D
David Goodstein
Researcher at Joint Genome Institute
Publications - 60
Citations - 29269
David Goodstein is an academic researcher from Joint Genome Institute. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 29, co-authored 54 publications receiving 25442 citations. Previous affiliations of David Goodstein include IBM & Lawrence Berkeley National Laboratory.
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Journal ArticleDOI
JBrowse: a dynamic web platform for genome visualization and analysis
Robert Buels,Eric Yao,Colin Diesh,Richard D. Hayes,Richard D. Hayes,Monica Munoz-Torres,Gregg Helt,David Goodstein,David Goodstein,Christine G. Elsik,Suzanna E. Lewis,Lincoln Stein,Ian Holmes,Ian Holmes +13 more
TL;DR: Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets.
Journal ArticleDOI
The Genome Portal of the Department of Energy Joint Genome Institute
Igor V. Grigoriev,Henrik P. Nordberg,Igor Shabalov,Andrea Aerts,Michael N. Cantor,David Goodstein,Alan Kuo,Simon Minovitsky,Roman Nikitin,Robin A. Ohm,Robert Otillar,Alexander Poliakov,Igor Ratnere,Robert Riley,Tatyana Smirnova,Daniel S. Rokhsar,Inna Dubchak +16 more
TL;DR: The general organization of the JGI Genome Portal is described and the most recent addition, MycoCosm, a new integrated fungal genomics resource is described.
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) - eScholarship
Gerald A. Tuskan,Stephen P. DiFazio,Stefan Jansson,Joerg Bohlmann,Igor V. Grigoriev,Uffe Hellsten,Nicholas H. Putnam,Steven G. Ralph,Stephane Rombauts,Asaf Salamov,Jacquie Schein,Lieven Sterck,Andrea Aerts,Rishikeshi Bhalerao,Rishikesh P. Bhalerao,Damien Blaudez,Wout Boerjan,Annick Brun,Amy M. Brunner,Victor Busov,Malcolm M. Campbell,John E. Carlson,Michel Chalot,Jarrod Chapman,G.-L. Chen,Dawn Cooper,Pedro M. Coutinho,Jérémy Couturier,Sarah F. Covert,Quentin C. B. Cronk,R. Cunningham,J. Davis,Sven Degroeve,Annabelle Déjardin,C. dePamphillis,John C. Detter,Bill Dirks,Inna Dubchak,Sébastien Duplessis,J. Ehiting,Brian E. Ellis,Karla C Gendler,David Goodstein,Michael Gribskov,Jane Grimwood,Andrew Groover,Lee E. Gunter,Björn Hamberger,Berthold Heinze,Yrjö Helariutta,Bernard Henrissat,D. Holligan,Robert A. Holt,Wenyu Huang,N. Islam-Faridi,Steven J.M. Jones,M. Jones-Rhoades,Richard A. Jorgensen,Chandrashekhar P. Joshi,Jaakko Kangasjärvi,Jan Karlsson,Colin T. Kelleher,Robert Kirkpatrick,Matias Kirst,Annegret Kohler,Udaya C. Kalluri,Frank W. Larimer,Jim Leebens-Mack,Jean-Charles Leplé,Philip F. LoCascio,Y. Lou,Susan Lucas,Francis Martin,Barbara Montanini,Carolyn A. Napoli,David R. Nelson,D. Nelson,Kaisa Nieminen,Ove Nilsson,Gary F. Peter,Ryan N. Philippe,Gilles Pilate,Alexander Poliakov,J. Razumovskaya,Paul G. Richardson +84 more
TL;DR: Analyzing the draft genome of the black cottonwood tree, Populus trichocarpa, revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome.
Journal ArticleDOI
The DNA sequence and biology of human chromosome 19
Jane Grimwood,Laurie Gordon,Laurie Gordon,Anne S. Olsen,Anne S. Olsen,Astrid Terry,Jeremy Schmutz,Jane Lamerdin,Jane Lamerdin,Uffe Hellsten,David Goodstein,Olivier Couronne,Mary Bao Tran-Gyamfi,Mary Bao Tran-Gyamfi,Andrea Aerts,Michael R. Altherr,Michael R. Altherr,Linda K. Ashworth,Linda K. Ashworth,Eva Bajorek,Stacey Black,Elbert Branscomb,Elbert Branscomb,Sean Caenepeel,Anthony V. Carrano,Anthony V. Carrano,Chenier Caoile,Yee Man Chan,Mari Christensen,Mari Christensen,Catherine A. Cleland,Catherine A. Cleland,Alex Copeland,Eileen Dalin,Paramvir S. Dehal,Mirian Denys,John C. Detter,Julio Escobar,Dave Flowers,Dea Fotopulos,Carmen Rosa Albacete García,Anca M. Georgescu,Anca M. Georgescu,Tijana Glavina,Maria Gomez,Eidelyn Gonzales,Matthew Groza,Matthew Groza,Nancy Hammon,Trevor Hawkins,Lauren Haydu,Isaac Ho,Wayne Huang,Sanjay Israni,Jamie Jett,Kristen Kadner,Heather Kimball,Arthur Kobayashi,Arthur Kobayashi,Vladimer Larionov,Sun-Hee Leem,Frederick Lopez,Yunian Lou,Steve Lowry,Stephanie Malfatti,Stephanie Malfatti,Diego Martinez,Paula McCready,Paula McCready,Catherine Medina,Jenna Morgan,Kathryn Nelson,Kathryn Nelson,Matt Nolan,Ivan Ovcharenko,Ivan Ovcharenko,Sam Pitluck,Martin Pollard,Anthony P. Popkie,Paul Predki,Glenda Quan,Glenda Quan,Lucía Ramírez,Sam Rash,James Retterer,Alex Rodriguez,Stephanine Rogers,Asaf Salamov,Angelica Salazar,Xinwei She,Doug Smith,Tom Slezak,Tom Slezak,Victor V. Solovyev,Nina Thayer,Nina Thayer,Hope Tice,Ming Tsai,Anna Ustaszewska,Nu Vo,Mark C. Wagner,Mark C. Wagner,Jeremy Wheeler,Kevin Wu,Gary Xie,Gary Xie,Joan Yang,Inna Dubchak,Terrence S. Furey,Pieter J. deJong,Mark Dickson,David Gordon,Evan E. Eichler,Len A. Pennacchio,Paul G. Richardson,Lisa Stubbs,Lisa Stubbs,Daniel S. Rokhsar,Richard M. Myers,Edward M. Rubin,Susan Lucas +120 more
TL;DR: Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.
Journal ArticleDOI
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.
Daniel Lang,Kristian K. Ullrich,Florent Murat,Joerg Fuchs,Jerry Jenkins,Fabian B. Haas,Mathieu Piednoël,Heidrun Gundlach,Michiel Van Bel,Rabea Meyberg,Cristina Vives,Jordi Morata,Aikaterini Symeonidi,Manuel Hiss,Wellington Muchero,Yasuko Kamisugi,Omar Abu Saleh,Guillaume Blanc,Eva L. Decker,Nico van Gessel,Jane Grimwood,Richard D. Hayes,Sean W. Graham,Lee E. Gunter,Stuart F. McDaniel,Sebastian N. W. Hoernstein,Anders Larsson,Fay-Wei Li,Pierre-François Perroud,Jeremy Phillips,Priya Ranjan,Daniel S. Rokshar,Daniel S. Rokshar,Carl J. Rothfels,Lucas Schneider,Shengqiang Shu,Dennis W. Stevenson,Fritz Thümmler,Michael Tillich,Juan Carlos Villarreal Aguilar,Thomas Widiez,Thomas Widiez,Gane Ka-Shu Wong,Ann M. Wymore,Yong Zhang,Andreas Zimmer,Ralph S. Quatrano,Klaus F. X. Mayer,David Goodstein,Josep M. Casacuberta,Klaas Vandepoele,Ralf Reski,Andrew C. Cuming,Gerald A. Tuskan,Florian Maumus,Jérôme Salse,Jeremy Schmutz,Stefan A. Rensing,Stefan A. Rensing +58 more
TL;DR: More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes, it is found that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle.