S
Sean Humphray
Researcher at Illumina
Publications - 86
Citations - 69908
Sean Humphray is an academic researcher from Illumina. The author has contributed to research in topics: Genome & Contig. The author has an hindex of 53, co-authored 86 publications receiving 60294 citations. Previous affiliations of Sean Humphray include Wellcome Trust Sanger Institute & Washington University in St. Louis.
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Journal ArticleDOI
Analyses of pig genomes provide insight into porcine demography and evolution
Martien A. M. Groenen,Alan Archibald,Hirohide Uenishi,Christopher K. Tuggle,Yasuhiro Takeuchi,Max F. Rothschild,Claire Rogel-Gaillard,Chankyu Park,Denis Milan,Hendrik-Jan Megens,Shengting Li,Denis M. Larkin,Heebal Kim,Laurent A. F. Frantz,Mario Caccamo,Hyeonju Ahn,Bronwen Aken,Anna Anselmo,Christian Anthon,Loretta Auvil,Bouabid Badaoui,Craig W. Beattie,Christian Bendixen,Daniel Berman,Frank Blecha,Jonas Blomberg,Lars Bolund,Mirte Bosse,Sara Botti,Zhan Bujie,Megan Bystrom,Boris Capitanu,Denise Carvalho-Silva,Patrick Chardon,Celine Chen,Ryan Cheng,Sang-Haeng Choi,William Chow,Richard Clark,C M Clee,Richard P. M. A. Crooijmans,Harry D. Dawson,Patrice Dehais,Fioravante De Sapio,Bert Dibbits,Nizar Drou,Zhi-Qiang Du,Kellye Eversole,João Fadista,João Fadista,Susan Fairley,Thomas Faraut,Geoffrey J. Faulkner,Geoffrey J. Faulkner,Katie E. Fowler,Merete Fredholm,Eric Fritz,James G. R. Gilbert,Elisabetta Giuffra,Elisabetta Giuffra,Jan Gorodkin,Darren K. Griffin,Jennifer Harrow,Alexander Hayward,Kerstin Howe,Zhi-Liang Hu,Sean Humphray,Sean Humphray,Toby Hunt,Henrik Hornshøj,Jin-Tae Jeon,Patric Jern,Matthew Jones,Jerzy Jurka,Hiroyuki Kanamori,Ronan Kapetanovic,Jaebum Kim,Jaebum Kim,Jae-Hwan Kim,Kyu-Won Kim,Tae-Hun Kim,Greger Larson,Kyooyeol Lee,Kyung-Tai Lee,Richard M. Leggett,Harris A. Lewin,Yingrui Li,Wan Sheng Liu,Jane E. Loveland,Yao Lu,Joan K. Lunney,Jian Ma,Ole Madsen,Katherine M. Mann,Katherine M. Mann,Lucy Matthews,Stuart McLaren,Takeya Morozumi,Michael P. Murtaugh,Jitendra Narayan,Dinh Truong Nguyen,Peixiang Ni,Song-Jung Oh,Suneel Kumar Onteru,Frank Panitz,Eung-Woo Park,Hong-Seog Park,Géraldine Pascal,Yogesh Paudel,Miguel Pérez-Enciso,Ricardo H. Ramirez-Gonzalez,James M. Reecy,Sandra L. Rodriguez-Zas,Gary A. Rohrer,Lauretta A. Rund,Yongming Sang,Kyle M. Schachtschneider,Joshua G. Schraiber,John C. Schwartz,Linda Scobie,Carol Scott,Stephen M. J. Searle,Bertrand Servin,Bruce R. Southey,Göran O. Sperber,Peter F. Stadler,Jonathan V. Sweedler,Hakim Tafer,Bo Thomsen,Rashmi Wali,Jian Wang,Jun Wang,Simon D. M. White,Xun Xu,Martine Yerle,Guojie Zhang,Jianguo Zhang,Jie Zhang,Shuhong Zhao,Jane Rogers,Carol Churcher,Lawrence B. Schook +141 more
TL;DR: The assembly and analysis of the genome sequence of a female domestic Duroc pig and a comparison with the genomes of wild and domestic pigs from Europe and Asia reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago.
Journal ArticleDOI
The Medicago genome provides insight into the evolution of rhizobial symbioses
Nevin D. Young,Frédéric Debellé,Frédéric Debellé,Giles E. D. Oldroyd,René Geurts,Steven B. Cannon,Steven B. Cannon,Michael K. Udvardi,Vagner A. Benedito,Klaus F. X. Mayer,Jérôme Gouzy,Jérôme Gouzy,Heiko Schoof,Yves Van de Peer,Sebastian Proost,Douglas R. Cook,Blake C. Meyers,Manuel Spannagl,Foo Cheung,Stéphane De Mita,Vivek Krishnakumar,Heidrun Gundlach,Shiguo Zhou,Joann Mudge,Arvind K. Bharti,Jeremy D. Murray,Marina Naoumkina,Benjamin D. Rosen,Kevin A. T. Silverstein,Haibao Tang,Stephane Rombauts,Patrick X. Zhao,Peng Zhou,Valérie Barbe,Philippe Bardou,Philippe Bardou,Michael Bechner,Arnaud Bellec,Anne Berger,Hélène Bergès,Shelby L. Bidwell,Ton Bisseling,Ton Bisseling,Nathalie Choisne,Arnaud Couloux,Roxanne Denny,Shweta Deshpande,Xinbin Dai,Jeff J. Doyle,Anne Marie Dudez,Anne Marie Dudez,Andrew Farmer,Stéphanie Fouteau,Carolien Franken,Chrystel Gibelin,Chrystel Gibelin,John Gish,Steven A. Goldstein,Alvaro J. González,Pamela J. Green,Asis Hallab,Marijke Hartog,Axin Hua,Sean Humphray,Dong-Hoon Jeong,Yi Jing,Anika Jöcker,Steve Kenton,Dong-Jin Kim,Dong-Jin Kim,Kathrin Klee,Hongshing Lai,Chunting Lang,Shaoping Lin,Simone L. Macmil,Ghislaine Magdelenat,Lucy Matthews,Jamison McCorrison,Erin L. Monaghan,Jeong Hwan Mun,Jeong Hwan Mun,Fares Z. Najar,Christine Nicholson,Céline Noirot,Majesta O'Bleness,Charles Paule,Julie Poulain,Florent Prion,Florent Prion,Baifang Qin,Chunmei Qu,Ernest F. Retzel,Claire Riddle,Erika Sallet,Erika Sallet,Sylvie Samain,Nicolas Samson,Nicolas Samson,Iryna Sanders,Olivier Saurat,Olivier Saurat,Claude Scarpelli,Thomas Schiex,Béatrice Segurens,Andrew J. Severin,D. Janine Sherrier,Ruihua Shi,Sarah Sims,Susan R. Singer,Senjuti Sinharoy,Lieven Sterck,Agnès Viollet,Bing Bing Wang,Keqin Wang,Mingyi Wang,Xiaohong Wang,Jens Warfsmann,Jean Weissenbach,Doug White,James D. White,Graham B. Wiley,Patrick Wincker,Yanbo Xing,Limei Yang,Ziyun Yao,Fu Ying,Jixian Zhai,Liping Zhou,Antoine Zuber,Antoine Zuber,Jean Dénarié,Jean Dénarié,Richard A. Dixon,Gregory D. May,David C. Schwartz,Jane Rogers,Francis Quetier,Christopher D. Town,Bruce A. Roe +138 more
TL;DR: The draft sequence of the M. truncatula genome sequence is described, a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics, which provides significant opportunities to expand al falfa’s genomic toolbox.
Journal ArticleDOI
Mapping copy number variation by population-scale genome sequencing
Ryan E. Mills,Klaudia Walter,Chip Stewart,Robert E. Handsaker,Ken Chen,Can Alkan,Alexej Abyzov,Seungtai Yoon,Kai Ye,R. Keira Cheetham,Asif T. Chinwalla,Donald F. Conrad,Yutao Fu,Fabian Grubert,Iman Hajirasouliha,Fereydoun Hormozdiari,Lilia M. Iakoucheva,Zamin Iqbal,Shuli Kang,Jeffrey M. Kidd,Miriam K. Konkel,Joshua M. Korn,Ekta Khurana,Deniz Kural,Hugo Y. K. Lam,Jing Leng,Ruiqiang Li,Yingrui Li,Chang-Yun Lin,Ruibang Luo,Xinmeng Jasmine Mu,James Nemesh,Heather E. Peckham,Tobias Rausch,Aylwyn Scally,Xinghua Shi,Michael Strömberg,Adrian M. Sütz,Alexander E. Urban,Jerilyn A. Walker,Jiantao Wu,Yujun Zhang,Zhengdong D. Zhang,Mark A. Batzer,Li Ding,Gabor T. Marth,Gil McVean,Jonathan Sebat,Michael Snyder,Jun Wang,Jun Wang,Kenny Ye,Evan E. Eichler,Mark Gerstein,Matthew E. Hurles,Charles Lee,Steven A. McCarroll,Steven A. McCarroll,Jan O. Korbel,Francis S. Collins,D. L. Altshuler,Richard Durbin,Gonçalo R. Abecasis,David R. Bentley,Aravinda Chakravarti,Andrew G. Clark,F. M. De La Vega,Peter Donnelly,Michael Egholm,Paul Flicek,S. Gabriel,Richard A. Gibbs,Bartha Maria Knoppers,Eric S. Lander,Hans Lehrach,Elaine R. Mardis,Gilean McVean,Deborah A. Nickerson,Leena Peltonen,Alan J. Schafer,Stephen T. Sherry,Richard K. Wilson,David Rio Deiros,Michael L. Metzker,Donna Muzny,Jeffrey S. Reid,D Wheeler,Jingxiang Li,Min Jian,Guoqing Li,Huiqing Liang,Geng Tian,Bo Wang,Wei Wang,Huanming Yang,Xiuqing Zhang,Huisong Zheng,Lauren Ambrogio,Toby Bloom,Kristian Cibulskis,T. J. Fennell,David B. Jaffe,Erica Shefler,Carrie Sougnez,Niall Anthony Gormley,Sean Humphray,Zoya Kingsbury,P. Koko-Gonzales,Jennifer Stone,Kevin McKernan,Gianna Costa,Jeffrey K. Ichikawa,Cheng-Sheng Lee,Ralf Sudbrak,Tatjana Borodina,Andreas Dahl,Alexey N. Davydov,P. Marquardt,Florian Mertes,Wilfried Nietfeld,Philip Rosenstiel,Stuart L. Schreiber,Alexey Soldatov,Bernd Timmermann,M. Tolzmann,Jason P. Affourtit,D. Ashworth,S. Attiya,M. Bachorski,E. Buglione,A. Burke,A. Caprio,Christopher Celone,S. Clark,D. Conners,B. Desany,L. Gu,L. Guccione,K. Kao,A. Kebbel,J. Knowlton,M. Labrecque,L. McDade,Craig Elder Mealmaker,M. Minderman,A. Nawrocki,Faheem Niazi,K. Pareja,Ramenani Ravi K,D. Riches,W. Song,Cynthia L. Turcotte,S. Wang,David J. Dooling,Linnea Fulton,Robert S. Fulton,George M. Weinstock,James O. Burton,David M. Carter,Carol Churcher,Alison J. Coffey,Anthony J. Cox,A. Palotie,Michael A. Quail,Tara Skelly,Jim Stalker,Harold Swerdlow,Dan Turner,A. De Witte,S. Giles,Matthew N. Bainbridge,Danny Challis,Aniko Sabo,Fuli Yu,Jin Yu,Xiaodong Fang,Xiaosen Guo,Shuaishuai Tai,Honglong Wu,Xiaole Zheng,Yan Zhou,E. P. Garrison,Weichun Huang,Amit Indap,Wan-Ping Lee,Wen Fung Leong,Aaron R. Quinlan,Alistair Ward,Mark J. Daly,Mark A. DePristo,A. D. Ball,Eric Banks,Brian L. Browning,Kiran V. Garimella,Sharon R. Grossman,Megan Hanna,Christopher Hartl,Andrew Kernytsky,J. M. Korn,Heng Li,Jared Maguire,Aaron McKenna,James Nemesh,Anthony A. Philippakis,Ryan Poplin,Amanda J. Price,Manual Rivas,Pardis C. Sabeti,Stephen F. Schaffner,Ilya Shlyakhter,David Neil Cooper,Edward V. Ball,Matthew Mort,Adam Phillips,Peter D. Stenson,Vladimir Makarov,Carlos Bustamante,Adam R. Boyko,Jeremiah D. Degenhardt,Simon Gravel,Ryan N. Gutenkunst,Mark Kaganovich,Alon Keinan,Philippe Lacroute,Xin Ma,Alex Reynolds,Laura Clarke,Fiona Cunningham,Javier Herrero,S. Keenen,Eugene Kulesha,Rasko Leinonen,William M. McLaren,Rajesh Radhakrishnan,Raffaella Smith,Vadim Zalunin,Xiangqun Zheng-Bradley,Adrian M. Stütz,Michael Bauer,Tony Cox,Michael A. Eberle,Terena James,Scott Kahn,Lucinda Murray,Fiona Hyland,Jonathan M. Manning,Stephen F. McLaughlin,Onur Sakarya,Yongming A. Sun,Eric F. Tsung,M. Albrecht,Vyacheslav Amstislavskiy,Ralf Herwig,Dmitri Parkhomchuk,Richa Agarwala,H. M. Khouri,Aleksandr Morgulis,Justin Paschall,Lon Phan,Kirill Rotmistrovsky,Robert Sanders,Martin Shumway,Chunlin Xiao,Adam Auton,Gerton Lunter,Jonathan Marchini,Loukas Moutsianas,Simon Myers,Afidalina Tumian,Jo Knight,Roger Winer,David Craig,Stephen M. Beckstrom-Sternberg,Alexis Christoforides,Ahmet Kurdoglu,John V. Pearson,Shripad Sinari,Waibhav Tembe,David Haussler,Angie S. Hinrichs,Sol Katzman,Andrew D. Kern,Robert M. Kuhn,Molly Przeworski,Ryan D. Hernandez,Bryan Howie,Joanna L. Kelley,S. C. Melton,Paige Anderson,Thomas W. Blackwell,Wei Chen,William O.C.M. Cookson,Jun Ding,Hyun Min Kang,Mark Lathrop,Liming Liang,Miriam F. Moffatt,Paul Scheet,C Sidore,Xiaowei Zhan,Sebastian Zöllner,Philip Awadalla,Ferran Casals,Youssef Idaghdour,Jon Keebler,Eric A. Stone,Martine Zilversmit,Lynn B. Jorde,Jinchuan Xing,Gozde Aksay,Suleyman Cenk Sahinalp,Peter H. Sudmant,Daniel C. Koboldt,Michael D. McLellan,John W. Wallis,Michael C. Wendl,Qunyuan Zhang,Cornelis A. Albers,Qasim Ayub,Senduran Balasubramaniam,Jeffrey C. Barrett,Yuan Chen,Petr Danecek,Emmanouil T. Dermitzakis,Min Hu,Ni Huang,Han-Jun Jin,Luke Jostins,Thomas M. Keane,Si Quang Le,Susan Lindsay,Quan Long,Daniel G. MacArthur,Stephen B. Montgomery,Leopold Parts,Chris Tyler-Smith,Shankar Balasubramanian,Robert D. Bjornson,Jiang Du,Lukas Habegger,Rajini R Haraksingh,Justin Jee,H. Y. Lam,J. Jeng,Zhaolei Zhang,E. Bank,S. Yoon,J. Kidd,C. Coafra,Huyen Dinh,Christie Kovar,Sandra J. Lee,Lynne V. Nazareth,Jane Wilkinson,H. M. Khouri,Carol Scott,Neda Gharani,Jane Kaye,Alastair Kent,T. Li,Amy L. McGuire,Pilar N. Ossorio,Charles N. Rotimi,Yeyang Su,Lorraine Toji,Lisa D Brooks,Adam Felsenfeld,Jean E. McEwen,Assya Abdallah,C. R. Juenger,N. C. Clemm,Audrey Duncanson,Eric D. Green,Mark S. Guyer,Jessica L. Peterson +374 more
TL;DR: A map of unbalanced SVs is constructed based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations, and serves as a resource for sequencing-based association studies.
Journal ArticleDOI
A physical map of the human genome.
John Douglas Mcpherson,Marco A. Marra,Marco A. Marra,LaDeana W. Hillier,Robert H. Waterston,Asif T. Chinwalla,John W. Wallis,Mandeep Sekhon,Kristine M. Wylie,Elaine R. Mardis,Richard K. Wilson,Robert S. Fulton,Tamara A. Kucaba,Caryn Wagner-McPherson,William B. Barbazuk,Simon G. Gregory,Sean Humphray,Lisa French,R Evans,Graeme Bethel,Adam Whittaker,Jane L. Holden,Owen T. McCann,Andrew Dunham,Carol Soderlund,Carol Scott,David R. Bentley,Gregory D. Schuler,Hsiu Chuan Chen,Wonhee Jang,Eric D. Green,Jacquelyn R. Idol,Valerie Maduro,Kate Montgomery,Eunice Lee,Ashley Miller,Suzanne Emerling,Raju Kucherlapati,Richard A. Gibbs,Steve Scherer,J. Harley Gorrell,Erica Sodergren,Kerstin P. Clerc-Blankenburg,Paul E. Tabor,S. Naylor,Dawn Garcia,J. de Jong,J. de Jong,J. de Jong,Joseph J. Catanese,Joseph J. Catanese,Joseph J. Catanese,Norma J. Nowak,Kazutoyo Osoegawa,Kazutoyo Osoegawa,Kazutoyo Osoegawa,Shizhen Qin,Lee Rowen,Anuradha Madan,Monica Dors,Leroy Hood,Barbara J. Trask,Cynthia Friedman,Hillary Massa,Vivian G. Cheung,Ilan R. Kirsch,Thomas Reid,Raluca Yonescu,Jean Weissenbach,Thomas Brüls,Roland Heilig,Elbert Branscomb,Anne S. Olsen,Norman A. Doggett,Jan Fang Cheng,Trevor Hawkins,Richard M. Myers,Jin Shang,Lucía Ramírez,Jeremy Schmutz,Olivia Velasquez,Kami Dixon,Nancy E. Stone,David R. Cox,David Haussler,W. James Kent,Terrence S. Furey,Sanja Rogic,Scot Kennedy,Steven J.M. Jones,André Rosenthal,Gaiping Wen,Markus Schilhabel,Gernot Gloeckner,Gerald Nyakatura,Reiner Siebert,Brigitte Schlegelberger,Julie R. Korenberg,Xiao Ning Chen,Asao Fujiyama,Masahira Hattori,Atsushi Toyoda,Tetsushi Yada,Hong Seok Park,Yoshiyuki Sakaki,Nobuyoshi Shimizu,Shuichi Asakawa,Kazuhiko Kawasaki,Takashi Sasaki,Ai Shintani,Atsushi Shimizu,Kazunori Shibuya,Jun Kudoh,Shinsei Minoshima,Juliane Ramser,Peter Seranski,Céline Hoff,Annemarie Poustka,Richard Reinhardt,Hans Lehrach +119 more
TL;DR: The construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions are reported.
Journal ArticleDOI
Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas
Claire Palles,Jean-Baptiste Cazier,Kimberley Howarth,Enric Domingo,Angela M. Jones,Peter Broderick,Zoe Kemp,Sarah L. Spain,Estrella Guarino,Israel Salguero,Amy L. Sherborne,Daniel Chubb,Luis G. Carvajal-Carmona,Yusanne Ma,Kulvinder Kaur,Sara E. Dobbins,Ella Barclay,Maggie Gorman,Lynn Martin,Michal Kovac,Michal Kovac,Sean Humphray,Anneke Lucassen,Christopher Holmes,David Bentley,Peter Donnelly,Peter Donnelly,Jenny C. Taylor,Christos Petridis,Rebecca Roylance,Elinor J. Sawyer,David J. Kerr,Susan K. Clark,Jonathan M. Grimes,Stephen E. Kearsey,Huw Thomas,Gilean McVean,Richard S. Houlston,Ian Tomlinson +38 more
TL;DR: A recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain, predicted to cause a defect in the correction of mispaired bases inserted during DNA replication.