Journal ArticleDOI
Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints
Danilo A. Tagle,Ben F. Koop,Morris Goodman,Jerry L. Slightom,Jerry L. Slightom,David L. Hess,Richard T. Jones +6 more
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TLDR
It is concluded that gamma E evolved into gamma F in stem-simians and an elevated non-synonymous substitution rate characterizes this transition.About:
This article is published in Journal of Molecular Biology.The article was published on 1988-09-20. It has received 354 citations till now. The article focuses on the topics: Galago & Sequence analysis.read more
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Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
Richard A. Gibbs,George M. Weinstock,Michael L. Metzker,Donna M. Muzny,Erica Sodergren,Steven E. Scherer,Graham R. Scott,David Steffen,Kim C. Worley,Paula E. Burch,Geoffrey Okwuonu,Sandra Hines,Lora Lewis,Christine Deramo,Oliver Delgado,Shannon Dugan-Rocha,George Miner,Margaret Morgan,Alicia Hawes,Rachel Gill,Robert A. Holt,Robert A. Holt,Mark Raymond Adams,Mark Raymond Adams,Peter G. Amanatides,Peter G. Amanatides,Holly Baden-Tillson,Holly Baden-Tillson,Mary Barnstead,Soo H. Chin,Cheryl A. Evans,Steve Ferriera,Steve Ferriera,Carl Fosler,A. Glodek,Zhiping Gu,Don Jennings,Cheryl L. Kraft,Cheryl L. Kraft,Trixie Nguyen,Cynthia Pfannkoch,Cynthia Pfannkoch,Cynthia Sitter,Granger G. Sutton,J. Craig Venter,J. Craig Venter,Trevor Woodage,Douglas Smith,Hong Mei Lee,Erik Gustafson,Patrick Cahill,Arnold Kana,Lynn Doucette-Stamm,Keith Weinstock,Kim Fechtel,Robert B. Weiss,Diane M. Dunn,Eric D. Green,Robert W. Blakesley,Gerard G. Bouffard,Pieter J. de Jong,Kazutoyo Osoegawa,Baoli Zhu,Marco A. Marra,Jacqueline E. Schein,Ian Bosdet,Chris Fjell,Steven J.M. Jones,Martin Krzywinski,Carrie Mathewson,Asim Sarosh Siddiqui,Natasja Wye,John Douglas Mcpherson,John Douglas Mcpherson,Shaying Zhao,Claire M. Fraser,Jyoti Shetty,Sofiya Shatsman,Keita Geer,Yixin Chen,Sofyia Abramzon,William C. Nierman,Paul Havlak,Rui Chen,K. James Durbin,Amy Egan,Yanru Ren,Xing Zhi Song,Bingshan Li,Yue Liu,Xiang Qin,Simon Cawley,Austin J. Cooney,Lisa M. D'Souza,Kirt Martin,Jia Qian Wu,Manuel L. Gonzalez-Garay,Andrew R. Jackson,Kenneth J. Kalafus,Michael P. McLeod,Aleksandar Milosavljevic,Davinder Virk,Andrei Volkov,David A. Wheeler,Zhengdong D. Zhang,Jeffrey A. Bailey,Evan E. Eichler,Eray Tüzün,Ewan Birney,Emmanuel Mongin,Abel Ureta-Vidal,Cara Woodwark,Evgeny M. Zdobnov,Peer Bork,Mikita Suyama,David Torrents,Marina Alexandersson,Barbara J. Trask,Janet M. Young,Hui Huang,Huajun Wang,Heming Xing,Sue Daniels,Darryl Gietzen,Jeanette Schmidt,Kristian Stevens,Ursula Vitt,Jim Wingrove,Francisco Camara,M. Mar Albà,Josep F. Abril,Roderic Guigó,Arian F.A. Smit,Inna Dubchak,Inna Dubchak,Edward M. Rubin,Edward M. Rubin,Olivier Couronne,Olivier Couronne,Alexander Poliakov,Norbert Hubner,Detlev Ganten,Claudia Goesele,Claudia Goesele,Oliver Hummel,Oliver Hummel,Thomas Kreitler,Thomas Kreitler,Young-Ae Lee,Jan Monti,Herbert Schulz,Heike Zimdahl,Heinz Himmelbauer,Hans Lehrach,Howard J. Jacob,Susan Bromberg,Jo Gullings-Handley,Michael I. Jensen-Seaman,Anne E. Kwitek,Jozef Lazar,Dean Pasko,Peter J. Tonellato,Simon N. Twigger,Chris P. Ponting,Jose M. Duarte,Stephen Rice,Leo Goodstadt,Scott A. Beatson,Richard D. Emes,Eitan E. Winter,Caleb Webber,Petra Brandt,Gerald Nyakatura,Margaret Adetobi,Francesca Chiaromonte,Laura Elnitski,Pallavi Eswara,Ross C. Hardison,Minmei Hou,Diana L. Kolbe,Kateryna D. Makova,Webb Miller,Anton Nekrutenko,Cathy Riemer,Scott Schwartz,James Taylor,Shan Yang,Yi Zhang,Klaus Lindpaintner,T. Dan Andrews,Mario Caccamo,Michele Clamp,Laura Clarke,Valerie Curwen,Richard Durbin,Eduardo Eyras,Stephen M. J. Searle,Gregory M. Cooper,Serafim Batzoglou,Michael Brudno,Arend Sidow,Eric A. Stone,Bret A. Payseur,Guillaume Bourque,Carlos López-Otín,Xose S. Puente,Kushal Chakrabarti,Sourav Chatterji,Colin N. Dewey,Lior Pachter,Nicolas Bray,Von Bing Yap,Anat Caspi,San Diego Glenn Tesler,Pavel A. Pevzner,Santa Cruz David Haussler,Krishna M. Roskin,Robert Baertsch,Hiram Clawson,Terrence S. Furey,Angie S. Hinrichs,Donna Karolchik,W. J. Kent,Kate R. Rosenbloom,Heather Trumbower,Matt Weirauch,Matt Weirauch,David Neil Cooper,Peter D. Stenson,Bin Ma,Michael R. Brent,Manimozhiyan Arumugam,David Shteynberg,Richard R. Copley,Martin S. Taylor,Harold Riethman,Uma Mudunuri,Jane Peterson,Mark S. Guyer,Adam Felsenfeld,Susan Old,Stephen C. Mockrin,Francis S. Collins +242 more
TL;DR: This first comprehensive analysis of the genome sequence of the Brown Norway (BN) rat strain is reported, which is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution.
Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRat Genome Sequencing Project ConsortiumNature200442849352115057822
Richard A. Gibbs,George M. Weinstock,Michael L. Metzker,Donna M. Muzny,Erica Sodergren,Steven E. Scherer,Graham R. Scott,David Steffen,Kim C. Worley,Paula E. Burch,Geoffrey Okwuonu,Sandra Hines,Lora Lewis,C. DeRamo,Oliver Delgado,S. Dugan Rocha,George Miner,Margaret Morgan,Alicia Hawes,Rachel Gill,Robert A. Holt,Mark Raymond Adams,Peter G. Amanatides,H. Baden Tillson,Mary Barnstead,Soo H. Chin,Cheryl A. Evans,Steve Ferriera,Carl Fosler,A. Glodek,Gu Zp,D. Jennings,Cheryl L. Kraft,T. Nguyen,Cynthia Pfannkoch,Cynthia Sitter,Granger G. Sutton,J. C. Venter,Trevor Woodage,Douglas Smith,H. M. Lee,Erik Gustafson,Patrick Cahill,A. Kana,L. Doucette Stamm,Keith Weinstock,Kim Fechtel,Robert B. Weiss,Diane M. Dunn,Eric D. Green,Robert W. Blakesley,Gerard G. Bouffard,P. J. De Jong,Kazutoyo Osoegawa,Zhu Bl,Marco A. Marra,Jacqueline E. Schein,Ian Bosdet,Chris Fjell,Steven J.M. Jones,Martin Krzywinski,Carrie Mathewson,Asim Sarosh Siddiqui,Natasja Wye,John Douglas Mcpherson,Zhao Sy,Claire M. Fraser,Jyoti Shetty,Sofiya Shatsman,Keita Geer,Chen Yx,S. Abramzon,William C. Nierman,Paul Havlak,Rui Chen,K. J. Durbin,Amy Egan,Ren Yr,Xing Zhi Song,Li Bs,Yue Liu,Xiang Qin,Simon Cawley,Austin J. Cooney,Lisa M. D'Souza,Kirt Martin,Jia Qian Wu,M. L. Gonzalez Garay,Andrew R. Jackson,K. J. Kalafus,Michael P. McLeod,Aleksandar Milosavljevic,D. Virk,A. Volkov,David A. Wheeler,Zhang Zd,Jeffrey A. Bailey,Evan E. Eichler,Eray Tüzün,Ewan Birney,Emmanuel Mongin,A. Ureta Vidal,C. Woodwark,Evgeny M. Zdobnov,Peer Bork,Mikita Suyama,David Torrents,Marina Alexandersson,Barbara J. Trask,Janet M. Young,Hui Huang,Wang Hj,Xing Hm,Sue Daniels,Darryl Gietzen,Jeanette Schmidt,K. Stevens,Ursula Vitt,Jim Wingrove,Francisco Camara,M. Mar Albà,Josep F. Abril,Roderic Guigó,Arian F.A. Smit,Inna Dubchak,Edward M. Rubin,Olivier Couronne,Alexander Poliakov,Norbert Hubner,Detlev Ganten,C. Goesele,Oliver Hummel,Thomas Kreitler,Young-Ae Lee,Jan Monti,Herbert Schulz,Heike Zimdahl,Heinz Himmelbauer,Hans Lehrach,Howard J. Jacob,Susan Bromberg,J. Gullings Handley,M. I. Jensen Seaman,Anne E. Kwitek,Jozef Lazar,Dean Pasko,Peter J. Tonellato,Simon N. Twigger,Chris P. Ponting,Jose M. Duarte,Stephen Rice,Leo Goodstadt,Scott A. Beatson,Richard D. Emes,Eitan E. Winter,Caleb Webber,Petra Brandt,Gerald Nyakatura,M. Adetobi,Francesca Chiaromonte,Laura Elnitski,Pallavi Eswara,Ross C. Hardison,Hou Mm,Diana L. Kolbe,Kateryna D. Makova,Webb Miller,Anton Nekrutenko,Cathy Riemer,Scott Schwartz,James Taylor,Shan Yang,Yi Zhang,Klaus Lindpaintner,T. D. Andrews,Mario Caccamo,Michele Clamp,Laura Clarke,V. Curwen,Richard Durbin,Eduardo Eyras,Stephen M. J. Searle,Gregory M. Cooper,Serafim Batzoglou,Michael Brudno,Arend Sidow,Eric A. Stone,Bret A. Payseur,Guillaume Bourque,C. Lopez Otin,Xose S. Puente,Kushal Chakrabarti,Sourav Chatterji,Colin N. Dewey,Lior Pachter,Nicolas Bray,Von Bing Yap,Anat Caspi,G. Tesler,Pavel A. Pevzner,David Haussler,Krishna M. Roskin,Robert Baertsch,Hiram Clawson,Terrence S. Furey,Angie S. Hinrichs,Donna Karolchik,W. J. Kent,Kate R. Rosenbloom,Heather Trumbower,M. Weirauch,David Neil Cooper,Peter D. Stenson,Bin Ma,Michael R. Brent,Manimozhiyan Arumugam,David Shteynberg,Richard R. Copley,Martin S. Taylor,Harold Riethman,Uma Mudunuri,Jane Peterson,Mark S. Guyer,Adam Felsenfeld,Susan Old,Stephen C. Mockrin,Francis S. Collins +226 more
Abstract: The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality ‘draft’ covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
Journal ArticleDOI
Molecular Signatures of Natural Selection
TL;DR: This review provides a nonmathematical description of the issues involved in detecting selection from DNA sequences and SNP data and is intended for readers who are not familiar with population genetic theory.
Journal ArticleDOI
Applied bioinformatics for the identification of regulatory elements
TL;DR: The purpose and mechanisms of the leading algorithms, with a particular emphasis on metazoan sequence analysis, are introduced and key issues that users should take into consideration in interpreting the results are identified.
References
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Arapid alkaline extraction procedure forscreening recombinant plasmid DNA
TL;DR: The method is simple enough to permit the analysis by gel electrophoresis of 100 or more clones per day yet yields plasmid DNA which is pure enough to be digestible by restriction enzymes, and achievesequate pH control without using a pH meter.
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TL;DR: This letter extends the heuristic homology algorithm of Needleman & Wunsch (1970) to find a pair of segments, one from each of two long sequences, such that there is no other Pair of segments with greater similarity (homology).
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