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
A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci
Robert S. Illingworth,Alastair R.W. Kerr,Dina DeSousa,Helle F. Jørgensen,Peter Ellis,Jim Stalker,David Jackson,Chris Clee,Robert W. Plumb,Jane Rogers,Sean Humphray,Tony Cox,Cordelia Langford,Adrian Bird +13 more
TL;DR: It is established that 6%–8% of CGIs are methylated in genomic DNA of human blood, brain, muscle, and spleen, and CGIs showing tissue-specific methylation were overrepresented at numerous genetic loci that are essential for development, including HOX and PAX family members.
Journal ArticleDOI
DNA sequence and analysis of human chromosome 9
Andrew J. Mungall,Sophie Palmer,Sarah Sims,C A Edwards,Jennifer L. Ashurst,Laurens G. Wilming,Matthew Jones,Roger Horton,Sarah E. Hunt,Carol Scott,James G. R. Gilbert,Michele Clamp,Graeme Bethel,Sarah Milne,R Ainscough,J P Almeida,K D Ambrose,T D Andrews,R I S Ashwell,A K Babbage,C L Bagguley,J Bailey,Ruby Banerjee,Darren Barker,K F Barlow,K Bates,David Beare,Helen Beasley,O. Beasley,Christine P. Bird,S. Blakey,S Bray-Allen,J Brook,A J Brown,J Y Brown,D C Burford,W Burrill,John Burton,C Carder,Nigel P. Carter,J C Chapman,S Y Clark,Graeme T Clark,C M Clee,S. M. Clegg,V. Cobley,R. E. Collier,Joanna Collins,L K Colman,N Corby,G. J. Coville,K M Culley,Pawandeep Dhami,Jim Davies,Matthew Dunn,M Earthrowl,A E Ellington,K A Evans,L M Faulkner,Matthew D. Francis,Adam Frankish,J Frankland,Lisa French,P Garner,J Garnett,Mohammed J. R. Ghori,L M Gilby,Christopher J. Gillson,Rebecca Glithero,Darren Grafham,M Grant,Susan M. Gribble,C Griffiths,Mark Griffiths,Rebekah Hall,K S Halls,S Hammond,Joanna Harley,E. Hart,Paul Heath,R Heathcott,S. Holmes,Philip Howden,Kevin L. Howe,Gareth R. Howell,Elizabeth J. Huckle,Sean Humphray,Matthew Humphries,Adrienne Hunt,Christopher M. Johnson,A Joy,M. Kay,Stephen Keenan,A M Kimberley,A. King,Gavin K. Laird,Cordelia Langford,S Lawlor,Daniel Leongamornlert,Margaret A. Leversha,Christine Lloyd,D. M. Lloyd,Jane E. Loveland,J Lovell,Sancha Martin,M Mashreghi-Mohammadi,Gareth Maslen,Lucy Matthews,O. T. McCann,S J McLaren,Kirsten McLay,Amanda McMurray,M. J F Moore,James C. Mullikin,David Niblett,T Nickerson,K L Novik,Karen Oliver,E K Overton-Larty,Anne Parker,R Patel,A. V. Pearce,A I Peck,Benjamin Phillimore,Sam Phillips,Robert W. Plumb,K M Porter,Y. Ramsey,S A Ranby,Catherine M. Rice,Mark T. Ross,S. Searle,Harminder Sehra,E Sheridan,C. D. Skuce,Sarah E. Smith,Michelle Smith,L Spraggon,S. Squares,Charles A. Steward,N Sycamore,G Tamlyn-Hall,J Tester,A J Theaker,Duncan W. Thomas,A Thorpe,Alan Tracey,A Tromans,B Tubby,Melanie M. Wall,J. M. Wallis,Anthony P. West,S S White,S. Whitehead,H Whittaker,A Wild,Dave Willey,T. E. Wilmer,Jonathan Wood,Paul Wray,J C Wyatt,L Young,R M Younger,David R. Bentley,Alan Coulson,Richard Durbin,Tim Hubbard,John Sulston,Ian Dunham,Jane Rogers,Stephan Beck +170 more
TL;DR: Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block, and detects recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.
A map of human genome variation from population-scale sequencing
Richard Durbin,David Altshuler,Gonçalo R. Abecasis,David R. Bentley,Aravinda Chakravarti,Andrew G. Clark,Francis S. Collins,Francisco M. De La Vega,Peter Donnelly,Michael Egholm,Paul Flicek,Stacey Gabriel,Richard A. Gibbs,Bartha Maria Knoppers,Eric S. Lander,Hans Lehrach,Elaine R. Mardis,Gil McVean,Deborah A. Nickerson,Leena Peltonen,Alan J. Schafer,Stephen T. Sherry,Jun Wang,Richard K. Wilson,David Rio Deiros,Mike Metzker,Donna M. Muzny,Jeffrey S. Reid,David C. Wheeler,Jingxiang Li,Min Jian,Guoqing Li,Ruiqiang Li,Huiqing Liang,Geng Tian,Bo Wang,Jian Wang,Wei Wang,Huanming Yang,Xiuqing Zhang,Huisong Zheng,Lauren Ambrogio,Toby Bloom,Kristian Cibulskis,Timothy Fennell,David B. Jaffe,Erica Shefler,Carrie Sougnez,Niall Anthony Gormley,Sean Humphray,Zoya Kingsbury,Paula Koko-Gonzales,Jennifer Stone,Kevin McKernan,Gina Costa,Jeffrey K. Ichikawa,Clarence Lee,Ralf Sudbrak,Tatiana A. Borodina,Andreas Dahl,Alexey N. Davydov,Peter Marquardt,Florian Mertes,Wilfiried Nietfeld,Philip Rosenstiel,Stefan Schreiber,Aleksey V. Soldatov,Bernd Timmermann,Marius Tolzmann,Jason P. Affourtit,Dana Ashworth,Said Attiya,Melissa Bachorski,Eli Buglione,Adam Burke,Amanda Caprio,Christopher Celone,Shauna Clark,David Conners,Brian Desany,Lisa Gu,Lorri Guccione,Kalvin Kao,Andrew Kebbel,Jennifer Knowlton,Matthew Labrecque,Louise McDade,Craig Elder Mealmaker,Melissa Minderman,Anne Nawrocki,Faheem Niazi,Kristen Pareja,Ramenani Ravi K,David Riches,Wanmin Song,Cynthia L. Turcotte,Shally Wang,David J. Dooling,Lucinda Fulton,Robert S. Fulton,George M. Weinstock,John Burton,David M. Carter,Carol Churcher,Alison J. Coffey,Anthony J. Cox,Aarno Palotie,Michael A. Quail,Tom Skelly,James Stalker,Harold Swerdlow,Daniel J. Turner,Anniek De Witte,Shane Giles,Matthew N. Bainbridge,Danny Challis,Aniko Sabo,Fuli Yu,Jin Yu,Xiaodong Fang,Xiaosen Guo,Yingrui Li,Ruibang Luo,Shuaishuai Tai,Honglong Wu,Hancheng Zheng,Xiaole Zheng,Yan Zhou,Gabor T. Marth,Erik Garrison,Weichun Huang,Amit Indap,Deniz Kural,Wan-Ping Lee,Wen Fung Leong,Aaron R. Quinlan,Chip Stewart,Michael Strömberg,Alistair Ward,Jiantao Wu,Charles Kai-Wu Lee,Ryan E. Mills,Xinghua Shi,Mark J. Daly,Mark A. DePristo,Aaron D. Ball,Eric Banks,Brian L. Browning,Kiran V. Garimella,Sharon R. Grossman,Robert E. Handsaker,Matt Hanna,Christopher Hartl,Andrew Kernytsky,Joshua M. Korn,Heng Li,Jared Maguire,Steven A. McCarroll,Aaron McKenna,James Nemesh,Anthony A. Philippakis,Ryan Poplin,Alkes L. Price,Manuel A. Rivas,Pardis C. Sabeti,Stephen F. Schaffner,Ilya Shlyakhter,David Neil Cooper,Edward V. Ball,Matthew Mort,Andrew David Phillips,Peter D. Stenson,Jonathan Sebat,Vladimir Makarov,Kenny Ye,Seungtai Yoon,Carlos Bustamante,Adam R. Boyko,Jeremiah D. Degenhardt,Simon Gravel,Ryan N. Gutenkunst,Mark Kaganovich,Alon Keinan,Phil Lacroute,Xin Ma,Andrew R. Reynolds,Laura Clarke,Fiona Cunningham,Javier Herrero,Stephen Keenen,Eugene Kulesha,Rasko Leinonen,William M. McLaren,Rajesh Radhakrishnan,Richard Smith,Vadim Zalunin,Xiangqun Zheng-Bradley,Jan O. Korbel,Adrian M. Stütz,Markus J. Bauer,R. Keira Cheetham,Tony Cox,Michael A. Eberle,Terena James,Scott Kahn,Lisa Murray,Kai Ye,Yutao Fu,Fiona Hyland,Jonathan M. Manning,Stephen F. McLaughlin,Heather E. Peckham,Onur Sakarya,Yongming A. Sun,Eric F. Tsung,Mark A. Batzer,Miriam K. Konkel,Jerilyn A. Walker,M. Albrecht,Vyacheslav Amstislavskiy,Ralf Herwig,Dimitri V. Parkhomchuk,Richa Agarwala,Hoda M. Khouri,Aleksandr Morgulis,Justin Paschall,Lon Phan,Kirill Rotmistrovsky,Robert Sanders,Martin Shumway,Chunlin Xiao,Adam Auton,Zamin Iqbal,Gerton Lunter,Jonathan Marchini,Loukas Moutsianas,Simon Myers,Afidalina Tumian,James R. Knight,Roger Winer,David Craig,Steve 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. Cord Melton,Yun Li,Paul 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,Carlo Sidore,Matthew W. Snyder,Xiaowei Zhan,Sebastian Zöllner,Philip Awadalla,Ferran Casals,Youssef Idaghdour,John Keebler,Eric A. Stone,Martine Zilversmit,Lynn B. Jorde,Jinchuan Xing,Evan E. Eichler,Gozde Aksay,Can Alkan,Iman Hajirasouliha,Fereydoun Hormozdiari,Jeffrey M. Kidd,S. Cenk Sahinalp,Peter H. Sudmant,Ken Chen,Asif T. Chinwalla,Li Ding,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,Donald F. Conrad,Petr Danecek,Emmanouil T. Dermitzakis,Min Hu,Ni Huang,Matthew E. Hurles,Han-Jun Jin,Luke Jostins,Thomas M. Keane,Si Quang Le,Sarah J. Lindsay,Quan Long,Daniel G. MacArthur,Stephen B. Montgomery,Leopold Parts,Chris Tyler-Smith,Klaudia Walter,Yujun Zhang,Mark Gerstein,Michael Snyder,Alexej Abyzov,Suganthi Balasubramanian,Robert D. Bjornson,Jiang Du,Fabian Grubert,Lukas Habegger,Rajini R Haraksingh,Justin Jee,Ekta Khurana,Hugo Y. K. Lam,Jing Leng,Xinmeng Jasmine Mu,Alexander E. Urban,Zhengdong D. Zhang,Cristian Coafra,Huyen Dinh,Christie Kovar,Sandy Lee,Lynne V. Nazareth,Jane E. Wilkinson,Allison Coffey,Carol Scott,Neda Gharani,Jane Kaye,Alastair Kent,Taosha Li,Amy L. McGuire,Pilar N. Ossorio,Charles N. Rotimi,Yeyang Su,Lorraine Toji,Lisa D. Brooks,Adam Felsenfeld,Jean E. McEwen,Assya Abdallah,Christopher R. Juenger,Nicholas C. Clemm,Audrey Duncanson,Eric D. Green,Mark S. Guyer,Jane Peterson +361 more
TL;DR: The pilot phase of the 1000 Genomes Project is presented, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms, and the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants are described.
Journal ArticleDOI
Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units
Carol J Saunders,Neil A. Miller,Neil A. Miller,Sarah E Soden,Sarah E Soden,Darrell L. Dinwiddie,Aaron Noll,Noor Abu Alnadi,Nevene Andraws,Melanie Patterson,Lisa Ann Krivohlavek,Joel Fellis,Sean Humphray,Peter Saffrey,Zoya Kingsbury,Jacqueline Weir,Jason Betley,Russell J. Grocock,Elliott H. Margulies,Emily G. Farrow,Michael Artman,Michael Artman,Nicole P. Safina,Nicole P. Safina,Joshua E. Petrikin,Kevin Hall,Stephen F. Kingsmore +26 more
TL;DR: A method that uses whole-genome sequencing (WGS) to achieve a differential diagnosis of genetic disorders in 50 hours rather than the 4 to 6 weeks is described and is intended to be a prototype for use in neonatal intensive care units.
Journal ArticleDOI
Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome
Laura Baxter,Sucheta Tripathy,Naveed Ishaque,Nico Boot,Adriana Cabral,Eric Kemen,Marco Thines,Marco Thines,Audrey M. V. Ah-Fong,Ryan G. Anderson,Wole Badejoko,Peter D. Bittner-Eddy,Jeffrey L. Boore,Marcus C. Chibucos,Mary Coates,Paramvir S. Dehal,Kim D. Delehaunty,Suomeng Dong,Suomeng Dong,Polly Downton,Bernard Dumas,Bernard Dumas,Georgina Fabro,Catrina Fronick,Susan I. Fuerstenberg,Lucinda Fulton,Elodie Gaulin,Elodie Gaulin,Francine Govers,Linda Karen Hughes,Sean Humphray,Rays H. Y. Jiang,Rays H. Y. Jiang,Howard S. Judelson,Sophien Kamoun,Kim Kyung,Harold J. G. Meijer,Patrick Minx,Paul Morris,Joanne O. Nelson,Vipa Phuntumart,Dinah Qutob,Anne P. Rehmany,Alejandra Rougon-Cardoso,Peter Ryden,Trudy Torto-Alalibo,David J. Studholme,Yuanchao Wang,Joe Win,Jonathan Wood,Sandra W. Clifton,Jane Rogers,Guido Van den Ackerveken,Jonathan D. G. Jones,John M. McDowell,Jim Beynon,Brett M. Tyler,Brett M. Tyler +57 more
TL;DR: The genome sequence of the oomycete Hyaloperonospora arabidopsidis is reported, an obligate biotroph and natural pathogen of Arabidopsis thaliana, which exhibits dramatic reductions in genes encoding RXLR effectors, proteins associated with zoospore formation and motility, and enzymes for assimilation of inorganic nitrogen and sulfur.