Stephen C J Parker

Stephen C J Parker

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Stephen C J Parker

Stephen C J Parker

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Machine learning to predict anti-TNF drug responses of rheumatoid arthritis patients by integrating clinical and genetic markers.

Arthritis Rheumatol 2019 Jul 24. Epub 2019 Jul 24.

Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China, 400000.

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http://dx.doi.org/10.1002/art.41056DOI Listing
July 2019

Genomic annotation of disease-associated variants reveals shared functional contexts.

Diabetologia 2019 05 12;62(5):735-743. Epub 2019 Feb 12.

Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, 2049 Palmer Commons Building, Ann Arbor, MI, 48109, USA.

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http://dx.doi.org/10.1007/s00125-019-4823-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451673PMC
May 2019

Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression.

Genetics 2019 02 28;211(2):549-562. Epub 2018 Dec 28.

Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109

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http://dx.doi.org/10.1534/genetics.118.301525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366912PMC
February 2019

Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function.

Cell Rep 2019 Jan;26(3):788-801.e6

The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.12.083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389269PMC
January 2019

YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU.

Bioinformatics 2018 10;34(20):3578-3580

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6184538PMC
October 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

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

Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.

Authors:
M Carola Zillikens Serkalem Demissie Yi-Hsiang Hsu Laura M Yerges-Armstrong Wen-Chi Chou Lisette Stolk Gregory Livshits Linda Broer Toby Johnson Daniel L Koller Zoltán Kutalik Jian'an Luan Ida Malkin Janina S Ried Albert V Smith Gudmar Thorleifsson Liesbeth Vandenput Jing Hua Zhao Weihua Zhang Ali Aghdassi Kristina Åkesson Najaf Amin Leslie J Baier Inês Barroso David A Bennett Lars Bertram Rainer Biffar Murielle Bochud Michael Boehnke Ingrid B Borecki Aron S Buchman Liisa Byberg Harry Campbell Natalia Campos Obanda Jane A Cauley Peggy M Cawthon Henna Cederberg Zhao Chen Nam H Cho Hyung Jin Choi Melina Claussnitzer Francis Collins Steven R Cummings Philip L De Jager Ilja Demuth Rosalie A M Dhonukshe-Rutten Luda Diatchenko Gudny Eiriksdottir Anke W Enneman Mike Erdos Johan G Eriksson Joel Eriksson Karol Estrada Daniel S Evans Mary F Feitosa Mao Fu Melissa Garcia Christian Gieger Thomas Girke Nicole L Glazer Harald Grallert Jagvir Grewal Bok-Ghee Han Robert L Hanson Caroline Hayward Albert Hofman Eric P Hoffman Georg Homuth Wen-Chi Hsueh Monica J Hubal Alan Hubbard Kim M Huffman Lise B Husted Thomas Illig Erik Ingelsson Till Ittermann John-Olov Jansson Joanne M Jordan Antti Jula Magnus Karlsson Kay-Tee Khaw Tuomas O Kilpeläinen Norman Klopp Jacqueline S L Kloth Heikki A Koistinen William E Kraus Stephen Kritchevsky Teemu Kuulasmaa Johanna Kuusisto Markku Laakso Jari Lahti Thomas Lang Bente L Langdahl Lenore J Launer Jong-Young Lee Markus M Lerch Joshua R Lewis Lars Lind Cecilia Lindgren Yongmei Liu Tian Liu Youfang Liu Östen Ljunggren Mattias Lorentzon Robert N Luben William Maixner Fiona E McGuigan Carolina Medina-Gomez Thomas Meitinger Håkan Melhus Dan Mellström Simon Melov Karl Michaëlsson Braxton D Mitchell Andrew P Morris Leif Mosekilde Anne Newman Carrie M Nielson Jeffrey R O'Connell Ben A Oostra Eric S Orwoll Aarno Palotie Stephen C J Parker Munro Peacock Markus Perola Annette Peters Ozren Polasek Richard L Prince Katri Räikkönen Stuart H Ralston Samuli Ripatti John A Robbins Jerome I Rotter Igor Rudan Veikko Salomaa Suzanne Satterfield Eric E Schadt Sabine Schipf Laura Scott Joban Sehmi Jian Shen Chan Soo Shin Gunnar Sigurdsson Shad Smith Nicole Soranzo Alena Stančáková Elisabeth Steinhagen-Thiessen Elizabeth A Streeten Unnur Styrkarsdottir Karin M A Swart Sian-Tsung Tan Mark A Tarnopolsky Patricia Thompson Cynthia A Thomson Unnur Thorsteinsdottir Emmi Tikkanen Gregory J Tranah Jaakko Tuomilehto Natasja M van Schoor Arjun Verma Peter Vollenweider Henry Völzke Jean Wactawski-Wende Mark Walker Michael N Weedon Ryan Welch H-Erich Wichmann Elisabeth Widen Frances M K Williams James F Wilson Nicole C Wright Weijia Xie Lei Yu Yanhua Zhou John C Chambers Angela Döring Cornelia M van Duijn Michael J Econs Vilmundur Gudnason Jaspal S Kooner Bruce M Psaty Timothy D Spector Kari Stefansson Fernando Rivadeneira André G Uitterlinden Nicholas J Wareham Vicky Ossowski Dawn Waterworth Ruth J F Loos David Karasik Tamara B Harris Claes Ohlsson Douglas P Kiel

Nat Commun 2017 11 7;8(1):1414. Epub 2017 Nov 7.

Hebrew SeniorLife, Institute for Aging Research, Roslindale, MA, 02131, USA.

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http://dx.doi.org/10.1038/s41467-017-01008-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676783PMC
November 2017

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.

Authors:
M Carola Zillikens Serkalem Demissie Yi-Hsiang Hsu Laura M Yerges-Armstrong Wen-Chi Chou Lisette Stolk Gregory Livshits Linda Broer Toby Johnson Daniel L Koller Zoltán Kutalik Jian'an Luan Ida Malkin Janina S Ried Albert V Smith Gudmar Thorleifsson Liesbeth Vandenput Jing Hua Zhao Weihua Zhang Ali Aghdassi Kristina Åkesson Najaf Amin Leslie J Baier Inês Barroso David A Bennett Lars Bertram Rainer Biffar Murielle Bochud Michael Boehnke Ingrid B Borecki Aron S Buchman Liisa Byberg Harry Campbell Natalia Campos Obanda Jane A Cauley Peggy M Cawthon Henna Cederberg Zhao Chen Nam H Cho Hyung Jin Choi Melina Claussnitzer Francis Collins Steven R Cummings Philip L De Jager Ilja Demuth Rosalie A M Dhonukshe-Rutten Luda Diatchenko Gudny Eiriksdottir Anke W Enneman Mike Erdos Johan G Eriksson Joel Eriksson Karol Estrada Daniel S Evans Mary F Feitosa Mao Fu Melissa Garcia Christian Gieger Thomas Girke Nicole L Glazer Harald Grallert Jagvir Grewal Bok-Ghee Han Robert L Hanson Caroline Hayward Albert Hofman Eric P Hoffman Georg Homuth Wen-Chi Hsueh Monica J Hubal Alan Hubbard Kim M Huffman Lise B Husted Thomas Illig Erik Ingelsson Till Ittermann John-Olov Jansson Joanne M Jordan Antti Jula Magnus Karlsson Kay-Tee Khaw Tuomas O Kilpeläinen Norman Klopp Jacqueline S L Kloth Heikki A Koistinen William E Kraus Stephen Kritchevsky Teemu Kuulasmaa Johanna Kuusisto Markku Laakso Jari Lahti Thomas Lang Bente L Langdahl Lenore J Launer Jong-Young Lee Markus M Lerch Joshua R Lewis Lars Lind Cecilia Lindgren Yongmei Liu Tian Liu Youfang Liu Östen Ljunggren Mattias Lorentzon Robert N Luben William Maixner Fiona E McGuigan Carolina Medina-Gomez Thomas Meitinger Håkan Melhus Dan Mellström Simon Melov Karl Michaëlsson Braxton D Mitchell Andrew P Morris Leif Mosekilde Anne Newman Carrie M Nielson Jeffrey R O'Connell Ben A Oostra Eric S Orwoll Aarno Palotie Stephen C J Parker Munro Peacock Markus Perola Annette Peters Ozren Polasek Richard L Prince Katri Räikkönen Stuart H Ralston Samuli Ripatti John A Robbins Jerome I Rotter Igor Rudan Veikko Salomaa Suzanne Satterfield Eric E Schadt Sabine Schipf Laura Scott Joban Sehmi Jian Shen Chan Soo Shin Gunnar Sigurdsson Shad Smith Nicole Soranzo Alena Stančáková Elisabeth Steinhagen-Thiessen Elizabeth A Streeten Unnur Styrkarsdottir Karin M A Swart Sian-Tsung Tan Mark A Tarnopolsky Patricia Thompson Cynthia A Thomson Unnur Thorsteinsdottir Emmi Tikkanen Gregory J Tranah Jaakko Tuomilehto Natasja M van Schoor Arjun Verma Peter Vollenweider Henry Völzke Jean Wactawski-Wende Mark Walker Michael N Weedon Ryan Welch H-Erich Wichmann Elisabeth Widen Frances M K Williams James F Wilson Nicole C Wright Weijia Xie Lei Yu Yanhua Zhou John C Chambers Angela Döring Cornelia M van Duijn Michael J Econs Vilmundur Gudnason Jaspal S Kooner Bruce M Psaty Timothy D Spector Kari Stefansson Fernando Rivadeneira André G Uitterlinden Nicholas J Wareham Vicky Ossowski Dawn Waterworth Ruth J F Loos David Karasik Tamara B Harris Claes Ohlsson Douglas P Kiel

Nat Commun 2017 07 19;8(1):80. Epub 2017 Jul 19.

Hebrew SeniorLife, Institute for Aging Research, Roslindale, MA, 02131, USA.

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http://dx.doi.org/10.1038/s41467-017-00031-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517526PMC
July 2017

HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS.

Pac Symp Biocomput 2017 ;22:635-639

Biomedical Informatics Training Program, Stanford University 3165 Porter Dr., Room 2270, Palo Alto, CA 94304, USA,

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http://dx.doi.org/10.1142/9789813207813_0058DOI Listing
March 2017

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

Super Enhancers in Cancers, Complex Disease, and Developmental Disorders.

Genes (Basel) 2015 Nov 9;6(4):1183-200. Epub 2015 Nov 9.

Medical Scientist Training Program, Medical School, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.3390/genes6041183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690034PMC
November 2015

Motif signatures in stretch enhancers are enriched for disease-associated genetic variants.

Epigenetics Chromatin 2015 16;8:23. Epub 2015 Jul 16.

National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1186/s13072-015-0015-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4502539PMC
July 2015

Super-enhancers delineate disease-associated regulatory nodes in T cells.

Nature 2015 Apr 16;520(7548):558-62. Epub 2015 Feb 16.

Lymphocyte Cell Biology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.

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http://dx.doi.org/10.1038/nature14154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409450PMC
April 2015

GBshape: a genome browser database for DNA shape annotations.

Nucleic Acids Res 2015 Jan 17;43(Database issue):D103-9. Epub 2014 Oct 17.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Departments of Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA

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http://dx.doi.org/10.1093/nar/gku977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384032PMC
January 2015

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data.

PLoS One 2011 17;6(8):e23683. Epub 2011 Aug 17.

Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023683PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157463PMC
February 2012

A computational method to search for DNA structural motifs in functional genomic elements.

Methods Mol Biol 2011 ;759:367-79

Bioinformatics Program, Boston University, Boston, MA, USA.

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http://dx.doi.org/10.1007/978-1-61779-173-4_21DOI Listing
December 2011

Accurate and comprehensive sequencing of personal genomes.

Genome Res 2011 Sep 19;21(9):1498-505. Epub 2011 Jul 19.

Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1101/gr.123638.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166834PMC
September 2011

DNA shape, genetic codes, and evolution.

Curr Opin Struct Biol 2011 Jun 23;21(3):342-7. Epub 2011 Mar 23.

Genome Informatics Section, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.sbi.2011.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112471PMC
June 2011

Family-based analysis of candidate genes for polycystic ovary syndrome.

J Clin Endocrinol Metab 2010 May 3;95(5):2306-15. Epub 2010 Mar 3.

Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1210/jc.2009-2703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869537PMC
May 2010

The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome.

Genome Inform 2008 ;20:199-211

Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA.

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July 2009

Local DNA topography correlates with functional noncoding regions of the human genome.

Science 2009 Apr 12;324(5925):389-92. Epub 2009 Mar 12.

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1126/science.1169050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749491PMC
April 2009

Detection of DNA structural motifs in functional genomic elements.

Genome Res 2007 Jun;17(6):940-6

Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.5602807
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http://dx.doi.org/10.1101/gr.5602807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891352PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

BMC Genomics 2006 Oct 19;7:265. Epub 2006 Oct 19.

Bioinformatics Graduate Program, Boston University, Boston, MA 02215 USA.

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http://dx.doi.org/10.1186/1471-2164-7-265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624830PMC
October 2006