Initial sequencing and analysis of the human genome.
Eric S. Lander,Lauren Linton,Bruce W. Birren,Chad Nusbaum,Michael C. Zody,Jennifer Baldwin,Keri Devon,Ken Dewar,Michael Doyle,William Fitzhugh,Roel Funke,Diane Gage,Katrina Harris,Andrew Heaford,John Howland,Lisa Kann,Jessica A. Lehoczky,Rosie Levine,Paul A. McEwan,Kevin McKernan,James Meldrim,Jill P. Mesirov,Cher Miranda,William Morris,Jerome Naylor,Christina Raymond,Mark Rosetti,Ralph Santos,Andrew Sheridan,Carrie Sougnez,Nicole Stange-Thomann,Nikola Stojanovic,Aravind Subramanian,Dudley Wyman,Jane Rogers,John Sulston,R Ainscough,Stephan Beck,David Bentley,John Burton,C M Clee,Nigel P. Carter,Alan Coulson,Rebecca Deadman,Panos Deloukas,Andrew Dunham,Ian Dunham,Richard Durbin,Lisa French,Darren Grafham,Simon G. Gregory,Tim Hubbard,Sean Humphray,Adrienne Hunt,Matthew Jones,Christine Lloyd,Amanda McMurray,Lucy Matthews,Simon Mercer,Sarah Milne,James C. Mullikin,Andrew J. Mungall,Robert W. Plumb,Mark T. Ross,Ratna Shownkeen,Sarah Sims,Robert H. Waterston,Richard K. Wilson,LaDeana W. Hillier,John Douglas Mcpherson,Marco A. Marra,Elaine R. Mardis,Lucinda Fulton,Asif T. Chinwalla,Kymberlie H. Pepin,Warren Gish,Stephanie L. Chissoe,Michael C. Wendl,Kim D. Delehaunty,Tracie L. Miner,Andrew Delehaunty,Jason B. Kramer,Lisa Cook,Robert S. Fulton,Douglas L. Johnson,Patrick Minx,Sandra W. Clifton,Trevor Hawkins,Elbert Branscomb,Paul Predki,Paul G. Richardson,Sarah Wenning,Tom Slezak,Norman A. Doggett,Jan Fang Cheng,Anne S. Olsen,Susan Lucas,Christopher J. Elkin,Edward Uberbacher,Marvin Frazier,Richard A. Gibbs,Donna M. Muzny,Steven E. Scherer,John Bouck,Erica Sodergren,Kim C. Worley,Catherine M. Rives,James H. Gorrell,Michael L. Metzker,Susan L. Naylor,Raju Kucherlapati,David L. Nelson,George M. Weinstock,Yoshiyuki Sakaki,Asao Fujiyama,Masahira Hattori,Tetsushi Yada,Atsushi Toyoda,Takehiko Itoh,Chiharu Kawagoe,Hidemi Watanabe,Yasushi Totoki,Todd D. Taylor,Jean Weissenbach,Roland Heilig,William Saurin,François Artiguenave,Philippe Brottier,Thomas Brüls,Eric Pelletier,Catherine Robert,Patrick Wincker,André Rosenthal,Matthias Platzer,Gerald Nyakatura,Stefan Taudien,Andreas Rump,Douglas R. Smith,Lynn Doucette-Stamm,Marc Rubenfield,Keith Weinstock,Mei Lee Hong,Joann Dubois,Huanming Yang,Jun Yu,Jian Wang,Guyang Huang,Jun Gu,Leroy Hood,Lee Rowen,Anup Madan,Shizen Qin,Ronald W. Davis,Nancy A. Federspiel,A. Pia Abola,Michael Proctor,Bruce A. Roe,Feng Chen,Huaqin Pan,Juliane Ramser,Hans Lehrach,Richard Reinhardt,W. Richard McCombie,Melissa De La Bastide,Neilay Dedhia,H. Blöcker,K. Hornischer,Gabriele Nordsiek,Richa Agarwala,L. Aravind,Jeffrey A. Bailey,Alex Bateman,Serafim Batzoglou,Ewan Birney,Peer Bork,Daniel G. Brown,Christopher B. Burge,Lorenzo Cerutti,Hsiu Chuan Chen,Deanna M. Church,Michele Clamp,Richard R. Copley,Tobias Doerks,Sean R. Eddy,Evan E. Eichler,Terrence S. Furey,James E. Galagan,James G. R. Gilbert,Cyrus L. Harmon,Yoshihide Hayashizaki,David Haussler,Henning Hermjakob,Karsten Hokamp,Wonhee Jang,L. Steven Johnson,Thomas A. Jones,Simon Kasif,Arek Kaspryzk,Scot Kennedy,W. James Kent,Paul Kitts,Eugene V. Koonin,Ian F Korf,David Kulp,Doron Lancet,Todd M. Lowe,Aoife McLysaght,Tarjei S. Mikkelsen,John V. Moran,Nicola Mulder,Victor J. Pollara,Chris P. Ponting,Greg Schuler,Jörg Schultz,Guy Slater,Arian F.A. Smit,Elia Stupka,Joseph Szustakowki,Danielle Thierry-Mieg,Jean Thierry-Mieg,Lukas Wagner,John W. Wallis,Raymond Wheeler,Alan Williams,Yuri I. Wolf,Kenneth H. Wolfe,Shiaw Pyng Yang,Ru Fang Yeh,Francis S. Collins,Mark S. Guyer,Jane Peterson,Adam Felsenfeld,Kris A. Wetterstrand,Richard M. Myers,Jeremy Schmutz,Mark Dickson,Jane Grimwood,David R. Cox,Maynard V. Olson,Rajinder Kaul,Christopher K. Raymond,Nobuyoshi Shimizu,Kazuhiko Kawasaki,Shinsei Minoshima,Glen A. Evans,Maria Athanasiou,Roger A. Schultz,Aristides Patrinos,Michael J. Morgan +248 more
TLDR
The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.Abstract:
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.read more
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Regulatory evolution of innate immunity through co-option of endogenous retroviruses
TL;DR: It is found that ERVs have shaped the evolution of a transcriptional network underlying the interferon (IFN) response, a major branch of innate immunity, and that lineage-specific ERV have dispersed numerous IFN-inducible enhancers independently in diverse mammalian genomes.
Journal ArticleDOI
Recent improvements to the SMART domain-based sequence annotation resource
Ivica Letunic,Leo Goodstadt,Nicholas J. Dickens,Tobias Doerks,Jörg Schultz,Richard Mott,Francesca D. Ciccarelli,Richard R. Copley,Chris P. Ponting,Peer Bork +9 more
TL;DR: The SMART database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats and new advanced queries provide direct access to the SMART relational database using SQL.
Journal ArticleDOI
The Hierarchy of the 3D Genome
Johan H. Gibcus,Job Dekker +1 more
TL;DR: The experimental and theoretical data on this hierarchy of structures and a key role for the recently discovered topologically associating domains are reviewed and proposed.
Journal ArticleDOI
The genome of the western clawed frog xenopus tropicalis
Uffe Hellsten,Richard M. Harland,Michael J. Gilchrist,David A. Hendrix,Jerzy Jurka,Vladimir V. Kapitonov,Ivan Ovcharenko,Nicholas H. Putnam,Shengqiang Shu,Leila Taher,Ira L. Blitz,Bruce Blumberg,Darwin S. Dichmann,Inna Dubchak,Enrique Amaya,John C. Detter,Russell B. Fletcher,Daniela S. Gerhard,David Goodstein,Tina Graves,Igor V. Grigoriev,Jane Grimwood,Takeshi Kawashima,Takeshi Kawashima,Erika Lindquist,Susan Lucas,Paul E. Mead,Therese Mitros,Hajime Ogino,Yuko Ohta,Alexander Poliakov,Nicolas Pollet,Jacques Robert,Asaf Salamov,Amy K. Sater,Jeremy Schmutz,Astrid Terry,Peter D. Vize,Wesley C. Warren,Dan E. Wells,Andrea E. Wills,Richard K. Wilson,Lyle B. Zimmerman,Aaron M. Zorn,Robert M. Grainger,Timothy C. Grammer,Mustafa K. Khokha,Paul G. Richardson,Daniel S. Rokhsar,Daniel S. Rokhsar +49 more
TL;DR: The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frogs Xenopus laevis with more tractable genetics.
Journal ArticleDOI
What is a gene, post-ENCODE? History and updated definition
Mark Gerstein,Joel Rozowsky,Deyou Zheng,Jiang Du,Jan O. Korbel,Olof Emanuelsson,Zhengdong D. Zhang,Sherman M. Weissman,Michael Snyder +8 more
TL;DR: This definition side-steps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene.
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TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
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Identification of common molecular subsequences.
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Sequence and organization of the human mitochondrial genome
Stephen Anderson,Alan T. Bankier,Bart Barrell,M.H.L. de Bruijn,Alan Coulson,J. Drouin,J. Drouin,Ian C. Eperon,Donald P. Nierlich,Donald P. Nierlich,Bruce A. Roe,Bruce A. Roe,Frederick Sanger,P. H. Schreier,Andrew J.H. Smith,Rodger Staden,Ian G. Young,Ian G. Young +17 more
TL;DR: The complete sequence of the 16,569-base pair human mitochondrial genome is presented and shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
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