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Keith O'Neill
Researcher at Broad Institute
Publications - 12
Citations - 4977
Keith O'Neill is an academic researcher from Broad Institute. The author has contributed to research in topics: Genome & Phytophthora infestans. The author has an hindex of 10, co-authored 12 publications receiving 4659 citations. Previous affiliations of Keith O'Neill include Harvard University & Virginia Bioinformatics Institute.
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Journal ArticleDOI
Genome sequence, comparative analysis and haplotype structure of the domestic dog
Kerstin Lindblad-Toh,Claire M. Wade,Claire M. Wade,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Elinor K. Karlsson,Elinor K. Karlsson,David B. Jaffe,Michael Kamal,Michele Clamp,Jean L. Chang,Edward J. Kulbokas,Michael C. Zody,Evan Mauceli,Xiaohui Xie,Matthew Breen,Robert K. Wayne,Elaine A. Ostrander,Chris P. Ponting,Francis Galibert,Douglas Smith,Pieter J. deJong,Ewen F. Kirkness,Pablo Alvarez,Tara Biagi,William Brockman,Jonathan Butler,Chee-Wye Chin,April Cook,James Cuff,Mark J. Daly,Mark J. Daly,David DeCaprio,Sante Gnerre,Manfred Grabherr,Manolis Kellis,Michael Kleber,Carolyne Bardeleben,Leo Goodstadt,Andreas Heger,Christophe Hitte,Lisa Kim,Klaus-Peter Koepfli,Heidi G. Parker,John P. Pollinger,Stephen M. J. Searle,Nathan B. Sutter,Rachael Thomas,Caleb Webber,Jennifer Baldwin,Jennifer Baldwin,Adal Abebe,Amr Abouelleil,Lynne Aftuck,Mostafa Ait-zahra,Tyler Aldredge,Nicole R. Allen,Peter An,Scott Anderson,Claudel Antoine,Harindra Arachchi,Ali Aslam,Laura Ayotte,Pasang Bachantsang,Andrew Barry,Tashi Bayul,Mostafa Benamara,Aaron M. Berlin,Daniel Bessette,Berta Blitshteyn,Toby Bloom,Jason Blye,Leonid Boguslavskiy,Claude Bonnet,Boris Boukhgalter,Adam Brown,Patrick Cahill,Nadia Calixte,Jody Camarata,Yama Cheshatsang,Jeffrey Chu,Mieke Citroen,Alville Collymore,Patrick Cooke,Tenzin Dawoe,Riza M. Daza,Karin Decktor,Stuart DeGray,Norbu Dhargay,Kimberly Dooley,Kathleen Dooley,Passang Dorje,Kunsang Dorjee,Lester Dorris,Noah Duffey,Alan Dupes,Osebhajajeme Egbiremolen,Richard Elong,Jill Falk,Abderrahim Farina,Susan Faro,Diallo Ferguson,Patricia Ferreira,Sheila A. Fisher,Michael Fitzgerald,Karen Foley,Chelsea D. Foley,Alicia Franke,Dennis C. Friedrich,Diane Gage,Manuel Garber,Gary Gearin,Georgia Giannoukos,Tina Goode,Audra Goyette,Joseph Graham,Edward Grandbois,Kunsang Gyaltsen,Nabil Hafez,Daniel S. Hagopian,Birhane Hagos,Jennifer Ruth Sadler Hall,Claire M. Healy,Ryan Hegarty,Tracey Honan,Andrea Horn,Nathan Houde,Leanne Hughes,Leigh Anne Hunnicutt,M. Husby,Benjamin Jester,Charlien Jones,Asha Kamat,Ben Kanga,Cristyn Kells,Dmitry Khazanovich,Alix Chinh Kieu,Peter Kisner,Mayank Kumar,Krista Lance,Thomas E. Landers,Marcia Lara,William H. Lee,Jean-Pierre Leger,Niall J. Lennon,Lisa Leuper,Sarah LeVine,Jinlei Liu,Xiaohong Liu,Yeshi Lokyitsang,Tashi Lokyitsang,Annie Lui,Jan Macdonald,John E. Major,Richard Marabella,Kebede Maru,Charles Matthews,Susan McDonough,Teena Mehta,James Meldrim,Alexandre Melnikov,Louis Meneus,Atanas Mihalev,Tanya Mihova,Karen Hughes Miller,Rachel Mittelman,Valentine Mlenga,Leonidas Mulrain,Glen Munson,Adam Navidi,Jerome Naylor,Tuyen T. Nguyen,Nga Nguyen,Cindy Nguyen,Thu Nguyen,Robert Nicol,Nyima Norbu,Choe Norbu,Nathaniel Novod,Tenchoe Nyima,Peter Olandt,Barry O'Neill,Keith O'Neill,Sahal Osman,Lucien Oyono,Christopher Patti,Danielle Perrin,Pema Phunkhang,Fritz Pierre,Margaret Priest,Anthony Rachupka,Sujaa Raghuraman,Rayale Rameau,Verneda Ray,Christina Raymond,Filip Rege,Cecil Rise,Julie Rogers,Peter Rogov,Julie Sahalie,Sampath Settipalli,Ted Sharpe,Terrance Shea,Mechele Sheehan,Ngawang Sherpa,Jianying Shi,Diana M. Shih,Jessie Sloan,Cherylyn Smith,Todd Sparrow,John Stalker,Nicole Stange-Thomann,Sharon Stavropoulos,Catherine Stone,Sabrina M. Stone,Sean M. Sykes,Pierre Tchuinga,Pema Tenzing,Senait Tesfaye,Dawa Thoulutsang,Yama Thoulutsang,Kerri Topham,Ira Topping,Tsamla Tsamla,Helen Vassiliev,Vijay Venkataraman,Andy Vo,Tsering Wangchuk,Tsering Wangdi,Michael Weiand,Jane E. Wilkinson,Adam Wilson,Shailendra Yadav,Shuli Yang,Xiaoping Yang,Geneva Young,Qing Yu,Joanne Zainoun,Lisa Zembek,Andrew Zimmer,Eric S. Lander,Eric S. Lander +241 more
TL;DR: A high-quality draft genome sequence of the domestic dog is reported, together with a dense map of single nucleotide polymorphisms (SNPs) across breeds, to shed light on the structure and evolution of genomes and genes.
Journal ArticleDOI
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.
Brian J. Haas,Sophien Kamoun,Sophien Kamoun,Michael C. Zody,Michael C. Zody,Rays H. Y. Jiang,Rays H. Y. Jiang,Robert E. Handsaker,Liliana M. Cano,Manfred Grabherr,Chinnappa D. Kodira,Chinnappa D. Kodira,Sylvain Raffaele,Trudy Torto-Alalibo,Trudy Torto-Alalibo,Tolga O. Bozkurt,Audrey M. V. Ah-Fong,Lucia Alvarado,Vicky L. Anderson,Miles R. Armstrong,Anna O. Avrova,Laura Baxter,Jim Beynon,Petra C. Boevink,Stephanie R. Bollmann,Jorunn I. B. Bos,Vincent Bulone,Guohong Cai,Cahid Cakir,James C. Carrington,Megan Chawner,Lucio Conti,Stefano Costanzo,Richard Ewan,Noah Fahlgren,Michael A. Fischbach,Johanna Fugelstad,Eleanor M. Gilroy,Sante Gnerre,Pamela J. Green,Laura J. Grenville-Briggs,John Griffith,Niklaus J. Grünwald,Karolyn Horn,Neil R. Horner,Chia-Hui Hu,Edgar Huitema,Dong-Hoon Jeong,Alexandra M. E. Jones,Jonathan D. G. Jones,Richard W. Jones,Elinor K. Karlsson,Sridhara G. Kunjeti,Kurt Lamour,Zhenyu Liu,Li-Jun Ma,Dan MacLean,Marcus C. Chibucos,Hayes McDonald,Jessica McWalters,Harold J. G. Meijer,William Morgan,Paul Morris,Carol A. Munro,Keith O'Neill,Keith O'Neill,Manuel D. Ospina-Giraldo,Andrés Pinzón,Leighton Pritchard,Bernard H Ramsahoye,Qinghu Ren,Silvia Restrepo,Sourav Roy,Ari Sadanandom,Alon Savidor,Sebastian Schornack,David C. Schwartz,Ulrike Schumann,Ben Schwessinger,Lauren Seyer,Ted Sharpe,Cristina Silvar,Jing Song,David J. Studholme,Sean M. Sykes,Marco Thines,Marco Thines,Peter J. I. van de Vondervoort,Vipaporn Phuntumart,Stephan Wawra,R. Weide,Joe Win,Carolyn A. Young,Shiguo Zhou,William E. Fry,Blake C. Meyers,Pieter van West,Jean B. Ristaino,Francine Govers,Paul R. J. Birch,Stephen C. Whisson,Howard S. Judelson,Chad Nusbaum +102 more
TL;DR: The sequence of the P. infestans genome is reported, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates and probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Journal ArticleDOI
Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing
Roman K. Thomas,Elizabeth Nickerson,Jan Fredrik Simons,Pasi A. Jänne,Torstein Tengs,Torstein Tengs,Yuki Yuza,Levi A. Garraway,Levi A. Garraway,Thomas LaFramboise,Thomas LaFramboise,Jeffrey C. Lee,Jeffrey C. Lee,Kinjal Shah,Kinjal Shah,Keith O'Neill,Hidefumi Sasaki,Neal I. Lindeman,Kwok-Kin Wong,Ana M. Borras,Edward J. Gutmann,Konstantin H. Dragnev,Ralph M. Debiasi,Ralph M. Debiasi,Tzu Hsiu Chen,Tzu Hsiu Chen,Karen A. Glatt,Heidi Greulich,Heidi Greulich,Brian Desany,Christine Lubeski,William Brockman,Pablo Alvarez,Stephen K. Hutchison,John H. Leamon,Michael T. Ronan,Gregory S. Turenchalk,Michael Egholm,William R. Sellers,William R. Sellers,Jonathan M. Rothberg,Matthew Meyerson +41 more
TL;DR: It is shown that microreactor-based pyrosequencing can detect rare cancer-associated sequence variations by independent and parallel sampling of multiple representatives of a given DNA fragment and can thereby facilitate accurate molecular diagnosis of heterogeneous cancer specimens and enable patient selection for targeted cancer therapies.
Journal ArticleDOI
Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain.
Jeffrey C. Lee,Jeffrey C. Lee,Igor Vivanco,Rameen Beroukhim,Rameen Beroukhim,Julie H. Y Huang,Whei Feng,Whei Feng,Ralph M. Debiasi,Ralph M. Debiasi,Koji Yoshimoto,J. King,Phioanh L. Nghiemphu,Yuki Yuza,Qing-Qing Xu,Heidi Greulich,Heidi Greulich,Roman K. Thomas,Roman K. Thomas,J. Guillermo Paez,J. Guillermo Paez,Timothy C. Peck,Timothy C. Peck,David Linhart,David Linhart,Karen A. Glatt,Gad Getz,Robert C. Onofrio,Liuda Ziaugra,Ross L. Levine,Stacey Gabriel,Tomohiro Kawaguchi,Keith O'Neill,Haumith Khan,Linda M. Liau,Stanley F. Nelson,P. Nagesh Rao,Paul S. Mischel,Russell O. Pieper,Timothy F. Cloughesy,Daniel J. Leahy,William R. Sellers,William R. Sellers,Charles L. Sawyers,Matthew Meyerson,Matthew Meyerson,Ingo K. Mellinghoff +46 more
TL;DR: The results suggest extracellular missense mutations as a novel mechanism for oncogenic EGFR activation and may help identify patients who can benefit from EGFR kinase inhibitors for treatment of glioblastoma.
Journal ArticleDOI
Assembly of polymorphic genomes: algorithms and application to Ciona savignyi.
Jade P. Vinson,David B. Jaffe,Keith O'Neill,Elinor K. Karlsson,Nicole Stange-Thomann,Scott Anderson,Jill P. Mesirov,Nori Satoh,Yutaka Satou,Chad Nusbaum,Bruce W. Birren,James E. Galagan,Eric S. Lander +12 more
TL;DR: This method was developed to assemble the genome of the sea squirt Ciona savignyi, which was sequenced to a depth of 12.7 x from a single wild individual and determined that the sequenced individual had an extremely high heterozygosity rate.