Nick Patterson

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Extreme Polygenicity of Complex Traits Is Explained by Negative Selection.

Am J Hum Genet 2019 Jul 29. Epub 2019 Jul 29.

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.07.003DOI Listing
July 2019

Estimating cross-population genetic correlations of causal effect sizes.

Genet Epidemiol 2019 03 25;43(2):180-188. Epub 2018 Nov 25.

Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts.

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http://dx.doi.org/10.1002/gepi.22173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375794PMC
March 2019

The genomic history of the Iberian Peninsula over the past 8000 years.

Authors:
Iñigo Olalde Swapan Mallick Nick Patterson Nadin Rohland Vanessa Villalba-Mouco Marina Silva Katharina Dulias Ceiridwen J Edwards Francesca Gandini Maria Pala Pedro Soares Manuel Ferrando-Bernal Nicole Adamski Nasreen Broomandkhoshbacht Olivia Cheronet Brendan J Culleton Daniel Fernandes Ann Marie Lawson Matthew Mah Jonas Oppenheimer Kristin Stewardson Zhao Zhang Juan Manuel Jiménez Arenas Isidro Jorge Toro Moyano Domingo C Salazar-García Pere Castanyer Marta Santos Joaquim Tremoleda Marina Lozano Pablo García Borja Javier Fernández-Eraso José Antonio Mujika-Alustiza Cecilio Barroso Francisco J Bermúdez Enrique Viguera Mínguez Josep Burch Neus Coromina David Vivó Artur Cebrià Josep Maria Fullola Oreto García-Puchol Juan Ignacio Morales F Xavier Oms Tona Majó Josep Maria Vergès Antònia Díaz-Carvajal Imma Ollich-Castanyer F Javier López-Cachero Ana Maria Silva Carmen Alonso-Fernández Germán Delibes de Castro Javier Jiménez Echevarría Adolfo Moreno-Márquez Guillermo Pascual Berlanga Pablo Ramos-García José Ramos-Muñoz Eduardo Vijande Vila Gustau Aguilella Arzo Ángel Esparza Arroyo Katina T Lillios Jennifer Mack Javier Velasco-Vázquez Anna Waterman Luis Benítez de Lugo Enrich María Benito Sánchez Bibiana Agustí Ferran Codina Gabriel de Prado Almudena Estalrrich Álvaro Fernández Flores Clive Finlayson Geraldine Finlayson Stewart Finlayson Francisco Giles-Guzmán Antonio Rosas Virginia Barciela González Gabriel García Atiénzar Mauro S Hernández Pérez Armando Llanos Yolanda Carrión Marco Isabel Collado Beneyto David López-Serrano Mario Sanz Tormo António C Valera Concepción Blasco Corina Liesau Patricia Ríos Joan Daura María Jesús de Pedro Michó Agustín A Diez-Castillo Raúl Flores Fernández Joan Francès Farré Rafael Garrido-Pena Victor S Gonçalves Elisa Guerra-Doce Ana Mercedes Herrero-Corral Joaquim Juan-Cabanilles Daniel López-Reyes Sarah B McClure Marta Merino Pérez Arturo Oliver Foix Montserrat Sanz Borràs Ana Catarina Sousa Julio Manuel Vidal Encinas Douglas J Kennett Martin B Richards Kurt Werner Alt Wolfgang Haak Ron Pinhasi Carles Lalueza-Fox David Reich

Science 2019 03;363(6432):1230-1234

Department of Genetics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1126/science.aav4040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436108PMC
March 2019

Reconstructing the Deep Population History of Central and South America.

Cell 2018 11 8;175(5):1185-1197.e22. Epub 2018 Nov 8.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183138
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http://dx.doi.org/10.1016/j.cell.2018.10.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327247PMC
November 2018

No evidence for unknown archaic ancestry in South Asia.

Nat Genet 2018 05;50(5):632-633

Department of Genetics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41588-018-0097-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433599PMC
May 2018

The genomic history of southeastern Europe.

Authors:
Iain Mathieson Songül Alpaslan-Roodenberg Cosimo Posth Anna Szécsényi-Nagy Nadin Rohland Swapan Mallick Iñigo Olalde Nasreen Broomandkhoshbacht Francesca Candilio Olivia Cheronet Daniel Fernandes Matthew Ferry Beatriz Gamarra Gloria González Fortes Wolfgang Haak Eadaoin Harney Eppie Jones Denise Keating Ben Krause-Kyora Isil Kucukkalipci Megan Michel Alissa Mittnik Kathrin Nägele Mario Novak Jonas Oppenheimer Nick Patterson Saskia Pfrengle Kendra Sirak Kristin Stewardson Stefania Vai Stefan Alexandrov Kurt W Alt Radian Andreescu Dragana Antonović Abigail Ash Nadezhda Atanassova Krum Bacvarov Mende Balázs Gusztáv Hervé Bocherens Michael Bolus Adina Boroneanţ Yavor Boyadzhiev Alicja Budnik Josip Burmaz Stefan Chohadzhiev Nicholas J Conard Richard Cottiaux Maja Čuka Christophe Cupillard Dorothée G Drucker Nedko Elenski Michael Francken Borislava Galabova Georgi Ganetsovski Bernard Gély Tamás Hajdu Veneta Handzhyiska Katerina Harvati Thomas Higham Stanislav Iliev Ivor Janković Ivor Karavanić Douglas J Kennett Darko Komšo Alexandra Kozak Damian Labuda Martina Lari Catalin Lazar Maleen Leppek Krassimir Leshtakov Domenico Lo Vetro Dženi Los Ivaylo Lozanov Maria Malina Fabio Martini Kath McSweeney Harald Meller Marko Menđušić Pavel Mirea Vyacheslav Moiseyev Vanya Petrova T Douglas Price Angela Simalcsik Luca Sineo Mario Šlaus Vladimir Slavchev Petar Stanev Andrej Starović Tamás Szeniczey Sahra Talamo Maria Teschler-Nicola Corinne Thevenet Ivan Valchev Frédérique Valentin Sergey Vasilyev Fanica Veljanovska Svetlana Venelinova Elizaveta Veselovskaya Bence Viola Cristian Virag Joško Zaninović Steve Zäuner Philipp W Stockhammer Giulio Catalano Raiko Krauß David Caramelli Gunita Zariņa Bisserka Gaydarska Malcolm Lillie Alexey G Nikitin Inna Potekhina Anastasia Papathanasiou Dušan Borić Clive Bonsall Johannes Krause Ron Pinhasi David Reich

Nature 2018 03 21;555(7695):197-203. Epub 2018 Feb 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://www.nature.com/doifinder/10.1038/nature25778
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http://dx.doi.org/10.1038/nature25778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091220PMC
March 2018

The Beaker phenomenon and the genomic transformation of northwest Europe.

Authors:
Iñigo Olalde Selina Brace Morten E Allentoft Ian Armit Kristian Kristiansen Thomas Booth Nadin Rohland Swapan Mallick Anna Szécsényi-Nagy Alissa Mittnik Eveline Altena Mark Lipson Iosif Lazaridis Thomas K Harper Nick Patterson Nasreen Broomandkhoshbacht Yoan Diekmann Zuzana Faltyskova Daniel Fernandes Matthew Ferry Eadaoin Harney Peter de Knijff Megan Michel Jonas Oppenheimer Kristin Stewardson Alistair Barclay Kurt Werner Alt Corina Liesau Patricia Ríos Concepción Blasco Jorge Vega Miguel Roberto Menduiña García Azucena Avilés Fernández Eszter Bánffy Maria Bernabò-Brea David Billoin Clive Bonsall Laura Bonsall Tim Allen Lindsey Büster Sophie Carver Laura Castells Navarro Oliver E Craig Gordon T Cook Barry Cunliffe Anthony Denaire Kirsten Egging Dinwiddy Natasha Dodwell Michal Ernée Christopher Evans Milan Kuchařík Joan Francès Farré Chris Fowler Michiel Gazenbeek Rafael Garrido Pena María Haber-Uriarte Elżbieta Haduch Gill Hey Nick Jowett Timothy Knowles Ken Massy Saskia Pfrengle Philippe Lefranc Olivier Lemercier Arnaud Lefebvre César Heras Martínez Virginia Galera Olmo Ana Bastida Ramírez Joaquín Lomba Maurandi Tona Majó Jacqueline I McKinley Kathleen McSweeney Balázs Gusztáv Mende Alessandra Modi Gabriella Kulcsár Viktória Kiss András Czene Róbert Patay Anna Endrődi Kitti Köhler Tamás Hajdu Tamás Szeniczey János Dani Zsolt Bernert Maya Hoole Olivia Cheronet Denise Keating Petr Velemínský Miroslav Dobeš Francesca Candilio Fraser Brown Raúl Flores Fernández Ana-Mercedes Herrero-Corral Sebastiano Tusa Emiliano Carnieri Luigi Lentini Antonella Valenti Alessandro Zanini Clive Waddington Germán Delibes Elisa Guerra-Doce Benjamin Neil Marcus Brittain Mike Luke Richard Mortimer Jocelyne Desideri Marie Besse Günter Brücken Mirosław Furmanek Agata Hałuszko Maksym Mackiewicz Artur Rapiński Stephany Leach Ignacio Soriano Katina T Lillios João Luís Cardoso Michael Parker Pearson Piotr Włodarczak T Douglas Price Pilar Prieto Pierre-Jérôme Rey Roberto Risch Manuel A Rojo Guerra Aurore Schmitt Joël Serralongue Ana Maria Silva Václav Smrčka Luc Vergnaud João Zilhão David Caramelli Thomas Higham Mark G Thomas Douglas J Kennett Harry Fokkens Volker Heyd Alison Sheridan Karl-Göran Sjögren Philipp W Stockhammer Johannes Krause Ron Pinhasi Wolfgang Haak Ian Barnes Carles Lalueza-Fox David Reich

Nature 2018 03 21;555(7695):190-196. Epub 2018 Feb 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature25738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973796PMC
March 2018

Erratum: The Beaker phenomenon and the genomic transformation of northwest Europe.

Authors:
Iñigo Olalde Selina Brace Morten E Allentoft Ian Armit Kristian Kristiansen Thomas Booth Nadin Rohland Swapan Mallick Anna Szécsényi-Nagy Alissa Mittnik Eveline Altena Mark Lipson Iosif Lazaridis Thomas K Harper Nick Patterson Nasreen Broomandkhoshbacht Yoan Diekmann Zuzana Faltyskova Daniel Fernandes Matthew Ferry Eadaoin Harney Peter de Knijff Megan Michel Jonas Oppenheimer Kristin Stewardson Alistair Barclay Kurt Werner Alt Corina Liesau Patricia Ríos Concepción Blasco Jorge Vega Miguel Roberto Menduiña García Azucena Avilés Fernández Eszter Bánffy Maria Bernabò-Brea David Billoin Clive Bonsall Laura Bonsall Tim Allen Lindsey Büster Sophie Carver Laura Castells Navarro Oliver E Craig Gordon T Cook Barry Cunliffe Anthony Denaire Kirsten Egging Dinwiddy Natasha Dodwell Michal Ernée Christopher Evans Milan Kuchařík Joan Francès Farré Chris Fowler Michiel Gazenbeek Rafael Garrido Pena María Haber-Uriarte Elżbieta Haduch Gill Hey Nick Jowett Timothy Knowles Ken Massy Saskia Pfrengle Philippe Lefranc Olivier Lemercier Arnaud Lefebvre César Heras Martínez Virginia Galera Olmo Ana Bastida Ramírez Joaquín Lomba Maurandi Tona Majó Jacqueline I McKinley Kathleen McSweeney Balázs Gusztáv Mende Alessandra Modi Gabriella Kulcsár Viktória Kiss András Czene Róbert Patay Anna Endrődi Kitti Köhler Tamás Hajdu Tamás Szeniczey János Dani Zsolt Bernert Maya Hoole Olivia Cheronet Denise Keating Petr Velemínský Miroslav Dobeš Francesca Candilio Fraser Brown Raúl Flores Fernández Ana-Mercedes Herrero-Corral Sebastiano Tusa Emiliano Carnieri Luigi Lentini Antonella Valenti Alessandro Zanini Clive Waddington Germán Delibes Elisa Guerra-Doce Benjamin Neil Marcus Brittain Mike Luke Richard Mortimer Jocelyne Desideri Marie Besse Günter Brücken Mirosław Furmanek Agata Hałuszko Maksym Mackiewicz Artur Rapiński Stephany Leach Ignacio Soriano Katina T Lillios João Luís Cardoso Michael Parker Pearson Piotr Włodarczak T Douglas Price Pilar Prieto Pierre-Jérôme Rey Roberto Risch Manuel A Rojo Guerra Aurore Schmitt Joël Serralongue Ana Maria Silva Václav Smrčka Luc Vergnaud João Zilhão David Caramelli Thomas Higham Mark G Thomas Douglas J Kennett Harry Fokkens Volker Heyd Alison Sheridan Karl-Göran Sjögren Philipp W Stockhammer Johannes Krause Ron Pinhasi Wolfgang Haak Ian Barnes Carles Lalueza-Fox David Reich

Nature 2018 03;555(7697):543

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http://dx.doi.org/10.1038/nature26164DOI Listing
March 2018

Effect of image registration on 3D absorbed dose calculations in Lu-DOTATOC peptide receptor radionuclide therapy.

Phys Med 2018 Jan 8;45:177-185. Epub 2018 Jan 8.

Department of Medical Physics, Velindre Cancer Centre, Cardiff, Wales, UK; School of Engineering, Cardiff University, Cardiff, Wales, UK.

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http://dx.doi.org/10.1016/j.ejmp.2017.11.021DOI Listing
January 2018

Mixed Model Association with Family-Biased Case-Control Ascertainment.

Am J Hum Genet 2017 Jan 22;100(1):31-39. Epub 2016 Dec 22.

Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223022PMC
January 2017

Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure.

Am J Hum Genet 2016 Nov 20;99(5):1130-1139. Epub 2016 Oct 20.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.09.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097941PMC
November 2016

Response to Shen et al.

Am J Hum Genet 2016 11;99(5):1220-1221

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.09.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097931PMC
November 2016

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Nature 2016 Oct 21;538(7624):201-206. Epub 2016 Sep 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature18964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161557PMC
October 2016

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans.

Curr Biol 2016 05 28;26(9):1241-7. Epub 2016 Mar 28.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://www.cell.com/current-biology/pdf/S0960-9822(16)30247-
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http://dx.doi.org/10.1016/j.cub.2016.03.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864120PMC
May 2016

A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years.

Proc Natl Acad Sci U S A 2016 May 2;113(20):5652-7. Epub 2016 May 2.

Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142; Department of Genetics, Harvard Medical School, Boston, MA 02115; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115

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http://dx.doi.org/10.1073/pnas.1514696113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878468PMC
May 2016

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia.

Am J Hum Genet 2016 Mar 25;98(3):456-472. Epub 2016 Feb 25.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.12.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4827102PMC
March 2016

An atlas of genetic correlations across human diseases and traits.

Nat Genet 2015 Nov 28;47(11):1236-41. Epub 2015 Sep 28.

Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.3406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797329PMC
November 2015

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes.

PLoS Genet 2015 Nov 12;11(11):e1005550. Epub 2015 Nov 12.

Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642934PMC
November 2015

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores.

Am J Hum Genet 2015 Oct;97(4):576-92

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://biorxiv.org/content/biorxiv/early/2015/03/01/015859.f
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http://linkinghub.elsevier.com/retrieve/pii/S000292971500365
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http://dx.doi.org/10.1016/j.ajhg.2015.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596916PMC
October 2015

Genetic evidence for two founding populations of the Americas.

Nature 2015 Sep 21;525(7567):104-8. Epub 2015 Jul 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature14895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982469PMC
September 2015

Mixed model with correction for case-control ascertainment increases association power.

Am J Hum Genet 2015 May 16;96(5):720-30. Epub 2015 Apr 16.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570278PMC
May 2015

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies.

Nat Genet 2015 Mar 2;47(3):291-5. Epub 2015 Feb 2.

1] Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [3] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.3211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495769PMC
March 2015

Efficient Bayesian mixed-model analysis increases association power in large cohorts.

Nat Genet 2015 Mar 2;47(3):284-90. Epub 2015 Feb 2.

1] Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [3] Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.3190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342297PMC
March 2015

Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.

Bioinformatics 2014 Oct 1;30(20):2906-14. Epub 2014 Jul 1.

Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90024, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, 90024, Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, 94143, Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, 02115, Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA, 02115, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, Department of Genetics Harvard Medical School, Boston, MA, 02115 and Division of Population Health Sciences and Education, St George's, University of London, UK Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90024, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, 90024, Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, 94143, Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, 02115, Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA, 02115, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, Department of Genetics Harvard Medical School, Boston, MA, 02115 and Division of Population Health Sciences and Education, St George's, University of London, UK Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90024, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, 90024, Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, 94143, Program in Genetic Epidemiology and Statistical Genetics, Har

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http://dx.doi.org/10.1093/bioinformatics/btu416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184260PMC
October 2014

Ancient human genomes suggest three ancestral populations for present-day Europeans.

Authors:
Iosif Lazaridis Nick Patterson Alissa Mittnik Gabriel Renaud Swapan Mallick Karola Kirsanow Peter H Sudmant Joshua G Schraiber Sergi Castellano Mark Lipson Bonnie Berger Christos Economou Ruth Bollongino Qiaomei Fu Kirsten I Bos Susanne Nordenfelt Heng Li Cesare de Filippo Kay Prüfer Susanna Sawyer Cosimo Posth Wolfgang Haak Fredrik Hallgren Elin Fornander Nadin Rohland Dominique Delsate Michael Francken Jean-Michel Guinet Joachim Wahl George Ayodo Hamza A Babiker Graciela Bailliet Elena Balanovska Oleg Balanovsky Ramiro Barrantes Gabriel Bedoya Haim Ben-Ami Judit Bene Fouad Berrada Claudio M Bravi Francesca Brisighelli George B J Busby Francesco Cali Mikhail Churnosov David E C Cole Daniel Corach Larissa Damba George van Driem Stanislav Dryomov Jean-Michel Dugoujon Sardana A Fedorova Irene Gallego Romero Marina Gubina Michael Hammer Brenna M Henn Tor Hervig Ugur Hodoglugil Aashish R Jha Sena Karachanak-Yankova Rita Khusainova Elza Khusnutdinova Rick Kittles Toomas Kivisild William Klitz Vaidutis Kučinskas Alena Kushniarevich Leila Laredj Sergey Litvinov Theologos Loukidis Robert W Mahley Béla Melegh Ene Metspalu Julio Molina Joanna Mountain Klemetti Näkkäläjärvi Desislava Nesheva Thomas Nyambo Ludmila Osipova Jüri Parik Fedor Platonov Olga Posukh Valentino Romano Francisco Rothhammer Igor Rudan Ruslan Ruizbakiev Hovhannes Sahakyan Antti Sajantila Antonio Salas Elena B Starikovskaya Ayele Tarekegn Draga Toncheva Shahlo Turdikulova Ingrida Uktveryte Olga Utevska René Vasquez Mercedes Villena Mikhail Voevoda Cheryl A Winkler Levon Yepiskoposyan Pierre Zalloua Tatijana Zemunik Alan Cooper Cristian Capelli Mark G Thomas Andres Ruiz-Linares Sarah A Tishkoff Lalji Singh Kumarasamy Thangaraj Richard Villems David Comas Rem Sukernik Mait Metspalu Matthias Meyer Evan E Eichler Joachim Burger Montgomery Slatkin Svante Pääbo Janet Kelso David Reich Johannes Krause

Nature 2014 Sep;513(7518):409-13

1] Institute for Archaeological Sciences, University of Tübingen, Tübingen 72074, Germany. [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany. [3] Max Planck Institut für Geschichte und Naturwissenschaften, Jena 07745, Germany.

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https://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_fil
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http://biorxiv.org/content/biorxiv/early/2013/12/23/001552.f
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http://www.geo.uni-tuebingen.de/fileadmin/website/arbeitsber
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http://www.nature.com/doifinder/10.1038/nature13673
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http://dx.doi.org/10.1038/nature13673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574PMC
September 2014

Reconstructing Austronesian population history in Island Southeast Asia.

Nat Commun 2014 Aug 19;5:4689. Epub 2014 Aug 19.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms5689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143916PMC
August 2014

The genomic landscape of Neanderthal ancestry in present-day humans.

Nature 2014 Mar 29;507(7492):354-7. Epub 2014 Jan 29.

1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://www.nature.com/articles/nature12961
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http://dx.doi.org/10.1038/nature12961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072735PMC
March 2014

Ancient west Eurasian ancestry in southern and eastern Africa.

Proc Natl Acad Sci U S A 2014 Feb 3;111(7):2632-7. Epub 2014 Feb 3.

Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115.

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http://dx.doi.org/10.1073/pnas.1313787111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932865PMC
February 2014

A novel approach to estimating heterozygosity from low-coverage genome sequence.

Genetics 2013 Oct 9;195(2):553-61. Epub 2013 Aug 9.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115.

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http://dx.doi.org/10.1534/genetics.113.154500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781980PMC
October 2013

Estimating and interpreting FST: the impact of rare variants.

Genome Res 2013 Sep 16;23(9):1514-21. Epub 2013 Jul 16.

Harvard-Massachusetts Institute of Technology (MIT), Division of Health, Science, and Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.154831.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759727PMC
September 2013

Genetic evidence for recent population mixture in India.

Am J Hum Genet 2013 Sep 8;93(3):422-38. Epub 2013 Aug 8.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.ajhg.2013.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769933PMC
September 2013

Efficient moment-based inference of admixture parameters and sources of gene flow.

Mol Biol Evol 2013 Aug 24;30(8):1788-802. Epub 2013 May 24.

Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology.

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http://dx.doi.org/10.1093/molbev/mst099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708505PMC
August 2013

Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

PLoS Genet 2013 May 30;9(5):e1003520. Epub 2013 May 30.

Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1371/journal.pgen.1003520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667752PMC
May 2013

Inferring admixture histories of human populations using linkage disequilibrium.

Genetics 2013 Apr 14;193(4):1233-54. Epub 2013 Feb 14.

Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1534/genetics.112.147330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3606100PMC
April 2013

The date of interbreeding between Neandertals and modern humans.

PLoS Genet 2012 4;8(10):e1002947. Epub 2012 Oct 4.

Department of Genetics, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464203PMC
March 2013

African ancestry and genetic risk for uterine leiomyomata.

Am J Epidemiol 2012 Dec 15;176(12):1159-68. Epub 2012 Nov 15.

Slone Epidemiology Center at Boston University, 1010 Commonwealth Avenue, 4th Floor, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/aje/kws276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571235PMC
December 2012

Ancient admixture in human history.

Genetics 2012 Nov 7;192(3):1065-93. Epub 2012 Sep 7.

Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.

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http://www.genetics.org/cgi/doi/10.1534/genetics.112.145037
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http://dx.doi.org/10.1534/genetics.112.145037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522152PMC
November 2012

A direct characterization of human mutation based on microsatellites.

Nat Genet 2012 Oct 23;44(10):1161-5. Epub 2012 Aug 23.

Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.2398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459271PMC
October 2012

Phasing of many thousands of genotyped samples.

Am J Hum Genet 2012 Aug;91(2):238-51

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.ajhg.2012.06.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415548PMC
August 2012

Testing for ancient admixture between closely related populations.

Mol Biol Evol 2011 Aug 15;28(8):2239-52. Epub 2011 Feb 15.

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

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http://dx.doi.org/10.1093/molbev/msr048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144383PMC
August 2011

The landscape of recombination in African Americans.

Nature 2011 Jul 20;476(7359):170-5. Epub 2011 Jul 20.

Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK.

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http://dx.doi.org/10.1038/nature10336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154982PMC
July 2011

The history of African gene flow into Southern Europeans, Levantines, and Jews.

PLoS Genet 2011 Apr 21;7(4):e1001373. Epub 2011 Apr 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080861PMC
April 2011

Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays.

Genet Epidemiol 2011 Jan;35(1):80-3

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1002/gepi.20550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386999PMC
January 2011

New approaches to population stratification in genome-wide association studies.

Nat Rev Genet 2010 Jul;11(7):459-63

Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nrg2813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975875PMC
July 2010

Admixture mapping of obesity-related traits in African Americans: the Atherosclerosis Risk in Communities (ARIC) Study.

Obesity (Silver Spring) 2010 Mar 20;18(3):563-72. Epub 2009 Aug 20.

Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/oby.2009.282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866099PMC
March 2010

Population differentiation as a test for selective sweeps.

Genome Res 2010 Mar 19;20(3):393-402. Epub 2010 Jan 19.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.100545.109
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http://dx.doi.org/10.1101/gr.100545.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840981PMC
March 2010

Genetic structure of a unique admixed population: implications for medical research.

Hum Mol Genet 2010 Feb 5;19(3):411-9. Epub 2009 Nov 5.

Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge Center, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/hmg/ddp505DOI Listing
February 2010

Combinatorics and next-generation sequencing.

Nat Biotechnol 2009 Sep;27(9):826-7

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http://dx.doi.org/10.1038/nbt0909-826DOI Listing
September 2009

Reconstructing Indian population history.

Nature 2009 Sep;461(7263):489-94

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://www.nature.com/articles/nature08365
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210PMC
September 2009