8):2231-7. Epub 2011 Mar 2.

Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California San Francisco, CA, USA.

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http://dx.doi.org/10.1093/molbev/msr049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144384PMC
August 2011

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes.

Nat Genet 2010 Oct 29;42(10):830-1. Epub 2010 Aug 29.

Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USA.

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http://dx.doi.org/10.1038/ng.651DOI Listing
October 2010

Genomics through the lens of next-generation sequencing.

Genome Biol 2010 25;11(6):306. Epub 2010 Jun 25.

Gladstone Institute of Cardiovascular Disease, University of California San Francisco, 1650 Owens Street, San Francisco, CA 94158, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2010-11-6-306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911104PMC
November 2010

Detecting ancient admixture and estimating demographic parameters in multiple human populations.

Mol Biol Evol 2009 Aug 6;26(8):1823-7. Epub 2009 May 6.

Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California San Francisco, CA, USA.

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http://dx.doi.org/10.1093/molbev/msp096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734152PMC
August 2009

Fast and flexible simulation of DNA sequence data.

Genome Res 2009 Jan 24;19(1):136-42. Epub 2008 Nov 24.

Department of Preventive Medicine, University of Southern California, Los Angeles, California 90033, USA.

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http://dx.doi.org/10.1101/gr.083634.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612967PMC
January 2009

Sex-biased evolutionary forces shape genomic patterns of human diversity.

PLoS Genet 2008 Sep 26;4(9):e1000202. Epub 2008 Sep 26.

ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, USA.

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http://dx.plos.org/10.1371/journal.pgen.1000202
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http://dx.doi.org/10.1371/journal.pgen.1000202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538571PMC
September 2008

A novel DNA sequence database for analyzing human demographic history.

Genome Res 2008 Aug 20;18(8):1354-61. Epub 2008 May 20.

Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1101/gr.075630.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493425PMC
August 2008

Exploring population genetic models with recombination using efficient forward-time simulations.

Genetics 2008 Apr;178(4):2417-27

Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA.

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http://dx.doi.org/10.1534/genetics.107.085332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323826PMC
April 2008

Inconsistencies in Neanderthal genomic DNA sequences.

PLoS Genet 2007 Oct 28;3(10):1862-6. Epub 2007 Aug 28.

Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.

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http://dx.doi.org/10.1371/journal.pgen.0030175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2014787PMC
October 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

Archaic admixture in the human genome.

Curr Opin Genet Dev 2006 Dec 5;16(6):606-10. Epub 2006 Oct 5.

Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1016/j.gde.2006.09.006DOI Listing
December 2006

Estimating recombination rates from single-nucleotide polymorphisms using summary statistics.

Genetics 2006 Nov 15;174(3):1517-28. Epub 2006 Sep 15.

Molecular and Computational Biology and Biostatistics Division, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA.

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http://www.genetics.org/lookup/doi/10.1534/genetics.106.0607
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http://dx.doi.org/10.1534/genetics.106.060723DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1667054PMC
November 2006

Possible ancestral structure in human populations.

PLoS Genet 2006 Jul;2(7):e105

Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.

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https://dx.plos.org/10.1371/journal.pgen.0020105
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http://dx.doi.org/10.1371/journal.pgen.0020105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523253PMC
July 2006

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

Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana.

Genetics 2006 Apr 19;172(4):2441-8. Epub 2005 Nov 19.

Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-2910, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.104.040311
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http://dx.doi.org/10.1534/genetics.104.040311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456404PMC
April 2006

Estimating recombination rates using three-site likelihoods.

Authors:
Jeffrey D Wall

Genetics 2004 Jul;167(3):1461-73

Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.103.025742
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http://dx.doi.org/10.1534/genetics.103.025742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470930PMC
July 2004

Close look at gene conversion hot spots.

Authors:
Jeffrey D Wall

Nat Genet 2004 Feb;36(2):114-5

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http://dx.doi.org/10.1038/ng0204-114DOI Listing
February 2004

Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.

Genetics 2003 Nov;165(3):1289-305

Department of Zoology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462864PMC
November 2003

Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates.

Am J Hum Genet 2003 Dec 18;73(6):1330-40. Epub 2003 Nov 18.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180398PMC
http://dx.doi.org/10.1086/380311DOI Listing
December 2003

Assessing the performance of the haplotype block model of linkage disequilibrium.

Am J Hum Genet 2003 Sep 11;73(3):502-15. Epub 2003 Aug 11.

Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S000292970762014
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180676PMC
http://dx.doi.org/10.1086/378099DOI Listing
September 2003

Haplotype blocks and linkage disequilibrium in the human genome.

Nat Rev Genet 2003 Aug;4(8):587-97

Department of Human Genetics, The University of Chicago, 920 East 58th Street, CLSC 507, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1038/nrg1123DOI Listing
August 2003

Estimating ancestral population sizes and divergence times.

Authors:
Jeffrey D Wall

Genetics 2003 Jan;163(1):395-404

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462435PMC
January 2003

Testing models of selection and demography in Drosophila simulans.

Genetics 2002 Sep;162(1):203-16

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462246PMC
September 2002