Y
Yufeng Shen
Researcher at Columbia University
Publications - 272
Citations - 24893
Yufeng Shen is an academic researcher from Columbia University. The author has contributed to research in topics: Exome sequencing & Mass spectrometry. The author has an hindex of 70, co-authored 237 publications receiving 20891 citations. Previous affiliations of Yufeng Shen include University of Cambridge & Environmental Molecular Sciences Laboratory.
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Journal ArticleDOI
The complete genome of an individual by massively parallel DNA sequencing
David A. Wheeler,Maithreyan Srinivasan,Michael Egholm,Yufeng Shen,Lei Chen,Amy L. McGuire,Wen He,Yi-Ju Chen,Vinod Makhijani,G. Thomas Roth,Xavier V. Gomes,Karrie R. Tartaro,Karrie R. Tartaro,Faheem Niazi,Cynthia L. Turcotte,Gerard P. Irzyk,James R. Lupski,James R. Lupski,Craig Chinault,Xingzhi Song,Yue Liu,Ye Yuan,Lynne V. Nazareth,Xiang Qin,Donna M. Muzny,Marcel Margulies,George M. Weinstock,George M. Weinstock,Richard A. Gibbs,Richard A. Gibbs,Jonathan M. Rothberg,Jonathan M. Rothberg +31 more
TL;DR: This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods and demonstrated the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing, which is the first genome sequenced by next-generation technologies.
Journal ArticleDOI
Evolutionary and biomedical insights from the rhesus macaque genome
Richard A. Gibbs,Jeffrey Rogers,Michael G. Katze,Roger E. Bumgarner,George M. Weinstock,Elaine R. Mardis,Karin A. Remington,Robert L. Strausberg,J. Craig Venter,Richard K. Wilson,Mark A. Batzer,Carlos Bustamante,Evan E. Eichler,Matthew W. Hahn,Ross C. Hardison,Kateryna D. Makova,Webb Miller,Aleksandar Milosavljevic,Robert E. Palermo,Adam Siepel,James M. Sikela,Tony Attaway,Stephanie Bell,Kelly E. Bernard,Christian J. Buhay,Mimi N. Chandrabose,Marvin Diep Dao,Clay Davis,Kimberly D. Delehaunty,Yan Ding,Huyen Dinh,Shannon Dugan-Rocha,Lucinda Fulton,Ramatu Ayiesha Gabisi,Toni T. Garner,Jennifer Godfrey,Alicia Hawes,Judith Hernandez,Sandra Hines,Michael Holder,Jennifer Hume,Shalini N. Jhangiani,Vandita Joshi,Ziad Khan,Ewen F. Kirkness,Andrew Cree,R. Gerald Fowler,Sandra L. Lee,Lora Lewis,Zhangwan Li,Yih-shin Liu,Stephanie M. Moore,Donna M. Muzny,Lynne V. Nazareth,Dinh Ngoc Ngo,Geoffrey Okwuonu,Grace Pai,David A. Parker,Heidie A. Paul,Cynthia Pfannkoch,Craig Pohl,Yu-Hui Rogers,San Juana Ruiz,Aniko Sabo,Jireh Santibanez,Brian W. Schneider,Scott M. Smith,Erica Sodergren,Amanda F. Svatek,Teresa Utterback,Selina Vattathil,Wesley C. Warren,Courtney Sherell White,Asif T. Chinwalla,Yucheng Feng,Aaron L. Halpern,LaDeana W. Hillier,Xiaoqiu Huang,Patrick Minx,Joanne O. Nelson,Kymberlie H. Pepin,Xiang Qin,Granger G. Sutton,Eli Venter,Brian P. Walenz,John W. Wallis,Kim C. Worley,Shiaw-Pyng Yang,Steven J. M. Jones,Marco A. Marra,Mariano Rocchi,Jacqueline E. Schein,Robert Baertsch,Laura Clarke,Miklós Csürös,Jarret Glasscock,R. Alan Harris,Paul Havlak,Andrew R. Jackson,Huaiyang Jiang,Yue Liu,David N. Messina,Yufeng Shen,Henry Xing-Zhi Song,Todd Wylie,Lan Zhang,Ewan Birney,Kyudong Han,Miriam K. Konkel,Jungnam Lee,Arian F.A. Smit,Brygg Ullmer,Hui Wang,Jinchuan Xing,Jinchuan Xing,Richard Burhans,Ze Cheng,John E. Karro,Jian Ma,Brian J. Raney,Xinwei She,Michael J. Cox,Jeffery P. Demuth,Laura J. Dumas,Sang-Gook Han,Janet A. Hopkins,Anis Karimpour-Fard,Young Ho Kim,Jonathan R. Pollack,Tomas Vinar,Charles Addo-Quaye,Jeremiah D. Degenhardt,Alexandra Denby,Melissa J. Hubisz,Amit Indap,Carolin Kosiol,Bruce T. Lahn,Heather A. Lawson,Alison Marklein,Rasmus Nielsen,Eric J. Vallender,Andrew G. Clark,Betsy Ferguson,Ryan D. Hernandez,Kashif Hirani,Hildegard Kehrer-Sawatzki,Jessica Kolb,Shobha Patil,Ling-Ling Pu,Yanru Ren,David Glenn Smith,David A. Wheeler,Ian Schenck,Edward V. Ball,Rui Chen,David Neil Cooper,Belinda Giardine,Fan Hsu,W. James Kent,Arthur M. Lesk,David L. Nelson,William E. O'Brien,Kay Prüfer,Peter D. Stenson,James C. Wallace,Hui Ke,Xiaoming Liu,Peng Wang,Andy Peng Xiang,Fan Yang,Galt P. Barber,David Haussler,David Haussler,Donna Karolchik,Andrew D. Kern,Robert M. Kuhn,Kayla E. Smith,Ann S. Zwieg +177 more
TL;DR: The genome sequence of an Indian-origin Macaca mulatta female is determined and compared with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families.
Journal ArticleDOI
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
Christine G. Elsik,Christine G. Elsik,Christine G. Elsik,Ross L. Tellam,Kim C. Worley,Kim C. Worley,Richard A. Gibbs,Donna M. Muzny,George M. Weinstock,George M. Weinstock,David L. Adelson,Evan E. Eichler,Evan E. Eichler,Laura Elnitski,Roderic Guigó,Debora L. Hamernik,Steve M. Kappes,Harris A. Lewin,David J. Lynn,Frank W. Nicholas,Alexandre Reymond,Monique Rijnkels,Loren C. Skow,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Lawrence B. Schook,James E. Womack,Tyler Alioto,Stylianos E. Antonarakis,Alex Astashyn,Charles E. Chappie,Hsiu Chuan Chen,Jacqueline Chrast,Francisco Câmara,Olga Ermolaeva,Charlotte N. Henrichsen,Wratko Hlavina,Yuri Kapustin,Boris Kiryutin,Paul Kitts,Felix Kokocinski,Melissa J. Landrum,Donna Maglott,Kim D. Pruitt,Victor Sapojnikov,Stephen M. J. Searle,Victor V. Solovyev,Alexandre Souvorov,Catherine Ucla,Carine Wyss,Juan Manuel Anzola,Daniel Gerlach,Daniel Gerlach,Eran Elhaik,Eran Elhaik,Dan Graur,Justin T. Reese,Robert C. Edgar,John C. McEwan,Gemma Marie Payne,Joy M. Raison,Thomas Junier,Thomas Junier,Evgenia V. Kriventseva,Eduardo Eyras,Mireya Plass,Ravikiran Donthu,Denis M. Larkin,James M. Reecy,Mary Qu Yang,Lin Chen,Ze Cheng,Carol G. Chitko-McKown,George E. Liu,Lakshmi K. Matukumalli,Lakshmi K. Matukumalli,Jiuzhou Song,Bin Zhu,Daniel G. Bradley,Fiona S. L. Brinkman,Lilian P.L. Lau,Matthew D. Whiteside,Angela K. Walker,Thomas T. Wheeler,Theresa Casey,J. Bruce German,J. Bruce German,Danielle G. Lemay,Nauman J. Maqbool,A.J. Molenaar,Seongwon Seo,Paul Stothard,Cynthia L. Baldwin,R. Baxter,Candice L. Brinkmeyer-Larigford,Wendy C. Brown,Christopher P. Childers,Timothy Connelley,Shirley A. Ellis,Krista L. Fritz,Elizabeth Glass,Carolyn T.A. Herzig,Antti Livanainen,Kevin K. Lahmers,Anna K. Bennett,C. Michael Dickens,James G. R. Gilbert,Darren E. Hagen,Hanni Salih,Jan Aerts,Alexandre Rodrigues Caetano,Brian P. Dalrymple,José Fernando Garcia,Clare A. Gill,Stefan Hiendleder,Erdogan Memili,D.M. Spurlock,John L. Williams,Lee Alexander,Michael J. Brownstein,Le Luo Guan,Robert A. Holt,Steven J.M. Jones,Marco A. Marra,Richard A. Moore,Stephen S. Moore,Andrew J. Roberts,Masaaki Taniguchi,Masaaki Taniguchi,Richard C. Waterman,Joseph Chacko,Mimi M. Chandrabose,Andy Cree,Marvin Diep Dao,Huyen Dinh,Ramatu Ayiesha Gabisi,Sandra Hines,Jennifer Hume,Shalini N. Jhangiani,Vandita Joshi,Christie Kovar,Lora Lewis,Yin Shin Liu,John Lopez,Margaret Morgan,Ngoc Nguyen,Geoffrey Okwuonu,San Juana Ruiz,Jireh Santibanez,Rita A. Wright,Christian J. Buhay,Yan Ding,Shannon Dugan-Rocha,Judith Herdandez,Michael Holder,Aniko Sabo,Amy Egan,Jason Goodell,Katarzyna Wilczek-Boney,Gerald R. Fowler,Matthew Hitchens,Ryan J. Lozado,Charles Moen,David Steffen,James T. Warren,Jingkun Zhang,Readman Chiu,Jacqueline E. Schein,K. James Durbin,K. James Durbin,Paul Havlak,Paul Havlak,Huaiyang Jiang,Yue Liu,Xiang Qin,Yanru Ren,Yufeng Shen,Yufeng Shen,Henry Song,Stephanie Bell,Clay Davis,Angela Jolivet Johnson,Sandra L. Lee,Lynne V. Nazareth,Bella Mayurkumar Patel,Ling Ling Pu,Selina Vattathil,Rex Lee Williams,Stacey M. Curry,Cerissa Hamilton,Erica Sodergren,Erica Sodergren,David A. Wheeler,Wes Barris,Gary L. Bennett,André Eggen,Ronnie D. Green,Gregory P. Harhay,Matthew Hobbs,Oliver C. Jann,John W. Keele,Matthew Peter Kent,Sigbjam Lien,Stephanie D. McKay,Sean McWilliam,Abhirami Ratnakumar,Robert D. Schnabel,Timothy P. L. Smith,Warren M. Snelling,Tad S. Sonstegard,Roger T. Stone,Yoshikazu Sugimoto,Akiko Takasuga,Jeremy F. Taylor,Curtis P. Van Tassell,Michael D. MacNeil,A.R.R. Abatepaulo,Colette A. Abbey,Virpi Ahola,Lassudara G. Almeida,Ariel Fernando Amadio,Elen Anatriello,Suria M. Bahadue,Fernando H. Biase,Clayton R. Boldt,Jeffery A. Carroll,W. A. Carvalho,Eliane P. Cervelatti,Elsa Chacko,Jennifer E. Chapin,Ye Cheng,Jung-Woo Choi,Adam J. Colley,Tatiana A. DeCampos,Marcos De Donato,Isabel Kinney Ferreira de Miranda Santos,Carlo José Freire de Oliveira,Heather M Deobald,Eve Devinoy,Kaitlin E. Donohue,Peter Dove,Annett Eberlein,Carolyn Fitzsimmons,Alessandra Mara Franzin,Gustavo Garcia,Sem Genini,Cody J. Gladney,Jason R. Grant,Marion L. Greaser,Jonathan A. Green,Darryl L. Hadsell,Hatam A. Hakimov,Rob Halgren,Jennifer Harrow,E. Hart,N. Hastings,Marta Hernández,Zhi-Liang Hu,Antti Iivanainen,Aaron Ingham,Terhi Iso-Touru,Catherine Jamis,Kirsty Jensen,Dimos Kapetis,Tovah Kerr,Sari S. Khalil,Hasan Khatib,D. Kolbehdari,D. Kolbehdari,Cham G. Kumar,Dinesh Kumar,Richard J. Leach,Justin C. Lee,Changxi Li,Krystin M. Logan,Roberto Malinverni,E. Marques,William F. Martin,Natália F. Martins,Sandra Regina Maruyama,Raffaele Mazza,Kim L. McLean,Juan F. Medrano,Barbara T. Moreno,Daniela D. Moré,Carl T. Muntean,Hari Prasad Nandakumar,Marcelo Fábio Gouveia Nogueira,Ingrid Olsaker,Sameer D. Pant,Francesca Panzitta,Rosemeire Conceição Parra Pastor,Mario Andres Poli,Nathan Poslusny,Satyanarayana Rachagani,Shoba Ranganathan,Shoba Ranganathan,Andrej Razpet,Penny K. Riggs,Gonzalo Rincon,Nelida Rodriguez-Osorio,Nelida Rodriguez-Osorio,Sandra L. Rodriguez-Zas,Natasha E. Romero,Anne G. Rosenwald,Lillian Sando,Sheila M. Schmutz,Libing Shen,Laura Sherman,Bruce R. Southey,Ylva Strandberg Lutzow,Jonathan V. Sweedler,Imke Tammen,Bhanu Prakash V.L. Telugu,Jennifer M. Urbanski,Yuri Tani Utsunomiya,Chris P. Verschoor,Ashley J. Waardenberg,Zhiquan Wang,Robert Ward,Rosemarie Weikard,Thomas H. Welsh,Stephen N. White,Stephen N. White,Laurens G. Wilming,Kris R. Wunderlich,Jianqi Yang,Feng-Qi Zhao +328 more
TL;DR: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage and provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
Journal ArticleDOI
The genome of the sea urchin Strongylocentrotus purpuratus.
Erica Sodergren,George M. Weinstock,Eric H. Davidson,R. Andrew Cameron,Richard A. Gibbs,Robert C. Angerer,Lynne M. Angerer,Maria Ina Arnone,David R. Burgess,Robert D. Burke,James A. Coffman,Michael Dean,Maurice R. Elphick,Charles A. Ettensohn,Kathy R. Foltz,Amro Hamdoun,Richard O. Hynes,William H. Klein,William F. Marzluff,David R. McClay,Robert L. Morris,Arcady Mushegian,Arcady Mushegian,Jonathan P. Rast,L. Courtney Smith,Michael C. Thorndyke,Victor D. Vacquier,Victor D. Vacquier,Gary M. Wessel,Greg Wray,Lan Zhang,Christine G. Elsik,Christine G. Elsik,Olga Ermolaeva,Wratko Hlavina,Gretchen E. Hofmann,Paul Kitts,Melissa J. Landrum,Melissa J. Landrum,Aaron J. Mackey,Aaron J. Mackey,Donna Maglott,Georgia Panopoulou,Albert J. Poustka,Kim D. Pruitt,Victor Sapojnikov,Xingzhi Song,Alexandre Souvorov,Victor V. Solovyev,Zheng Wei,Charles A. Whittaker,Kim C. Worley,K. James Durbin,Yufeng Shen,Olivier Fedrigo,David A. Garfield,Ralph Haygood,Alexander E Primus,Rahul Satija,Tonya F. Severson,Manuel L. Gonzalez-Garay,Andrew R. Jackson,Aleksandar Milosavljevic,Mark Y. Tong,Christopher E. Killian,Brian T. Livingston,Fred H. Wilt,Nikki Adams,Nikki Adams,Robert Bellé,Robert Bellé,Seth Carbonneau,Rocky Cheung,Patrick Cormier,Patrick Cormier,Bertrand Cosson,Bertrand Cosson,Jenifer C. Croce,Antonio Fernandez-Guerra,Antonio Fernandez-Guerra,Anne Marie Genevière,Anne Marie Genevière,Manisha Goel,Hemant Kelkar,Julia Morales,Julia Morales,Odile Mulner-Lorillon,Anthony J. Robertson,Jared V. Goldstone,Bryan J. Cole,David Epel,Bert Gold,Mark E. Hahn,Meredith Howard-Ashby,Mark Scally,John J. Stegeman,Erin L. Allgood,Jonah Cool,Kyle M. Judkins,Shawn S. McCafferty,Ashlan M. Musante,Robert A. Obar,Amanda P. Rawson,Blair J. Rossetti,I. R. Gibbons,Matthew P. Hoffman,Andrew Leone,Sorin Istrail,Stefan C. Materna,Manoj P. Samanta,Viktor Stolc,Waraporn Tongprasit,Qiang Tu,Karl Frederik Bergeron,Bruce P. Brandhorst,James R.R. Whittle,Kevin Berney,David J. Bottjer,Cristina Calestani,Kevin J. Peterson,Elly Suk Hen Chow,Qiu Autumn Yuan,Eran Elhaik,Dan Graur,Justin T. Reese,Ian Bosdet,Shin Heesun,Marco A. Marra,Jacqueline E. Schein,Michele K. Anderson,Virginia Brockton,Katherine M. Buckley,Avis H. Cohen,Sebastian D. Fugmann,Taku Hibino,Mariano Loza-Coll,Audrey J. Majeske,Cynthia Messier,Sham V. Nair,Zeev Pancer,David P. Terwilliger,Cavit Agca,Enrique Arboleda,Nansheng Chen,Allison M. Churcher,Finn Hallböök,Glen Humphrey,Mohammed M. Idris,Takae Kiyama,Shuguang Liang,Dan O Mellott,Xiuqian Mu,Greg Murray,Robert Piotr Olinski,Florian Raible,Matthew L. Rowe,John S. Taylor,Kristin Tessmar-Raible,D. Wang,Karen Wilson,Karen Wilson,Shunsuke Yaguchi,Terry Gaasterland,Blanca E. Galindo,Herath Jayantha Gunaratne,Celina E. Juliano,Masashi Kinukawa,Gary W. Moy,Anna T. Neill,Mamoru Nomura,Michael Raisch,Anna Reade,Michelle M. Roux,Jia L. Song,Yi-Hsien Su,Ian K. Townley,Ekaterina Voronina,Julian L. Wong,Gabriele Amore,Margherita Branno,Euan R. Brown,Vincenzo Cavalieri,Véronique Duboc,Louise Duloquin,Constantin N. Flytzanis,Constantin N. Flytzanis,Christian Gache,François Lapraz,Thierry Lepage,Annamaria Locascio,Pedro Martinez,Giorgio Matassi,Valeria Matranga,Ryan C. Range,Francesca Rizzo,Eric Röttinger,Karen Wilson,Wendy S. Beane,Cynthia A. Bradham,Christine A. Byrum,Christine A. Byrum,Thomas D. Glenn,Sofia Hussain,Mariano A. Loza,Gerard Manning,Esther Miranda,Rebecca Thomason,Rebecca Thomason,Katherine D. Walton,Athula Wikramanayke,Charles A. Whittaker,Shu-Yu Wu,Ronghui Xu,C. Titus Brown,Lili Chen,Rachel F. Gray,Pei Yun Lee,Jongmin Nam,Paola Oliveri,Joel Smith,Donna M. Muzny,Stephanie Bell,Joseph Chacko,Andrew Cree,Stacey M. Curry,Clay Davis,Huyen Dinh,Shannon Dugan-Rocha,Fowler J,Rachel Gill,Cerrissa Hamilton,Judith Hernandez,Sandra Hines,Jennifer Hume,La Ronda Jackson,Angela Jolivet,Christie Kovar,Sandra L. Lee,Lora Lewis,George Miner,Margaret Morgan,Lynne V. Nazareth,Geoffrey Okwuonu,David A. Parker,Ling Ling Pu,Rachel Thorn,Rita A. Wright +246 more
TL;DR: The sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus is reported, a model for developmental and systems biology and yields insights into the evolution of deuterostomes.
Journal ArticleDOI
The support of human genetic evidence for approved drug indications
Matthew R. Nelson,Hannah Tipney,Jeffery L. Painter,Judong Shen,Paola Nicoletti,Yufeng Shen,Aris Floratos,Pak C. Sham,Mulin Jun Li,Junwen Wang,Lon R. Cardon,John C. Whittaker,Philippe Sanseau +12 more
TL;DR: It is estimated that selecting genetically supported targets could double the success rate in clinical development, and using the growing wealth of human genetic data to select the best targets and indications should have a measurable impact on the successful development of new drugs.