Carlos D Bustamante

Carlos D Bustamante

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Carlos D Bustamante

Carlos D Bustamante

Publications by authors named "Carlos D Bustamante"

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Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis.

Genet Med 2019 09 24;21(9):2126-2134. Epub 2019 Jan 24.

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

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http://www.nature.com/articles/s41436-019-0439-8
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http://dx.doi.org/10.1038/s41436-019-0439-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752318PMC
September 2019

The inference of sex-biased human demography from whole-genome data.

PLoS Genet 2019 Sep 20;15(9):e1008293. Epub 2019 Sep 20.

Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

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http://dx.doi.org/10.1371/journal.pgen.1008293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6774570PMC
September 2019

Genetic analyses of diverse populations improves discovery for complex traits.

Nature 2019 Jun 19;570(7762):514-518. Epub 2019 Jun 19.

Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.1038/s41586-019-1310-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6785182PMC
June 2019

Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue.

J Mol Diagn 2019 May 31;21(3):375-383. Epub 2018 Dec 31.

Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15251578183017
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http://dx.doi.org/10.1016/j.jmoldx.2018.11.003DOI Listing
May 2019

A genetic counseling needs assessment of Mexico.

Mol Genet Genomic Med 2019 05 1;7(5):e668. Epub 2019 Apr 1.

Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California.

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https://onlinelibrary.wiley.com/doi/abs/10.1002/mgg3.668
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http://dx.doi.org/10.1002/mgg3.668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503023PMC
May 2019

An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos.

J Allergy Clin Immunol 2019 Mar 7;143(3):957-969. Epub 2018 Sep 7.

Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif; Department of Medicine, University of California, San Francisco, San Francisco, Calif.

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https://linkinghub.elsevier.com/retrieve/pii/S00916749183127
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http://dx.doi.org/10.1016/j.jaci.2016.08.057DOI Listing
March 2019

Rapid evolution of a skin-lightening allele in southern African KhoeSan.

Proc Natl Acad Sci U S A 2018 12 10;115(52):13324-13329. Epub 2018 Dec 10.

Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY 11794;

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http://dx.doi.org/10.1073/pnas.1801948115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310813PMC
December 2018

Polygenic risk scores: a biased prediction?

Genome Med 2018 12 27;10(1):100. Epub 2018 Dec 27.

Department of Biomedical Data Science, Stanford University School of Medicine, Campus Drive, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1186/s13073-018-0610-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309089PMC
December 2018

DeepTag: inferring diagnoses from veterinary clinical notes.

NPJ Digit Med 2018 24;1:60. Epub 2018 Oct 24.

1Department of Biomedical Data Science, Stanford University, Stanford, CA 94305 USA.

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http://dx.doi.org/10.1038/s41746-018-0067-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6550285PMC
October 2018

Population structure in Argentina.

PLoS One 2018 1;13(5):e0196325. Epub 2018 May 1.

Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196325PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5929549PMC
August 2018

Network enhancement as a general method to denoise weighted biological networks.

Nat Commun 2018 08 6;9(1):3108. Epub 2018 Aug 6.

Department of Computer Science, Stanford University, 353 Serra Mall, Stanford, 94305, CA, USA.

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http://dx.doi.org/10.1038/s41467-018-05469-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078978PMC
August 2018

In-solution Y-chromosome capture-enrichment on ancient DNA libraries.

BMC Genomics 2018 Aug 14;19(1):608. Epub 2018 Aug 14.

International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.

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http://dx.doi.org/10.1186/s12864-018-4945-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092841PMC
August 2018

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.

Lancet Oncol 2018 06 9;19(6):785-798. Epub 2018 May 9.

Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany; Hopp Children's Cancer Center at the NCT Heidelberg, Heidelberg, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S14702045183024
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http://dx.doi.org/10.1016/S1470-2045(18)30242-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984248PMC
June 2018

Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate.

Genome 2018 Apr 21;61(4):241-247. Epub 2017 Dec 21.

a School of Biological Sciences and Center for Reproductive Biology, Washington State University, 100 Dairy Road, Pullman, WA 99164, USA.

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http://dx.doi.org/10.1139/gen-2017-0188DOI Listing
April 2018

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia.

Genome Res 2018 04 22;28(4):423-431. Epub 2018 Mar 22.

Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.223693.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880234PMC
April 2018

Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars.

Cell 2017 Oct;171(2):427-439.e21

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.08.016DOI Listing
October 2017

Identification of a Novel Somatic Mutation Leading to Allele Dropout for EGFR L858R Genotyping in Non-Small Cell Lung Cancer.

Mol Diagn Ther 2017 08;21(4):431-436

Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.

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http://dx.doi.org/10.1007/s40291-017-0275-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5511778PMC
August 2017

A novel splice mutation within equine KIT and the W15 allele in the homozygous state lead to all white coat color phenotypes.

Anim Genet 2017 Aug 5;48(4):497-498. Epub 2017 Apr 5.

Equine Genetics, Etalon Inc., Menlo Park, CA, 94025, USA.

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http://dx.doi.org/10.1111/age.12554DOI Listing
August 2017

Patterns of genomic and phenomic diversity in wine and table grapes.

Hortic Res 2017 2;4:17035. Epub 2017 Aug 2.

Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada.

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http://dx.doi.org/10.1038/hortres.2017.35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5539807PMC
August 2017

Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations.

Am J Hum Genet 2017 Apr 30;100(4):635-649. Epub 2017 Mar 30.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center of Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384097PMC
April 2017

Population-specific single-nucleotide polymorphism confers increased risk of venous thromboembolism in African Americans.

Mol Genet Genomic Med 2016 Sep 21;4(5):513-20. Epub 2016 Jun 21.

Department of GeneticsStanford University School of MedicineStanfordCalifornia94305; Department of BioengineeringStanford University School of MedicineStanfordCalifornia94305.

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http://dx.doi.org/10.1002/mgg3.226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5023936PMC
September 2016

Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation.

Proc Natl Acad Sci U S A 2016 06 31;113(24):6701-6. Epub 2016 May 31.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305; Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1606950113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914177PMC
June 2016

Efficient analysis of large datasets and sex bias with ADMIXTURE.

BMC Bioinformatics 2016 May 23;17:218. Epub 2016 May 23.

Pacific Biosciences, Menlo Park, California, USA.

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http://dx.doi.org/10.1186/s12859-016-1082-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877806PMC
May 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

The Divergence of Neandertal and Modern Human Y Chromosomes.

Am J Hum Genet 2016 Apr;98(4):728-34

Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.02.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833433PMC
April 2016

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.

Am J Hum Genet 2016 Jan 31;98(1):216-24. Epub 2015 Dec 31.

Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.11.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716687PMC
January 2016

Privacy Risks from Genomic Data-Sharing Beacons.

Am J Hum Genet 2015 Nov 29;97(5):631-46. Epub 2015 Oct 29.

Department of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297150037
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http://dx.doi.org/10.1016/j.ajhg.2015.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667107PMC
November 2015

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Authors:
Maanasa Raghavan Matthias Steinrücken Kelley Harris Stephan Schiffels Simon Rasmussen Michael DeGiorgio Anders Albrechtsen Cristina Valdiosera María C Ávila-Arcos Anna-Sapfo Malaspinas Anders Eriksson Ida Moltke Mait Metspalu Julian R Homburger Jeff Wall Omar E Cornejo J Víctor Moreno-Mayar Thorfinn S Korneliussen Tracey Pierre Morten Rasmussen Paula F Campos Peter de Barros Damgaard Morten E Allentoft John Lindo Ene Metspalu Ricardo Rodríguez-Varela Josefina Mansilla Celeste Henrickson Andaine Seguin-Orlando Helena Malmström Thomas Stafford Suyash S Shringarpure Andrés Moreno-Estrada Monika Karmin Kristiina Tambets Anders Bergström Yali Xue Vera Warmuth Andrew D Friend Joy Singarayer Paul Valdes Francois Balloux Ilán Leboreiro Jose Luis Vera Hector Rangel-Villalobos Davide Pettener Donata Luiselli Loren G Davis Evelyne Heyer Christoph P E Zollikofer Marcia S Ponce de León Colin I Smith Vaughan Grimes Kelly-Anne Pike Michael Deal Benjamin T Fuller Bernardo Arriaza Vivien Standen Maria F Luz Francois Ricaut Niede Guidon Ludmila Osipova Mikhail I Voevoda Olga L Posukh Oleg Balanovsky Maria Lavryashina Yuri Bogunov Elza Khusnutdinova Marina Gubina Elena Balanovska Sardana Fedorova Sergey Litvinov Boris Malyarchuk Miroslava Derenko M J Mosher David Archer Jerome Cybulski Barbara Petzelt Joycelynn Mitchell Rosita Worl Paul J Norman Peter Parham Brian M Kemp Toomas Kivisild Chris Tyler-Smith Manjinder S Sandhu Michael Crawford Richard Villems David Glenn Smith Michael R Waters Ted Goebel John R Johnson Ripan S Malhi Mattias Jakobsson David J Meltzer Andrea Manica Richard Durbin Carlos D Bustamante Yun S Song Rasmus Nielsen Eske Willerslev

Science 2015 Aug 21;349(6250):aab3884. Epub 2015 Jul 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/10.1126/science.aab3884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733658PMC
August 2015

Estimating the mutation load in human genomes.

Nat Rev Genet 2015 Jun 12;16(6):333-43. Epub 2015 May 12.

McGill University, Department of Human Genetics and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, Quebec H3A 0G1, Canada.

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http://dx.doi.org/10.1038/nrg3931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959039PMC
June 2015

ClinGen--the Clinical Genome Resource.

N Engl J Med 2015 06 27;372(23):2235-42. Epub 2015 May 27.

From Harvard Medical School and Brigham and Women's Hospital and Partners HealthCare - all in Boston (H.L.R.); University of North Carolina, Chapel Hill (J.S.B., J.P.E.); National Human Genome Research Institute, National Institutes of Health (NIH) (L.D.B., E.M.R.), National Center for Biotechnology Information, National Library of Medicine, NIH (M.J.L., D.R.M., S.T.S.), and American College of Medical Genetics and Genomics (M.S.W.) - all in Bethesda, MD; Stanford University School of Medicine, Stanford (C.D.B.), and University of California, San Francisco, San Francisco (R.L.N.) - both in California; Geisinger Health System, Danville, PA (D.H.L., C.L.M.); and Baylor College of Medicine, Houston (S.E.P.).

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http://dx.doi.org/10.1056/NEJMsr1406261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474187PMC
June 2015

Beyond the reference genome.

Nat Biotechnol 2015 Jun;33(6):605-6

Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/nbt.3249DOI Listing
June 2015

Imputation-based assessment of next generation rare exome variant arrays.

Pac Symp Biocomput 2014 :241-52

Department of Genetics & Biomedical Informatics Training Program, Stanford University, Stanford, CA, 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3900244PMC
August 2014

Genetic recombination is targeted towards gene promoter regions in dogs.

PLoS Genet 2013 12;9(12):e1003984. Epub 2013 Dec 12.

Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003984DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861134PMC
August 2014

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.

Nat Commun 2014 Aug 12;5:4611. Epub 2014 Aug 12.

1] Department of Entomology, Ohio State University, 300 Aronoff Laboratory, 318W. 12th Avenue, Columbus, Ohio 43210, USA [2] Department of Evolution, Ecology and Organismal Biology, Ohio State University, 300 Aronoff Laboratory, 318W. 12th Avenue, Columbus, Ohio 43210, USA.

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http://dx.doi.org/10.1038/ncomms5611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164542PMC
August 2014

IQCB1 and PDE6B mutations cause similar early onset retinal degenerations in two closely related terrier dog breeds.

Invest Ophthalmol Vis Sci 2013 Oct 25;54(10):7005-19. Epub 2013 Oct 25.

Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York.

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http://dx.doi.org/10.1167/iovs.13-12915DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3809947PMC
October 2013

RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference.

Am J Hum Genet 2013 Aug 1;93(2):278-88. Epub 2013 Aug 1.

Department of Genetics, Stanford University, Stanford, CA 94305, USA; Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1016/j.ajhg.2013.06.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738819PMC
August 2013

Gene flow from North Africa contributes to differential human genetic diversity in southern Europe.

Proc Natl Acad Sci U S A 2013 Jul 3;110(29):11791-6. Epub 2013 Jun 3.

Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1073/pnas.1306223110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3718088PMC
July 2013

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

A tale of two haplotypes: the EDA2R/AR Intergenic region is the most divergent genomic segment between Africans and East Asians in the human genome.

Hum Biol 2012 Dec;84(6):641-94

Department of Genetics, Stanford University, Mail Stop 5120, Stanford, California 94305, USA.

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http://dx.doi.org/10.3378/027.084.0604DOI Listing
December 2012