Stephen F Schaffner

Stephen F Schaffner

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Stephen F Schaffner

Publications by authors named "Stephen F Schaffner"

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Development of a SNP barcode to genotype Babesia microti infections.

PLoS Negl Trop Dis 2019 03 25;13(3):e0007194. Epub 2019 Mar 25.

Broad Institute, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pntd.0007194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448979PMC
March 2019

Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018.

N Engl J Med 2018 11 17;379(18):1745-1753. Epub 2018 Oct 17.

From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.).

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http://dx.doi.org/10.1056/NEJMoa1804498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181183PMC
November 2018

hmmIBD: software to infer pairwise identity by descent between haploid genotypes.

Malar J 2018 May 15;17(1):196. Epub 2018 May 15.

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

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https://malariajournal.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12936-018-2349-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952413PMC
May 2018

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent.

PLoS Genet 2017 Oct 27;13(10):e1007065. Epub 2017 Oct 27.

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5678785PMC
October 2017

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Nature 2017 06 24;546(7658):401-405. Epub 2017 May 24.

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature22400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536180PMC
June 2017

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Nature 2017 04 12;544(7650):309-315. Epub 2017 Apr 12.

Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.

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http://dx.doi.org/10.1038/nature22040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712493PMC
April 2017

Genomic Analysis of Viral Outbreaks.

Annu Rev Virol 2016 09 3;3(1):173-195. Epub 2016 Aug 3.

FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138.

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http://dx.doi.org/10.1146/annurev-virology-110615-035747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210220PMC
September 2016

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.

Cell 2016 Jun;165(6):1519-1529

Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.04.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4957403PMC
June 2016

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

Cell 2015 Aug;162(4):738-50

FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://www.cell.com/cell/pdf/S0092-8674(15)00897-1.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S009286741500897
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http://dx.doi.org/10.1016/j.cell.2015.07.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537774PMC
August 2015

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Cell 2015 Jun;161(7):1516-26

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4503805PMC
June 2015

Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections.

PLoS Negl Trop Dis 2015 Mar 17;9(3):e0003539. Epub 2015 Mar 17.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America; Broad Institute, Cambridge, Massachusetts, United States of America; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pntd.0003539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362761PMC
March 2015

Data sharing: Make outbreak research open access.

Nature 2015 Feb;518(7540):477-9

Broad Institute and Harvard University in Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/518477aDOI Listing
February 2015

Cosi2: an efficient simulator of exact and approximate coalescent with selection.

Bioinformatics 2014 Dec 22;30(23):3427-9. Epub 2014 Aug 22.

Broad Institute of MIT and Harvard, MA 02142 and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296154PMC
December 2014

Epidemiology. Emerging disease or diagnosis?

Science 2012 Nov;338(6108):750-2

Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.

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http://dx.doi.org/10.1126/science.1225893DOI Listing
November 2012

Harnessing genomics and genome biology to understand malaria biology.

Nat Rev Genet 2012 Apr 12;13(5):315-28. Epub 2012 Apr 12.

Department of Immunology and Infectious Disease, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nrg3187DOI Listing
April 2012

Integrating common and rare genetic variation in diverse human populations.

Nature 2010 Sep;467(7311):52-8

Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nature09298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173859PMC
September 2010

A composite of multiple signals distinguishes causal variants in regions of positive selection.

Science 2010 Feb 7;327(5967):883-6. Epub 2010 Jan 7.

Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1126/science.1183863DOI Listing
February 2010

A second generation human haplotype map of over 3.1 million SNPs.

Authors:
Kelly A Frazer Dennis G Ballinger David R Cox David A Hinds Laura L Stuve Richard A Gibbs John W Belmont Andrew Boudreau Paul Hardenbol Suzanne M Leal Shiran Pasternak David A Wheeler Thomas D Willis Fuli Yu Huanming Yang Changqing Zeng Yang Gao Haoran Hu Weitao Hu Chaohua Li Wei Lin Siqi Liu Hao Pan Xiaoli Tang Jian Wang Wei Wang Jun Yu Bo Zhang Qingrun Zhang Hongbin Zhao Hui Zhao Jun Zhou Stacey B Gabriel Rachel Barry Brendan Blumenstiel Amy Camargo Matthew Defelice Maura Faggart Mary Goyette Supriya Gupta Jamie Moore Huy Nguyen Robert C Onofrio Melissa Parkin Jessica Roy Erich Stahl Ellen Winchester Liuda Ziaugra David Altshuler Yan Shen Zhijian Yao Wei Huang Xun Chu Yungang He Li Jin Yangfan Liu Yayun Shen Weiwei Sun Haifeng Wang Yi Wang Ying Wang Xiaoyan Xiong Liang Xu Mary M Y Waye Stephen K W Tsui Hong Xue J Tze-Fei Wong Luana M Galver Jian-Bing Fan Kevin Gunderson Sarah S Murray Arnold R Oliphant Mark S Chee Alexandre Montpetit Fanny Chagnon Vincent Ferretti Martin Leboeuf Jean-François Olivier Michael S Phillips Stéphanie Roumy Clémentine Sallée Andrei Verner Thomas J Hudson Pui-Yan Kwok Dongmei Cai Daniel C Koboldt Raymond D Miller Ludmila Pawlikowska Patricia Taillon-Miller Ming Xiao Lap-Chee Tsui William Mak You Qiang Song Paul K H Tam Yusuke Nakamura Takahisa Kawaguchi Takuya Kitamoto Takashi Morizono Atsushi Nagashima Yozo Ohnishi Akihiro Sekine Toshihiro Tanaka Tatsuhiko Tsunoda Panos Deloukas Christine P Bird Marcos Delgado Emmanouil T Dermitzakis Rhian Gwilliam Sarah Hunt Jonathan Morrison Don Powell Barbara E Stranger Pamela Whittaker David R Bentley Mark J Daly Paul I W de Bakker Jeff Barrett Yves R Chretien Julian Maller Steve McCarroll Nick Patterson Itsik Pe'er Alkes Price Shaun Purcell Daniel J Richter Pardis Sabeti Richa Saxena Stephen F Schaffner Pak C Sham Patrick Varilly David Altshuler Lincoln D Stein Lalitha Krishnan Albert Vernon Smith Marcela K Tello-Ruiz Gudmundur A Thorisson Aravinda Chakravarti Peter E Chen David J Cutler Carl S Kashuk Shin Lin Gonçalo R Abecasis Weihua Guan Yun Li Heather M Munro Zhaohui Steve Qin Daryl J Thomas Gilean McVean Adam Auton Leonardo Bottolo Niall Cardin Susana Eyheramendy Colin Freeman Jonathan Marchini Simon Myers Chris Spencer Matthew Stephens Peter Donnelly Lon R Cardon Geraldine Clarke David M Evans Andrew P Morris Bruce S Weir Tatsuhiko Tsunoda James C Mullikin Stephen T Sherry Michael Feolo Andrew Skol Houcan Zhang Changqing Zeng Hui Zhao Ichiro Matsuda Yoshimitsu Fukushima Darryl R Macer Eiko Suda Charles N Rotimi Clement A Adebamowo Ike Ajayi Toyin Aniagwu Patricia A Marshall Chibuzor Nkwodimmah Charmaine D M Royal Mark F Leppert Missy Dixon Andy Peiffer Renzong Qiu Alastair Kent Kazuto Kato Norio Niikawa Isaac F Adewole Bartha M Knoppers Morris W Foster Ellen Wright Clayton Jessica Watkin Richard A Gibbs John W Belmont Donna Muzny Lynne Nazareth Erica Sodergren George M Weinstock David A Wheeler Imtaz Yakub Stacey B Gabriel Robert C Onofrio Daniel J Richter Liuda Ziaugra Bruce W Birren Mark J Daly David Altshuler Richard K Wilson Lucinda L Fulton Jane Rogers John Burton Nigel P Carter Christopher M Clee Mark Griffiths Matthew C Jones Kirsten McLay Robert W Plumb Mark T Ross Sarah K Sims David L Willey Zhu Chen Hua Han Le Kang Martin Godbout John C Wallenburg Paul L'Archevêque Guy Bellemare Koji Saeki Hongguang Wang Daochang An Hongbo Fu Qing Li Zhen Wang Renwu Wang Arthur L Holden Lisa D Brooks Jean E McEwen Mark S Guyer Vivian Ota Wang Jane L Peterson Michael Shi Jack Spiegel Lawrence M Sung Lynn F Zacharia Francis S Collins Karen Kennedy Ruth Jamieson John Stewart

Nature 2007 Oct;449(7164):851-61

The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA.

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https://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/In
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http://www.nature.com/doifinder/10.1038/nature06258
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http://dx.doi.org/10.1038/nature06258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689609PMC
October 2007

Genome-wide detection and characterization of positive selection in human populations.

Authors:
Pardis C Sabeti Patrick Varilly Ben Fry Jason Lohmueller Elizabeth Hostetter Chris Cotsapas Xiaohui Xie Elizabeth H Byrne Steven A McCarroll Rachelle Gaudet Stephen F Schaffner Eric S Lander Kelly A Frazer Dennis G Ballinger David R Cox David A Hinds Laura L Stuve Richard A Gibbs John W Belmont Andrew Boudreau Paul Hardenbol Suzanne M Leal Shiran Pasternak David A Wheeler Thomas D Willis Fuli Yu Huanming Yang Changqing Zeng Yang Gao Haoran Hu Weitao Hu Chaohua Li Wei Lin Siqi Liu Hao Pan Xiaoli Tang Jian Wang Wei Wang Jun Yu Bo Zhang Qingrun Zhang Hongbin Zhao Hui Zhao Jun Zhou Stacey B Gabriel Rachel Barry Brendan Blumenstiel Amy Camargo Matthew Defelice Maura Faggart Mary Goyette Supriya Gupta Jamie Moore Huy Nguyen Robert C Onofrio Melissa Parkin Jessica Roy Erich Stahl Ellen Winchester Liuda Ziaugra David Altshuler Yan Shen Zhijian Yao Wei Huang Xun Chu Yungang He Li Jin Yangfan Liu Yayun Shen Weiwei Sun Haifeng Wang Yi Wang Ying Wang Xiaoyan Xiong Liang Xu Mary M Y Waye Stephen K W Tsui Hong Xue J Tze-Fei Wong Luana M Galver Jian-Bing Fan Kevin Gunderson Sarah S Murray Arnold R Oliphant Mark S Chee Alexandre Montpetit Fanny Chagnon Vincent Ferretti Martin Leboeuf Jean-François Olivier Michael S Phillips Stéphanie Roumy Clémentine Sallée Andrei Verner Thomas J Hudson Pui-Yan Kwok Dongmei Cai Daniel C Koboldt Raymond D Miller Ludmila Pawlikowska Patricia Taillon-Miller Ming Xiao Lap-Chee Tsui William Mak You Qiang Song Paul K H Tam Yusuke Nakamura Takahisa Kawaguchi Takuya Kitamoto Takashi Morizono Atsushi Nagashima Yozo Ohnishi Akihiro Sekine Toshihiro Tanaka Tatsuhiko Tsunoda Panos Deloukas Christine P Bird Marcos Delgado Emmanouil T Dermitzakis Rhian Gwilliam Sarah Hunt Jonathan Morrison Don Powell Barbara E Stranger Pamela Whittaker David R Bentley Mark J Daly Paul I W de Bakker Jeff Barrett Yves R Chretien Julian Maller Steve McCarroll Nick Patterson Itsik Pe'er Alkes Price Shaun Purcell Daniel J Richter Pardis Sabeti Richa Saxena Stephen F Schaffner Pak C Sham Patrick Varilly David Altshuler Lincoln D Stein Lalitha Krishnan Albert Vernon Smith Marcela K Tello-Ruiz Gudmundur A Thorisson Aravinda Chakravarti Peter E Chen David J Cutler Carl S Kashuk Shin Lin Gonçalo R Abecasis Weihua Guan Yun Li Heather M Munro Zhaohui Steve Qin Daryl J Thomas Gilean McVean Adam Auton Leonardo Bottolo Niall Cardin Susana Eyheramendy Colin Freeman Jonathan Marchini Simon Myers Chris Spencer Matthew Stephens Peter Donnelly Lon R Cardon Geraldine Clarke David M Evans Andrew P Morris Bruce S Weir Tatsuhiko Tsunoda Todd A Johnson James C Mullikin Stephen T Sherry Michael Feolo Andrew Skol Houcan Zhang Changqing Zeng Hui Zhao Ichiro Matsuda Yoshimitsu Fukushima Darryl R Macer Eiko Suda Charles N Rotimi Clement A Adebamowo Ike Ajayi Toyin Aniagwu Patricia A Marshall Chibuzor Nkwodimmah Charmaine D M Royal Mark F Leppert Missy Dixon Andy Peiffer Renzong Qiu Alastair Kent Kazuto Kato Norio Niikawa Isaac F Adewole Bartha M Knoppers Morris W Foster Ellen Wright Clayton Jessica Watkin Richard A Gibbs John W Belmont Donna Muzny Lynne Nazareth Erica Sodergren George M Weinstock David A Wheeler Imtaz Yakub Stacey B Gabriel Robert C Onofrio Daniel J Richter Liuda Ziaugra Bruce W Birren Mark J Daly David Altshuler Richard K Wilson Lucinda L Fulton Jane Rogers John Burton Nigel P Carter Christopher M Clee Mark Griffiths Matthew C Jones Kirsten McLay Robert W Plumb Mark T Ross Sarah K Sims David L Willey Zhu Chen Hua Han Le Kang Martin Godbout John C Wallenburg Paul L'Archevêque Guy Bellemare Koji Saeki Hongguang Wang Daochang An Hongbo Fu Qing Li Zhen Wang Renwu Wang Arthur L Holden Lisa D Brooks Jean E McEwen Mark S Guyer Vivian Ota Wang Jane L Peterson Michael Shi Jack Spiegel Lawrence M Sung Lynn F Zacharia Francis S Collins Karen Kennedy Ruth Jamieson John Stewart

Nature 2007 Oct;449(7164):913-8

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA.

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https://www.genome.gov/Pages/Newsroom/CurrentNewsReleases/Le
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http://www.nature.com/doifinder/10.1038/nature06250
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http://dx.doi.org/10.1038/nature06250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687721PMC
October 2007

Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens".

Science 2007 Apr;316(5823):370

Department of Genetics, Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

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http://dx.doi.org/10.1126/science.1137568DOI Listing
April 2007

Calibrating a coalescent simulation of human genome sequence variation.

Genome Res 2005 Nov;15(11):1576-83

Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.3709305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1310645PMC
November 2005

The X chromosome in population genetics.

Nat Rev Genet 2004 Jan;5(1):43-51

Whitehead/MIT Center for Genome Research, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nrg1247DOI Listing
January 2004

Human genome sequence variation and the influence of gene history, mutation and recombination.

Nat Genet 2002 Sep 5;32(1):135-42. Epub 2002 Aug 5.

Whitehead Institute/MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA.

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http://www.nature.com/articles/ng947z
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http://dx.doi.org/10.1038/ng947DOI Listing
September 2002