S
Simon D. M. White
Researcher at Baylor College of Medicine
Publications - 85
Citations - 16237
Simon D. M. White is an academic researcher from Baylor College of Medicine. The author has contributed to research in topics: Galaxy & Galaxy formation and evolution. The author has an hindex of 44, co-authored 85 publications receiving 14292 citations. Previous affiliations of Simon D. M. White include Wellcome Trust Sanger Institute & Max Planck Society.
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Journal ArticleDOI
The zebrafish reference genome sequence and its relationship to the human genome.
Kerstin Howe,Matthew D. Clark,Carlos Torroja,Carlos Torroja,James Torrance,Camille Berthelot,Matthieu Muffato,John E. Collins,Sean Humphray,Karen McLaren,Lucy Matthews,Stuart McLaren,Ian M Sealy,Mario Caccamo,Carol Churcher,Carol Scott,Jeffrey C. Barrett,Romke Koch,Gerd Jörg Rauch,Simon D. M. White,William Chow,Britt Kilian,Leonor T. Quintais,José Afonso Guerra-Assunção,Yi Zhou,Yong Gu,Jennifer Yen,Jan Hinnerk Vogel,Tina Eyre,Seth Redmond,Ruby Banerjee,Jianxiang Chi,Beiyuan Fu,Elizabeth Langley,Sean Maguire,Gavin K. Laird,D. M. Lloyd,Emma J. Kenyon,Sarah Donaldson,Harminder Sehra,Jeff Almeida-King,Jane E. Loveland,Stephen J. Trevanion,Matthew Jones,Michael A. Quail,Dave Willey,Adrienne Hunt,John Burton,Sarah Sims,Kirsten McLay,Bob Plumb,J. C. Davis,Chris Clee,Karen Oliver,Richard M. Clark,Clare Riddle,David Eliott,Glen Threadgold,Glenn Harden,Darren Ware,Beverly Mortimer,Giselle Kerry,Paul Heath,Benjamin Phillimore,Alan Tracey,N Corby,Matthew Dunn,Christopher M. Johnson,Jonathan Wood,Susan J. Clark,Sarah Pelan,Guy Griffiths,Michelle Smith,Rebecca Glithero,Philip Howden,Nick Barker,Christopher Stevens,Joanna Harley,Karen Holt,Georgios Panagiotidis,J Lovell,Helen Beasley,Carl Henderson,Daria Gordon,Katherine Auger,Debbie E. Wright,Joanna Collins,Claire Raisen,Lauren Dyer,Kenric Leung,Lauren Robertson,Kirsty Ambridge,Daniel Leongamornlert,Sarah McGuire,Ruth Gilderthorp,C Griffiths,Deepa Manthravadi,Sarah Nichol,Gary L A Barker,S. Whitehead,Michael Kay,Jacqueline Brown,Clare Murnane,Emma Gray,Matthew Humphries,N Sycamore,Darren Barker,David S. Saunders,J. M. Wallis,A K Babbage,S Hammond,M Mashreghi-Mohammadi,Lucy Barr,Sancha Martin,Paul Wray,Andrew D. Ellington,Nicholas Matthews,Matthew Ellwood,Rebecca Woodmansey,Graham Clark,James D. Cooper,A Tromans,Darren Grafham,C. D. Skuce,Richard Pandian,Robert Andrews,Elliot Harrison,A M Kimberley,J Garnett,Nigel Fosker,Rebekah Hall,P Garner,Daniel P. Kelly,Christine P. Bird,Sophie Palmer,Ines Gehring,Andrea Berger,Christopher M. Dooley,Christopher M. Dooley,Zübeyde Ersan-Ürün,Cigdem Eser,Horst Geiger,Maria Geisler,Lena Karotki,Anette Kirn,Judith Konantz,Martina Konantz,Martina Oberländer,Silke Rudolph-Geiger,Mathias Teucke,Kazutoyo Osoegawa,Baoli Zhu,Amanda Rapp,Sara Widaa,Cordelia Langford,Fengtang Yang,Nigel P. Carter,Jennifer Harrow,Zemin Ning,Javier Herrero,Steve Searle,Anton J. Enright,Robert Geisler,Robert Geisler,Ronald H.A. Plasterk,Charles Lee,Monte Westerfield,Pieter J. de Jong,Leonard I. Zon,John H. Postlethwait,Christiane Nüsslein-Volhard,Tim Hubbard,Hugues Roest Crollius,Jane Rogers,Derek L. Stemple +174 more
TL;DR: A high-quality sequence assembly of the zebrafish genome is generated, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map, providing a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebra fish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.
Journal ArticleDOI
The genomic basis of adaptive evolution in threespine sticklebacks
Felicity C. Jones,Manfred Grabherr,Manfred Grabherr,Yingguang Frank Chan,Pamela Russell,Evan Mauceli,Evan Mauceli,Jeremy Johnson,Ross Swofford,Mono Pirun,Mono Pirun,Michael C. Zody,Simon D. M. White,Ewan Birney,Stephen M. J. Searle,Jeremy Schmutz,Jane Grimwood,Mark Dickson,Richard M. Myers,Craig Miller,Craig Miller,Brian R. Summers,Anne K. Knecht,Shannon D. Brady,Haili Zhang,Alex A. Pollen,Timothy R. Howes,Chris T. Amemiya,Eric S. Lander,Federica Di Palma,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,David M. Kingsley,David M. Kingsley +33 more
TL;DR: A high-quality reference genome assembly for threespine stickleback fish is developed and it is indicated that reuse of globally shared standing genetic variation has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation.
The genomic basis of adaptive evolution in threespine sticklebacks
Felicity C. Jones,Manfred Grabherr,Yingguang Frank Chan,Pamela Russell,Evan Mauceli,Jeremy A. Johnson,Ross Swofford,Mono Pirun,Michael C. Zody,Simon D. M. White,Ewan Birney,Stephen M. J. Searle,Jeremy Schmutz,Jane Grimwood,Mark Dickson,Richard M. Myers,Craig Miller,Brian R. Summers,Anne K. Knecht,Shannon D. Brady,Haili Zhang,Alex A. Pollen,Timothy R. Howes,Chris T. Amemiya,Jen Baldwin,Toby Bloom,David B. Jaffe,Robert Nicol,Jane E. Wilkinson,Eric S. Lander,Federica Di Palma,Kerstin Lindblad-Toh,David M. Kingsley +32 more
Journal ArticleDOI
Analyses of pig genomes provide insight into porcine demography and evolution
Martien A. M. Groenen,Alan Archibald,Hirohide Uenishi,Christopher K. Tuggle,Yasuhiro Takeuchi,Max F. Rothschild,Claire Rogel-Gaillard,Chankyu Park,Denis Milan,Hendrik-Jan Megens,Shengting Li,Denis M. Larkin,Heebal Kim,Laurent A. F. Frantz,Mario Caccamo,Hyeonju Ahn,Bronwen Aken,Anna Anselmo,Christian Anthon,Loretta Auvil,Bouabid Badaoui,Craig W. Beattie,Christian Bendixen,Daniel Berman,Frank Blecha,Jonas Blomberg,Lars Bolund,Mirte Bosse,Sara Botti,Zhan Bujie,Megan Bystrom,Boris Capitanu,Denise Carvalho-Silva,Patrick Chardon,Celine Chen,Ryan Cheng,Sang-Haeng Choi,William Chow,Richard Clark,C M Clee,Richard P. M. A. Crooijmans,Harry D. Dawson,Patrice Dehais,Fioravante De Sapio,Bert Dibbits,Nizar Drou,Zhi-Qiang Du,Kellye Eversole,João Fadista,João Fadista,Susan Fairley,Thomas Faraut,Geoffrey J. Faulkner,Geoffrey J. Faulkner,Katie E. Fowler,Merete Fredholm,Eric Fritz,James G. R. Gilbert,Elisabetta Giuffra,Elisabetta Giuffra,Jan Gorodkin,Darren K. Griffin,Jennifer Harrow,Alexander Hayward,Kerstin Howe,Zhi-Liang Hu,Sean Humphray,Sean Humphray,Toby Hunt,Henrik Hornshøj,Jin-Tae Jeon,Patric Jern,Matthew Jones,Jerzy Jurka,Hiroyuki Kanamori,Ronan Kapetanovic,Jaebum Kim,Jaebum Kim,Jae-Hwan Kim,Kyu-Won Kim,Tae-Hun Kim,Greger Larson,Kyooyeol Lee,Kyung-Tai Lee,Richard M. Leggett,Harris A. Lewin,Yingrui Li,Wan Sheng Liu,Jane E. Loveland,Yao Lu,Joan K. Lunney,Jian Ma,Ole Madsen,Katherine M. Mann,Katherine M. Mann,Lucy Matthews,Stuart McLaren,Takeya Morozumi,Michael P. Murtaugh,Jitendra Narayan,Dinh Truong Nguyen,Peixiang Ni,Song-Jung Oh,Suneel Kumar Onteru,Frank Panitz,Eung-Woo Park,Hong-Seog Park,Géraldine Pascal,Yogesh Paudel,Miguel Pérez-Enciso,Ricardo H. Ramirez-Gonzalez,James M. Reecy,Sandra L. Rodriguez-Zas,Gary A. Rohrer,Lauretta A. Rund,Yongming Sang,Kyle M. Schachtschneider,Joshua G. Schraiber,John C. Schwartz,Linda Scobie,Carol Scott,Stephen M. J. Searle,Bertrand Servin,Bruce R. Southey,Göran O. Sperber,Peter F. Stadler,Jonathan V. Sweedler,Hakim Tafer,Bo Thomsen,Rashmi Wali,Jian Wang,Jun Wang,Simon D. M. White,Xun Xu,Martine Yerle,Guojie Zhang,Jianguo Zhang,Jie Zhang,Shuhong Zhao,Jane Rogers,Carol Churcher,Lawrence B. Schook +141 more
TL;DR: The assembly and analysis of the genome sequence of a female domestic Duroc pig and a comparison with the genomes of wild and domestic pigs from Europe and Asia reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago.
Journal ArticleDOI
The Ensembl gene annotation system.
Bronwen Aken,Bronwen Aken,Sarah Ayling,Daniel Barrell,Laura Clarke,Valery Curwen,Susan Fairley,Julio Fernandez Banet,Konstantinos Billis,Carlos García Girón,Thibaut Hourlier,Kevin L. Howe,Andreas Kähäri,Felix Kokocinski,Fergal J. Martin,Daniel N. Murphy,Rishi Nag,Magali Ruffier,Michael Schuster,Y. Amy Tang,Jan-Hinnerk Vogel,Simon D. M. White,Amonida Zadissa,Paul Flicek,Stephen M. J. Searle +24 more
TL;DR: The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects and generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets.