Publications by authors named "Mark DePristo"

57Publications

GenomeWarp: an alignment-based variant coordinate transformation.

Bioinformatics 2019 11;35(21):4389-4391

Verily Life Sciences, Mountain View, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821237PMC
November 2019

CrowdVariant: a crowdsourcing approach to classify copy number variants.

Pac Symp Biocomput 2019 ;24:224-235

Biomedical Informatics, Stanford University, Stanford, CA 94305, USA,

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August 2019

A guide to deep learning in healthcare.

Nat Med 2019 01 7;25(1):24-29. Epub 2019 Jan 7.

Google Research, San Jose, CA, USA.

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http://dx.doi.org/10.1038/s41591-018-0316-zDOI Listing
January 2019

Deep learning of genomic variation and regulatory network data.

Hum Mol Genet 2018 05;27(R1):R63-R71

Google Inc., Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1093/hmg/ddy115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499235PMC
May 2018

Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

Authors:
Jason Flannick Christian Fuchsberger Anubha Mahajan Tanya M Teslovich Vineeta Agarwala Kyle J Gaulton Lizz Caulkins Ryan Koesterer Clement Ma Loukas Moutsianas Davis J McCarthy Manuel A Rivas John R B Perry Xueling Sim Thomas W Blackwell Neil R Robertson N William Rayner Pablo Cingolani Adam E Locke Juan Fernandez Tajes Heather M Highland Josee Dupuis Peter S Chines Cecilia M Lindgren Christopher Hartl Anne U Jackson Han Chen Jeroen R Huyghe Martijn van de Bunt Richard D Pearson Ashish Kumar Martina Müller-Nurasyid Niels Grarup Heather M Stringham Eric R Gamazon Jaehoon Lee Yuhui Chen Robert A Scott Jennifer E Below Peng Chen Jinyan Huang Min Jin Go Michael L Stitzel Dorota Pasko Stephen C J Parker Tibor V Varga Todd Green Nicola L Beer Aaron G Day-Williams Teresa Ferreira Tasha Fingerlin Momoko Horikoshi Cheng Hu Iksoo Huh Mohammad Kamran Ikram Bong-Jo Kim Yongkang Kim Young Jin Kim Min-Seok Kwon Juyoung Lee Selyeong Lee Keng-Han Lin Taylor J Maxwell Yoshihiko Nagai Xu Wang Ryan P Welch Joon Yoon Weihua Zhang Nir Barzilai Benjamin F Voight Bok-Ghee Han Christopher P Jenkinson Teemu Kuulasmaa Johanna Kuusisto Alisa Manning Maggie C Y Ng Nicholette D Palmer Beverley Balkau Alena Stančáková Hanna E Abboud Heiner Boeing Vilmantas Giedraitis Dorairaj Prabhakaran Omri Gottesman James Scott Jason Carey Phoenix Kwan George Grant Joshua D Smith Benjamin M Neale Shaun Purcell Adam S Butterworth Joanna M M Howson Heung Man Lee Yingchang Lu Soo-Heon Kwak Wei Zhao John Danesh Vincent K L Lam Kyong Soo Park Danish Saleheen Wing Yee So Claudia H T Tam Uzma Afzal David Aguilar Rector Arya Tin Aung Edmund Chan Carmen Navarro Ching-Yu Cheng Domenico Palli Adolfo Correa Joanne E Curran Dennis Rybin Vidya S Farook Sharon P Fowler Barry I Freedman Michael Griswold Daniel Esten Hale Pamela J Hicks Chiea-Chuen Khor Satish Kumar Benjamin Lehne Dorothée Thuillier Wei Yen Lim Jianjun Liu Marie Loh Solomon K Musani Sobha Puppala William R Scott Loïc Yengo Sian-Tsung Tan Herman A Taylor Farook Thameem Gregory Wilson Tien Yin Wong Pål Rasmus Njølstad Jonathan C Levy Massimo Mangino Lori L Bonnycastle Thomas Schwarzmayr João Fadista Gabriela L Surdulescu Christian Herder Christopher J Groves Thomas Wieland Jette Bork-Jensen Ivan Brandslund Cramer Christensen Heikki A Koistinen Alex S F Doney Leena Kinnunen Tõnu Esko Andrew J Farmer Liisa Hakaste Dylan Hodgkiss Jasmina Kravic Valeri Lyssenko Mette Hollensted Marit E Jørgensen Torben Jørgensen Claes Ladenvall Johanne Marie Justesen Annemari Käräjämäki Jennifer Kriebel Wolfgang Rathmann Lars Lannfelt Torsten Lauritzen Narisu Narisu Allan Linneberg Olle Melander Lili Milani Matt Neville Marju Orho-Melander Lu Qi Qibin Qi Michael Roden Olov Rolandsson Amy Swift Anders H Rosengren Kathleen Stirrups Andrew R Wood Evelin Mihailov Christine Blancher Mauricio O Carneiro Jared Maguire Ryan Poplin Khalid Shakir Timothy Fennell Mark DePristo Martin Hrabé de Angelis Panos Deloukas Anette P Gjesing Goo Jun Peter Nilsson Jacquelyn Murphy Robert Onofrio Barbara Thorand Torben Hansen Christa Meisinger Frank B Hu Bo Isomaa Fredrik Karpe Liming Liang Annette Peters Cornelia Huth Stephen P O'Rahilly Colin N A Palmer Oluf Pedersen Rainer Rauramaa Jaakko Tuomilehto Veikko Salomaa Richard M Watanabe Ann-Christine Syvänen Richard N Bergman Dwaipayan Bharadwaj Erwin P Bottinger Yoon Shin Cho Giriraj R Chandak Juliana C N Chan Kee Seng Chia Mark J Daly Shah B Ebrahim Claudia Langenberg Paul Elliott Kathleen A Jablonski Donna M Lehman Weiping Jia Ronald C W Ma Toni I Pollin Manjinder Sandhu Nikhil Tandon Philippe Froguel Inês Barroso Yik Ying Teo Eleftheria Zeggini Ruth J F Loos Kerrin S Small Janina S Ried Ralph A DeFronzo Harald Grallert Benjamin Glaser Andres Metspalu Nicholas J Wareham Mark Walker Eric Banks Christian Gieger Erik Ingelsson Hae Kyung Im Thomas Illig Paul W Franks Gemma Buck Joseph Trakalo David Buck Inga Prokopenko Reedik Mägi Lars Lind Yossi Farjoun Katharine R Owen Anna L Gloyn Konstantin Strauch Tiinamaija Tuomi Jaspal Singh Kooner Jong-Young Lee Taesung Park Peter Donnelly Andrew D Morris Andrew T Hattersley Donald W Bowden Francis S Collins Gil Atzmon John C Chambers Timothy D Spector Markku Laakso Tim M Strom Graeme I Bell John Blangero Ravindranath Duggirala E Shyong Tai Gilean McVean Craig L Hanis James G Wilson Mark Seielstad Timothy M Frayling James B Meigs Nancy J Cox Rob Sladek Eric S Lander Stacey Gabriel Karen L Mohlke Thomas Meitinger Leif Groop Goncalo Abecasis Laura J Scott Andrew P Morris Hyun Min Kang David Altshuler Noël P Burtt Jose C Florez Michael Boehnke Mark I McCarthy

Sci Data 2018 01 23;5:180002. Epub 2018 Jan 23.

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http://dx.doi.org/10.1038/sdata.2018.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5779067PMC
January 2018

Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees.

Proc Natl Acad Sci U S A 2018 01 26;115(2):379-384. Epub 2017 Dec 26.

South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520.

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http://dx.doi.org/10.1073/pnas.1705859115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777025PMC
January 2018

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

Authors:
Jason Flannick Christian Fuchsberger Anubha Mahajan Tanya M Teslovich Vineeta Agarwala Kyle J Gaulton Lizz Caulkins Ryan Koesterer Clement Ma Loukas Moutsianas Davis J McCarthy Manuel A Rivas John R B Perry Xueling Sim Thomas W Blackwell Neil R Robertson N William Rayner Pablo Cingolani Adam E Locke Juan Fernandez Tajes Heather M Highland Josee Dupuis Peter S Chines Cecilia M Lindgren Christopher Hartl Anne U Jackson Han Chen Jeroen R Huyghe Martijn van de Bunt Richard D Pearson Ashish Kumar Martina Müller-Nurasyid Niels Grarup Heather M Stringham Eric R Gamazon Jaehoon Lee Yuhui Chen Robert A Scott Jennifer E Below Peng Chen Jinyan Huang Min Jin Go Michael L Stitzel Dorota Pasko Stephen C J Parker Tibor V Varga Todd Green Nicola L Beer Aaron G Day-Williams Teresa Ferreira Tasha Fingerlin Momoko Horikoshi Cheng Hu Iksoo Huh Mohammad Kamran Ikram Bong-Jo Kim Yongkang Kim Young Jin Kim Min-Seok Kwon Juyoung Lee Selyeong Lee Keng-Han Lin Taylor J Maxwell Yoshihiko Nagai Xu Wang Ryan P Welch Joon Yoon Weihua Zhang Nir Barzilai Benjamin F Voight Bok-Ghee Han Christopher P Jenkinson Teemu Kuulasmaa Johanna Kuusisto Alisa Manning Maggie C Y Ng Nicholette D Palmer Beverley Balkau Alena Stančáková Hanna E Abboud Heiner Boeing Vilmantas Giedraitis Dorairaj Prabhakaran Omri Gottesman James Scott Jason Carey Phoenix Kwan George Grant Joshua D Smith Benjamin M Neale Shaun Purcell Adam S Butterworth Joanna M M Howson Heung Man Lee Yingchang Lu Soo-Heon Kwak Wei Zhao John Danesh Vincent K L Lam Kyong Soo Park Danish Saleheen Wing Yee So Claudia H T Tam Uzma Afzal David Aguilar Rector Arya Tin Aung Edmund Chan Carmen Navarro Ching-Yu Cheng Domenico Palli Adolfo Correa Joanne E Curran Dennis Rybin Vidya S Farook Sharon P Fowler Barry I Freedman Michael Griswold Daniel Esten Hale Pamela J Hicks Chiea-Chuen Khor Satish Kumar Benjamin Lehne Dorothée Thuillier Wei Yen Lim Jianjun Liu Marie Loh Solomon K Musani Sobha Puppala William R Scott Loïc Yengo Sian-Tsung Tan Herman A Taylor Farook Thameem Gregory Wilson Tien Yin Wong Pål Rasmus Njølstad Jonathan C Levy Massimo Mangino Lori L Bonnycastle Thomas Schwarzmayr João Fadista Gabriela L Surdulescu Christian Herder Christopher J Groves Thomas Wieland Jette Bork-Jensen Ivan Brandslund Cramer Christensen Heikki A Koistinen Alex S F Doney Leena Kinnunen Tõnu Esko Andrew J Farmer Liisa Hakaste Dylan Hodgkiss Jasmina Kravic Valeri Lyssenko Mette Hollensted Marit E Jørgensen Torben Jørgensen Claes Ladenvall Johanne Marie Justesen Annemari Käräjämäki Jennifer Kriebel Wolfgang Rathmann Lars Lannfelt Torsten Lauritzen Narisu Narisu Allan Linneberg Olle Melander Lili Milani Matt Neville Marju Orho-Melander Lu Qi Qibin Qi Michael Roden Olov Rolandsson Amy Swift Anders H Rosengren Kathleen Stirrups Andrew R Wood Evelin Mihailov Christine Blancher Mauricio O Carneiro Jared Maguire Ryan Poplin Khalid Shakir Timothy Fennell Mark DePristo Martin Hrabé de Angelis Panos Deloukas Anette P Gjesing Goo Jun Peter Nilsson Jacquelyn Murphy Robert Onofrio Barbara Thorand Torben Hansen Christa Meisinger Frank B Hu Bo Isomaa Fredrik Karpe Liming Liang Annette Peters Cornelia Huth Stephen P O'Rahilly Colin N A Palmer Oluf Pedersen Rainer Rauramaa Jaakko Tuomilehto Veikko Salomaa Richard M Watanabe Ann-Christine Syvänen Richard N Bergman Dwaipayan Bharadwaj Erwin P Bottinger Yoon Shin Cho Giriraj R Chandak Juliana Cn Chan Kee Seng Chia Mark J Daly Shah B Ebrahim Claudia Langenberg Paul Elliott Kathleen A Jablonski Donna M Lehman Weiping Jia Ronald C W Ma Toni I Pollin Manjinder Sandhu Nikhil Tandon Philippe Froguel Inês Barroso Yik Ying Teo Eleftheria Zeggini Ruth J F Loos Kerrin S Small Janina S Ried Ralph A DeFronzo Harald Grallert Benjamin Glaser Andres Metspalu Nicholas J Wareham Mark Walker Eric Banks Christian Gieger Erik Ingelsson Hae Kyung Im Thomas Illig Paul W Franks Gemma Buck Joseph Trakalo David Buck Inga Prokopenko Reedik Mägi Lars Lind Yossi Farjoun Katharine R Owen Anna L Gloyn Konstantin Strauch Tiinamaija Tuomi Jaspal Singh Kooner Jong-Young Lee Taesung Park Peter Donnelly Andrew D Morris Andrew T Hattersley Donald W Bowden Francis S Collins Gil Atzmon John C Chambers Timothy D Spector Markku Laakso Tim M Strom Graeme I Bell John Blangero Ravindranath Duggirala E Shyong Tai Gilean McVean Craig L Hanis James G Wilson Mark Seielstad Timothy M Frayling James B Meigs Nancy J Cox Rob Sladek Eric S Lander Stacey Gabriel Karen L Mohlke Thomas Meitinger Leif Groop Goncalo Abecasis Laura J Scott Andrew P Morris Hyun Min Kang David Altshuler Noël P Burtt Jose C Florez Michael Boehnke Mark I McCarthy

Sci Data 2017 12 19;4:170179. Epub 2017 Dec 19.

Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/sdata.2017.179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5735917PMC
December 2017

A Low-Frequency Inactivating Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.

Authors:
Alisa Manning Heather M Highland Jessica Gasser Xueling Sim Taru Tukiainen Pierre Fontanillas Niels Grarup Manuel A Rivas Anubha Mahajan Adam E Locke Pablo Cingolani Tune H Pers Ana Viñuela Andrew A Brown Ying Wu Jason Flannick Christian Fuchsberger Eric R Gamazon Kyle J Gaulton Hae Kyung Im Tanya M Teslovich Thomas W Blackwell Jette Bork-Jensen Noël P Burtt Yuhui Chen Todd Green Christopher Hartl Hyun Min Kang Ashish Kumar Claes Ladenvall Clement Ma Loukas Moutsianas Richard D Pearson John R B Perry N William Rayner Neil R Robertson Laura J Scott Martijn van de Bunt Johan G Eriksson Antti Jula Seppo Koskinen Terho Lehtimäki Aarno Palotie Olli T Raitakari Suzanne B R Jacobs Jennifer Wessel Audrey Y Chu Robert A Scott Mark O Goodarzi Christine Blancher Gemma Buck David Buck Peter S Chines Stacey Gabriel Anette P Gjesing Christopher J Groves Mette Hollensted Jeroen R Huyghe Anne U Jackson Goo Jun Johanne Marie Justesen Massimo Mangino Jacquelyn Murphy Matt Neville Robert Onofrio Kerrin S Small Heather M Stringham Joseph Trakalo Eric Banks Jason Carey Mauricio O Carneiro Mark DePristo Yossi Farjoun Timothy Fennell Jacqueline I Goldstein George Grant Martin Hrabé de Angelis Jared Maguire Benjamin M Neale Ryan Poplin Shaun Purcell Thomas Schwarzmayr Khalid Shakir Joshua D Smith Tim M Strom Thomas Wieland Jaana Lindstrom Ivan Brandslund Cramer Christensen Gabriela L Surdulescu Timo A Lakka Alex S F Doney Peter Nilsson Nicholas J Wareham Claudia Langenberg Tibor V Varga Paul W Franks Olov Rolandsson Anders H Rosengren Vidya S Farook Farook Thameem Sobha Puppala Satish Kumar Donna M Lehman Christopher P Jenkinson Joanne E Curran Daniel Esten Hale Sharon P Fowler Rector Arya Ralph A DeFronzo Hanna E Abboud Ann-Christine Syvänen Pamela J Hicks Nicholette D Palmer Maggie C Y Ng Donald W Bowden Barry I Freedman Tõnu Esko Reedik Mägi Lili Milani Evelin Mihailov Andres Metspalu Narisu Narisu Leena Kinnunen Lori L Bonnycastle Amy Swift Dorota Pasko Andrew R Wood João Fadista Toni I Pollin Nir Barzilai Gil Atzmon Benjamin Glaser Barbara Thorand Konstantin Strauch Annette Peters Michael Roden Martina Müller-Nurasyid Liming Liang Jennifer Kriebel Thomas Illig Harald Grallert Christian Gieger Christa Meisinger Lars Lannfelt Solomon K Musani Michael Griswold Herman A Taylor Gregory Wilson Adolfo Correa Heikki Oksa William R Scott Uzma Afzal Sian-Tsung Tan Marie Loh John C Chambers Jobanpreet Sehmi Jaspal Singh Kooner Benjamin Lehne Yoon Shin Cho Jong-Young Lee Bok-Ghee Han Annemari Käräjämäki Qibin Qi Lu Qi Jinyan Huang Frank B Hu Olle Melander Marju Orho-Melander Jennifer E Below David Aguilar Tien Yin Wong Jianjun Liu Chiea-Chuen Khor Kee Seng Chia Wei Yen Lim Ching-Yu Cheng Edmund Chan E Shyong Tai Tin Aung Allan Linneberg Bo Isomaa Thomas Meitinger Tiinamaija Tuomi Liisa Hakaste Jasmina Kravic Marit E Jørgensen Torsten Lauritzen Panos Deloukas Kathleen E Stirrups Katharine R Owen Andrew J Farmer Timothy M Frayling Stephen P O'Rahilly Mark Walker Jonathan C Levy Dylan Hodgkiss Andrew T Hattersley Teemu Kuulasmaa Alena Stančáková Inês Barroso Dwaipayan Bharadwaj Juliana Chan Giriraj R Chandak Mark J Daly Peter J Donnelly Shah B Ebrahim Paul Elliott Tasha Fingerlin Philippe Froguel Cheng Hu Weiping Jia Ronald C W Ma Gilean McVean Taesung Park Dorairaj Prabhakaran Manjinder Sandhu James Scott Rob Sladek Nikhil Tandon Yik Ying Teo Eleftheria Zeggini Richard M Watanabe Heikki A Koistinen Y Antero Kesaniemi Matti Uusitupa Timothy D Spector Veikko Salomaa Rainer Rauramaa Colin N A Palmer Inga Prokopenko Andrew D Morris Richard N Bergman Francis S Collins Lars Lind Erik Ingelsson Jaakko Tuomilehto Fredrik Karpe Leif Groop Torben Jørgensen Torben Hansen Oluf Pedersen Johanna Kuusisto Gonçalo Abecasis Graeme I Bell John Blangero Nancy J Cox Ravindranath Duggirala Mark Seielstad James G Wilson Josee Dupuis Samuli Ripatti Craig L Hanis Jose C Florez Karen L Mohlke James B Meigs Markku Laakso Andrew P Morris Michael Boehnke David Altshuler Mark I McCarthy Anna L Gloyn Cecilia M Lindgren

Diabetes 2017 07 24;66(7):2019-2032. Epub 2017 Mar 24.

Program in Medical and Population Genetics, Broad Institute, Cambridge, MA.

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http://dx.doi.org/10.2337/db16-1329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482074PMC
July 2017

A framework for the detection of de novo mutations in family-based sequencing data.

Eur J Hum Genet 2017 02 23;25(2):227-233. Epub 2016 Nov 23.

Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/ejhg.2016.147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5255947PMC
February 2017

Analysis of protein-coding genetic variation in 60,706 humans.

Nature 2016 08;536(7616):285-91

Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

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http://www.nature.com/articles/nature19057
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http://dx.doi.org/10.1038/nature19057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018207PMC
August 2016

The genetic architecture of type 2 diabetes.

Authors:
Christian Fuchsberger Jason Flannick Tanya M Teslovich Anubha Mahajan Vineeta Agarwala Kyle J Gaulton Clement Ma Pierre Fontanillas Loukas Moutsianas Davis J McCarthy Manuel A Rivas John R B Perry Xueling Sim Thomas W Blackwell Neil R Robertson N William Rayner Pablo Cingolani Adam E Locke Juan Fernandez Tajes Heather M Highland Josee Dupuis Peter S Chines Cecilia M Lindgren Christopher Hartl Anne U Jackson Han Chen Jeroen R Huyghe Martijn van de Bunt Richard D Pearson Ashish Kumar Martina Müller-Nurasyid Niels Grarup Heather M Stringham Eric R Gamazon Jaehoon Lee Yuhui Chen Robert A Scott Jennifer E Below Peng Chen Jinyan Huang Min Jin Go Michael L Stitzel Dorota Pasko Stephen C J Parker Tibor V Varga Todd Green Nicola L Beer Aaron G Day-Williams Teresa Ferreira Tasha Fingerlin Momoko Horikoshi Cheng Hu Iksoo Huh Mohammad Kamran Ikram Bong-Jo Kim Yongkang Kim Young Jin Kim Min-Seok Kwon Juyoung Lee Selyeong Lee Keng-Han Lin Taylor J Maxwell Yoshihiko Nagai Xu Wang Ryan P Welch Joon Yoon Weihua Zhang Nir Barzilai Benjamin F Voight Bok-Ghee Han Christopher P Jenkinson Teemu Kuulasmaa Johanna Kuusisto Alisa Manning Maggie C Y Ng Nicholette D Palmer Beverley Balkau Alena Stančáková Hanna E Abboud Heiner Boeing Vilmantas Giedraitis Dorairaj Prabhakaran Omri Gottesman James Scott Jason Carey Phoenix Kwan George Grant Joshua D Smith Benjamin M Neale Shaun Purcell Adam S Butterworth Joanna M M Howson Heung Man Lee Yingchang Lu Soo-Heon Kwak Wei Zhao John Danesh Vincent K L Lam Kyong Soo Park Danish Saleheen Wing Yee So Claudia H T Tam Uzma Afzal David Aguilar Rector Arya Tin Aung Edmund Chan Carmen Navarro Ching-Yu Cheng Domenico Palli Adolfo Correa Joanne E Curran Denis Rybin Vidya S Farook Sharon P Fowler Barry I Freedman Michael Griswold Daniel Esten Hale Pamela J Hicks Chiea-Chuen Khor Satish Kumar Benjamin Lehne Dorothée Thuillier Wei Yen Lim Jianjun Liu Yvonne T van der Schouw Marie Loh Solomon K Musani Sobha Puppala William R Scott Loïc Yengo Sian-Tsung Tan Herman A Taylor Farook Thameem Gregory Wilson Tien Yin Wong Pål Rasmus Njølstad Jonathan C Levy Massimo Mangino Lori L Bonnycastle Thomas Schwarzmayr João Fadista Gabriela L Surdulescu Christian Herder Christopher J Groves Thomas Wieland Jette Bork-Jensen Ivan Brandslund Cramer Christensen Heikki A Koistinen Alex S F Doney Leena Kinnunen Tõnu Esko Andrew J Farmer Liisa Hakaste Dylan Hodgkiss Jasmina Kravic Valeriya Lyssenko Mette Hollensted Marit E Jørgensen Torben Jørgensen Claes Ladenvall Johanne Marie Justesen Annemari Käräjämäki Jennifer Kriebel Wolfgang Rathmann Lars Lannfelt Torsten Lauritzen Narisu Narisu Allan Linneberg Olle Melander Lili Milani Matt Neville Marju Orho-Melander Lu Qi Qibin Qi Michael Roden Olov Rolandsson Amy Swift Anders H Rosengren Kathleen Stirrups Andrew R Wood Evelin Mihailov Christine Blancher Mauricio O Carneiro Jared Maguire Ryan Poplin Khalid Shakir Timothy Fennell Mark DePristo Martin Hrabé de Angelis Panos Deloukas Anette P Gjesing Goo Jun Peter Nilsson Jacquelyn Murphy Robert Onofrio Barbara Thorand Torben Hansen Christa Meisinger Frank B Hu Bo Isomaa Fredrik Karpe Liming Liang Annette Peters Cornelia Huth Stephen P O'Rahilly Colin N A Palmer Oluf Pedersen Rainer Rauramaa Jaakko Tuomilehto Veikko Salomaa Richard M Watanabe Ann-Christine Syvänen Richard N Bergman Dwaipayan Bharadwaj Erwin P Bottinger Yoon Shin Cho Giriraj R Chandak Juliana C N Chan Kee Seng Chia Mark J Daly Shah B Ebrahim Claudia Langenberg Paul Elliott Kathleen A Jablonski Donna M Lehman Weiping Jia Ronald C W Ma Toni I Pollin Manjinder Sandhu Nikhil Tandon Philippe Froguel Inês Barroso Yik Ying Teo Eleftheria Zeggini Ruth J F Loos Kerrin S Small Janina S Ried Ralph A DeFronzo Harald Grallert Benjamin Glaser Andres Metspalu Nicholas J Wareham Mark Walker Eric Banks Christian Gieger Erik Ingelsson Hae Kyung Im Thomas Illig Paul W Franks Gemma Buck Joseph Trakalo David Buck Inga Prokopenko Reedik Mägi Lars Lind Yossi Farjoun Katharine R Owen Anna L Gloyn Konstantin Strauch Tiinamaija Tuomi Jaspal Singh Kooner Jong-Young Lee Taesung Park Peter Donnelly Andrew D Morris Andrew T Hattersley Donald W Bowden Francis S Collins Gil Atzmon John C Chambers Timothy D Spector Markku Laakso Tim M Strom Graeme I Bell John Blangero Ravindranath Duggirala E Shyong Tai Gilean McVean Craig L Hanis James G Wilson Mark Seielstad Timothy M Frayling James B Meigs Nancy J Cox Rob Sladek Eric S Lander Stacey Gabriel Noël P Burtt Karen L Mohlke Thomas Meitinger Leif Groop Goncalo Abecasis Jose C Florez Laura J Scott Andrew P Morris Hyun Min Kang Michael Boehnke David Altshuler Mark I McCarthy

Nature 2016 08 11;536(7614):41-47. Epub 2016 Jul 11.

Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

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http://hmg.oxfordjournals.org/content/early/2015/07/21/hmg.d
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http://www.nature.com/doifinder/10.1038/nature18642
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http://dx.doi.org/10.1038/nature18642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5034897PMC
August 2016

Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction.

Nature 2015 Feb 10;518(7537):102-6. Epub 2014 Dec 10.

1] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. [2] Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. [3] Department of Medicine, Harvard Medical School, Boston, Massachusetts 02114, USA. [4] Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://kooperberg.fhcrc.org/papers/2015do.pdf
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http://www.nature.com/doifinder/10.1038/nature13917
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http://dx.doi.org/10.1038/nature13917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319990PMC
February 2015

A framework for the interpretation of de novo mutation in human disease.

Nat Genet 2014 Sep 3;46(9):944-50. Epub 2014 Aug 3.

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

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http://dx.doi.org/10.1038/ng.3050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222185PMC
September 2014

Loss-of-function mutations in APOC3, triglycerides, and coronary disease.

N Engl J Med 2014 Jul 18;371(1):22-31. Epub 2014 Jun 18.

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http://dx.doi.org/10.1056/NEJMoa1307095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180269PMC
July 2014

A polygenic burden of rare disruptive mutations in schizophrenia.

Nature 2014 Feb 22;506(7487):185-90. Epub 2014 Jan 22.

1] Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2] Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [3] Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.

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http://dx.doi.org/10.1038/nature12975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136494PMC
February 2014

Pacific biosciences sequencing technology for genotyping and variation discovery in human data.

BMC Genomics 2012 Aug 5;13:375. Epub 2012 Aug 5.

Broad Institute of MIT and Harvard, Medical and Population Genetics Program, Cambridge, MA 02141, USA.

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http://dx.doi.org/10.1186/1471-2164-13-375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443046PMC
August 2012

Efficiency and power as a function of sequence coverage, SNP array density, and imputation.

PLoS Comput Biol 2012 12;8(7):e1002604. Epub 2012 Jul 12.

Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395607PMC
January 2013

ContEst: estimating cross-contamination of human samples in next-generation sequencing data.

Bioinformatics 2011 Sep 29;27(18):2601-2. Epub 2011 Jul 29.

Genome Sequencing Analysis Program and Platform, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167057PMC
September 2011

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Genome Res 2010 Sep 19;20(9):1297-303. Epub 2010 Jul 19.

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

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http://dx.doi.org/10.1101/gr.107524.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928508PMC
September 2010

Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome.

Mol Biol Evol 2010 Sep 28;27(9):2198-209. Epub 2010 Apr 28.

Department of Organismic and Evolutionary Biology, Harvard University, Boston, MA, USA.

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http://dx.doi.org/10.1093/molbev/msq108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2922621PMC
September 2010

Introducing simulated cellular architecture to the quantitative analysis of fluorescent microscopy.

Prog Biophys Mol Biol 2009 Sep-Oct;100(1-3):25-32. Epub 2009 Jul 21.

The Physiology Course, Marine Biological Laboratory, Woods Hole, MA 02543, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805826PMC
April 2010

Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways.

Mol Biol Evol 2009 Nov 14;26(11):2455-62. Epub 2009 Jul 14.

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

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http://dx.doi.org/10.1093/molbev/msp151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912465PMC
November 2009

The subtle benefits of being promiscuous: adaptive evolution potentiated by enzyme promiscuity.

Authors:
Mark A Depristo

HFSP J 2007 Jul 10;1(2):94-8. Epub 2007 Jul 10.

Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639842PMC
July 2007

Mutational reversions during adaptive protein evolution.

Mol Biol Evol 2007 Aug 7;24(8):1608-10. Epub 2007 Jun 7.

Department of Organismic and Evolutionary Biology, Harvard University, MA, USA.

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http://dx.doi.org/10.1093/molbev/msm118DOI Listing
August 2007

Knowledge-based real-space explorations for low-resolution structure determination.

Structure 2006 Aug;14(8):1313-20

Sanger Building, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.

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August 2006

Relation between native ensembles and experimental structures of proteins.

Proc Natl Acad Sci U S A 2006 Jul 7;103(29):10901-6. Epub 2006 Jul 7.

Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0511156103
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1544146PMC
July 2006

On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins.

Gene 2006 Aug 11;378:19-30. Epub 2006 May 11.

Department of Organismic and Evolutionary Biology, Hartl Lab, 16 Divinity Street, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1016/j.gene.2006.03.023DOI Listing
August 2006

The RNA degradosome: life in the fast lane of adaptive molecular evolution.

Trends Biochem Sci 2006 Jul;31(7):359-65

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

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http://dx.doi.org/10.1016/j.tibs.2006.05.005DOI Listing
July 2006

Darwinian evolution can follow only very few mutational paths to fitter proteins.

Science 2006 Apr;312(5770):111-4

Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1123539
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April 2006

Is one solution good enough?

Nat Struct Mol Biol 2006 Mar;13(3):184-5; discussion 185

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http://dx.doi.org/10.1038/nsmb0306-184DOI Listing
March 2006

Conformer generation under restraints.

Curr Opin Struct Biol 2006 Apr 17;16(2):160-5. Epub 2006 Feb 17.

Department of Molecular Biology and Center for Human Genetic Research, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114-2790, USA.

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http://dx.doi.org/10.1016/j.sbi.2006.02.001DOI Listing
April 2006

Crystallographic refinement by knowledge-based exploration of complex energy landscapes.

Structure 2005 Sep;13(9):1311-9

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.

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http://dx.doi.org/10.1016/j.str.2005.06.008DOI Listing
September 2005

Missense meanderings in sequence space: a biophysical view of protein evolution.

Nat Rev Genet 2005 Sep;6(9):678-87

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

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http://dx.doi.org/10.1038/nrg1672DOI Listing
September 2005

Simultaneous determination of protein structure and dynamics.

Nature 2005 Jan;433(7022):128-32

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

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http://dx.doi.org/10.1038/nature03199DOI Listing
January 2005

Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography.

Structure 2004 May;12(5):831-8

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.

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May 2004

Advantages of fine-grained side chain conformer libraries.

Protein Eng 2003 Dec;16(12):963-9

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

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http://dx.doi.org/10.1093/protein/gzg143DOI Listing
December 2003

Discrete restraint-based protein modeling and the Calpha-trace problem.

Protein Sci 2003 Sep;12(9):2032-46

Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England.

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http://dx.doi.org/10.1110/ps.0386903DOI Listing
September 2003

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

Proteins 2003 Apr;51(1):41-55

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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April 2003