David Goodstein

David Goodstein

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David Goodstein

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Construction and comparison of three reference-quality genome assemblies for soybean.

Authors:
Babu Valliyodan Steven B Cannon Philipp E Bayer Shengqiang Shu Anne V Brown Longhui Ren Jerry Jenkins Claire Yik-Lok Chung Ting-Fung Chan Christopher G Daum Christopher Plott Alex Hastie Kobi Baruch Kerrie W Barry Wei Huang Gunvant Patil Rajeev K Varshney Haifei Hu Jacqueline Batley Yuxuan Yuan Qijian Song Robert M Stupar David M Goodstein Gary Stacey Hon-Ming Lam Scott A Jackson Jeremy Schmutz Jane Grimwood David Edwards Henry T Nguyen

Plant J 2019 Aug 21. Epub 2019 Aug 21.

Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA.

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http://dx.doi.org/10.1111/tpj.14500DOI Listing
August 2019

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Authors:
Daniel Lang Kristian K Ullrich Florent Murat Jörg Fuchs Jerry Jenkins Fabian B Haas Mathieu Piednoel Heidrun Gundlach Michiel Van Bel Rabea Meyberg Cristina Vives Jordi Morata Aikaterini Symeonidi Manuel Hiss Wellington Muchero Yasuko Kamisugi Omar 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 Carl J Rothfels Lucas Schneider Shengqiang Shu Dennis W Stevenson Fritz Thümmler Michael Tillich Juan C Villarreal Aguilar Thomas Widiez Gane Ka-Shu Wong Ann Wymore Yong Zhang Andreas D 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 Jérome Salse Jeremy Schmutz Stefan A Rensing

Plant J 2018 02;93(3):515-533

Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany.

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http://dx.doi.org/10.1111/tpj.13801DOI Listing
February 2018

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.

Authors:
Xiaohan Yang Rongbin Hu Hengfu Yin Jerry Jenkins Shengqiang Shu Haibao Tang Degao Liu Deborah A Weighill Won Cheol Yim Jungmin Ha Karolina Heyduk David M Goodstein Hao-Bo Guo Robert C Moseley Elisabeth Fitzek Sara Jawdy Zhihao Zhang Meng Xie James Hartwell Jane Grimwood Paul E Abraham Ritesh Mewalal Juan D Beltrán Susanna F Boxall Louisa V Dever Kaitlin J Palla Rebecca Albion Travis Garcia Jesse A Mayer Sung Don Lim Ching Man Wai Paul Peluso Robert Van Buren Henrique Cestari De Paoli Anne M Borland Hong Guo Jin-Gui Chen Wellington Muchero Yanbin Yin Daniel A Jacobson Timothy J Tschaplinski Robert L Hettich Ray Ming Klaus Winter James H Leebens-Mack J Andrew C Smith John C Cushman Jeremy Schmutz Gerald A Tuskan

Nat Commun 2017 12 1;8(1):1899. Epub 2017 Dec 1.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.

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http://dx.doi.org/10.1038/s41467-017-01491-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711932PMC
December 2017

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

Authors:
Sean P Gordon Bruno Contreras-Moreira Daniel P Woods David L Des Marais Diane Burgess Shengqiang Shu Christoph Stritt Anne C Roulin Wendy Schackwitz Ludmila Tyler Joel Martin Anna Lipzen Niklas Dochy Jeremy Phillips Kerrie Barry Koen Geuten Hikmet Budak Thomas E Juenger Richard Amasino Ana L Caicedo David Goodstein Patrick Davidson Luis A J Mur Melania Figueroa Michael Freeling Pilar Catalan John P Vogel

Nat Commun 2017 12 19;8(1):2184. Epub 2017 Dec 19.

DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.

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http://dx.doi.org/10.1038/s41467-017-02292-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736591PMC
December 2017

JBrowse: a dynamic web platform for genome visualization and analysis.

Authors:
Robert Buels Eric Yao Colin M Diesh Richard D Hayes Monica Munoz-Torres Gregg Helt David M Goodstein Christine G Elsik Suzanna E Lewis Lincoln Stein Ian H Holmes

Genome Biol 2016 Apr 12;17:66. Epub 2016 Apr 12.

Department of Bioengineering, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1186/s13059-016-0924-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4830012PMC
April 2016

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Authors:
Damian Smedley Syed Haider Steffen Durinck Luca Pandini Paolo Provero James Allen Olivier Arnaiz Mohammad Hamza Awedh Richard Baldock Giulia Barbiera Philippe Bardou Tim Beck Andrew Blake Merideth Bonierbale Anthony J Brookes Gabriele Bucci Iwan Buetti Sarah Burge Cédric Cabau Joseph W Carlson Claude Chelala Charalambos Chrysostomou Davide Cittaro Olivier Collin Raul Cordova Rosalind J Cutts Erik Dassi Alex Di Genova Anis Djari Anthony Esposito Heather Estrella Eduardo Eyras Julio Fernandez-Banet Simon Forbes Robert C Free Takatomo Fujisawa Emanuela Gadaleta Jose M Garcia-Manteiga David Goodstein Kristian Gray José Afonso Guerra-Assunção Bernard Haggarty Dong-Jin Han Byung Woo Han Todd Harris Jayson Harshbarger Robert K Hastings Richard D Hayes Claire Hoede Shen Hu Zhi-Liang Hu Lucie Hutchins Zhengyan Kan Hideya Kawaji Aminah Keliet Arnaud Kerhornou Sunghoon Kim Rhoda Kinsella Christophe Klopp Lei Kong Daniel Lawson Dejan Lazarevic Ji-Hyun Lee Thomas Letellier Chuan-Yun Li Pietro Lio Chu-Jun Liu Jie Luo Alejandro Maass Jerome Mariette Thomas Maurel Stefania Merella Azza Mostafa Mohamed Francois Moreews Ibounyamine Nabihoudine Nelson Ndegwa Céline Noirot Cristian Perez-Llamas Michael Primig Alessandro Quattrone Hadi Quesneville Davide Rambaldi James Reecy Michela Riba Steven Rosanoff Amna Ali Saddiq Elisa Salas Olivier Sallou Rebecca Shepherd Reinhard Simon Linda Sperling William Spooner Daniel M Staines Delphine Steinbach Kevin Stone Elia Stupka Jon W Teague Abu Z Dayem Ullah Jun Wang Doreen Ware Marie Wong-Erasmus Ken Youens-Clark Amonida Zadissa Shi-Jian Zhang Arek Kasprzyk

Nucleic Acids Res 2015 Jul 20;43(W1):W589-98. Epub 2015 Apr 20.

Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia

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http://dx.doi.org/10.1093/nar/gkv350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489294PMC
July 2015

The Chlamydomonas genome project: a decade on.

Authors:
Ian K Blaby Crysten E Blaby-Haas Nicolas Tourasse Erik F Y Hom David Lopez Munevver Aksoy Arthur Grossman James Umen Susan Dutcher Mary Porter Stephen King George B Witman Mario Stanke Elizabeth H Harris David Goodstein Jane Grimwood Jeremy Schmutz Olivier Vallon Sabeeha S Merchant Simon Prochnik

Trends Plant Sci 2014 Oct 17;19(10):672-80. Epub 2014 Jun 17.

US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tplants.2014.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4185214PMC
October 2014

A reference genome for common bean and genome-wide analysis of dual domestications.

Authors:
Jeremy Schmutz Phillip E McClean Sujan Mamidi G Albert Wu Steven B Cannon Jane Grimwood Jerry Jenkins Shengqiang Shu Qijian Song Carolina Chavarro Mirayda Torres-Torres Valerie Geffroy Samira Mafi Moghaddam Dongying Gao Brian Abernathy Kerrie Barry Matthew Blair Mark A Brick Mansi Chovatia Paul Gepts David M Goodstein Michael Gonzales Uffe Hellsten David L Hyten Gaofeng Jia James D Kelly Dave Kudrna Rian Lee Manon M S Richard Phillip N Miklas Juan M Osorno Josiane Rodrigues Vincent Thareau Carlos A Urrea Mei Wang Yeisoo Yu Ming Zhang Rod A Wing Perry B Cregan Daniel S Rokhsar Scott A Jackson

Nat Genet 2014 Jul 8;46(7):707-13. Epub 2014 Jun 8.

Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.

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http://dx.doi.org/10.1038/ng.3008DOI Listing
July 2014

The genome of Eucalyptus grandis.

Authors:
Alexander A Myburg Dario Grattapaglia Gerald A Tuskan Uffe Hellsten Richard D Hayes Jane Grimwood Jerry Jenkins Erika Lindquist Hope Tice Diane Bauer David M Goodstein Inna Dubchak Alexandre Poliakov Eshchar Mizrachi Anand R K Kullan Steven G Hussey Desre Pinard Karen van der Merwe Pooja Singh Ida van Jaarsveld Orzenil B Silva-Junior Roberto C Togawa Marilia R Pappas Danielle A Faria Carolina P Sansaloni Cesar D Petroli Xiaohan Yang Priya Ranjan Timothy J Tschaplinski Chu-Yu Ye Ting Li Lieven Sterck Kevin Vanneste Florent Murat Marçal Soler Hélène San Clemente Naijib Saidi Hua Cassan-Wang Christophe Dunand Charles A Hefer Erich Bornberg-Bauer Anna R Kersting Kelly Vining Vindhya Amarasinghe Martin Ranik Sushma Naithani Justin Elser Alexander E Boyd Aaron Liston Joseph W Spatafora Palitha Dharmwardhana Rajani Raja Christopher Sullivan Elisson Romanel Marcio Alves-Ferreira Carsten Külheim William Foley Victor Carocha Jorge Paiva David Kudrna Sergio H Brommonschenkel Giancarlo Pasquali Margaret Byrne Philippe Rigault Josquin Tibbits Antanas Spokevicius Rebecca C Jones Dorothy A Steane René E Vaillancourt Brad M Potts Fourie Joubert Kerrie Barry Georgios J Pappas Steven H Strauss Pankaj Jaiswal Jacqueline Grima-Pettenati Jérôme Salse Yves Van de Peer Daniel S Rokhsar Jeremy Schmutz

Nature 2014 Jun 11;510(7505):356-62. Epub 2014 Jun 11.

1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA.

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http://dx.doi.org/10.1038/nature13308DOI Listing
June 2014

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.

Authors:
Ignazio Verde Albert G Abbott Simone Scalabrin Sook Jung Shengqiang Shu Fabio Marroni Tatyana Zhebentyayeva Maria Teresa Dettori Jane Grimwood Federica Cattonaro Andrea Zuccolo Laura Rossini Jerry Jenkins Elisa Vendramin Lee A Meisel Veronique Decroocq Bryon Sosinski Simon Prochnik Therese Mitros Alberto Policriti Guido Cipriani Luca Dondini Stephen Ficklin David M Goodstein Pengfei Xuan Cristian Del Fabbro Valeria Aramini Dario Copetti Susana Gonzalez David S Horner Rachele Falchi Susan Lucas Erica Mica Jonathan Maldonado Barbara Lazzari Douglas Bielenberg Raul Pirona Mara Miculan Abdelali Barakat Raffaele Testolin Alessandra Stella Stefano Tartarini Pietro Tonutti Pere Arús Ariel Orellana Christina Wells Dorrie Main Giannina Vizzotto Herman Silva Francesco Salamini Jeremy Schmutz Michele Morgante Daniel S Rokhsar

Nat Genet 2013 May 24;45(5):487-94. Epub 2013 Mar 24.

Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA)-Centro di Ricerca per la Frutticoltura, Rome, Italy.

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http://dx.doi.org/10.1038/ng.2586DOI Listing
May 2013

Phytozome: a comparative platform for green plant genomics.

Authors:
David M Goodstein Shengqiang Shu Russell Howson Rochak Neupane Richard D Hayes Joni Fazo Therese Mitros William Dirks Uffe Hellsten Nicholas Putnam Daniel S Rokhsar

Nucleic Acids Res 2012 Jan 22;40(Database issue):D1178-86. Epub 2011 Nov 22.

US Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1093/nar/gkr944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245001PMC
January 2012

The genome portal of the Department of Energy Joint Genome Institute.

Authors:
Igor V Grigoriev Henrik Nordberg Igor Shabalov Andrea Aerts Mike Cantor David Goodstein Alan Kuo Simon Minovitsky Roman Nikitin Robin A Ohm Robert Otillar Alex Poliakov Igor Ratnere Robert Riley Tatyana Smirnova Daniel Rokhsar Inna Dubchak

Nucleic Acids Res 2012 Jan 22;40(Database issue):D26-32. Epub 2011 Nov 22.

Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA.

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http://dx.doi.org/10.1093/nar/gkr947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245080PMC
January 2012

The Amphimedon queenslandica genome and the evolution of animal complexity.

Authors:
Mansi Srivastava Oleg Simakov Jarrod Chapman Bryony Fahey Marie E A Gauthier Therese Mitros Gemma S Richards Cecilia Conaco Michael Dacre Uffe Hellsten Claire Larroux Nicholas H Putnam Mario Stanke Maja Adamska Aaron Darling Sandie M Degnan Todd H Oakley David C Plachetzki Yufeng Zhai Marcin Adamski Andrew Calcino Scott F Cummins David M Goodstein Christina Harris Daniel J Jackson Sally P Leys Shengqiang Shu Ben J Woodcroft Michel Vervoort Kenneth S Kosik Gerard Manning Bernard M Degnan Daniel S Rokhsar

Nature 2010 Aug;466(7307):720-6

Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/nature09201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130542PMC
August 2010

The genome of the Western clawed frog Xenopus tropicalis.

Authors:
Uffe Hellsten Richard M Harland Michael J Gilchrist David Hendrix Jerzy Jurka Vladimir 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 Fletcher Daniela S Gerhard David Goodstein Tina Graves Igor V Grigoriev Jane Grimwood Takeshi Kawashima Erika Lindquist Susan M Lucas Paul E Mead Therese Mitros Hajime Ogino Yuko Ohta Alexander V Poliakov Nicolas Pollet Jacques Robert Asaf Salamov Amy K Sater Jeremy Schmutz Astrid Terry Peter D Vize Wesley C Warren Dan Wells Andrea Wills Richard K Wilson Lyle B Zimmerman Aaron M Zorn Robert Grainger Timothy Grammer Mustafa K Khokha Paul M Richardson Daniel S Rokhsar

Science 2010 Apr;328(5978):633-6

Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1126/science.1183670DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994648PMC
April 2010

The dynamic genome of Hydra.

Authors:
Jarrod A Chapman Ewen F Kirkness Oleg Simakov Steven E Hampson Therese Mitros Thomas Weinmaier Thomas Rattei Prakash G Balasubramanian Jon Borman Dana Busam Kathryn Disbennett Cynthia Pfannkoch Nadezhda Sumin Granger G Sutton Lakshmi Devi Viswanathan Brian Walenz David M Goodstein Uffe Hellsten Takeshi Kawashima Simon E Prochnik Nicholas H Putnam Shengquiang Shu Bruce Blumberg Catherine E Dana Lydia Gee Dennis F Kibler Lee Law Dirk Lindgens Daniel E Martinez Jisong Peng Philip A Wigge Bianca Bertulat Corina Guder Yukio Nakamura Suat Ozbek Hiroshi Watanabe Konstantin Khalturin Georg Hemmrich André Franke René Augustin Sebastian Fraune Eisuke Hayakawa Shiho Hayakawa Mamiko Hirose Jung Shan Hwang Kazuho Ikeo Chiemi Nishimiya-Fujisawa Atshushi Ogura Toshio Takahashi Patrick R H Steinmetz Xiaoming Zhang Roland Aufschnaiter Marie-Kristin Eder Anne-Kathrin Gorny Willi Salvenmoser Alysha M Heimberg Benjamin M Wheeler Kevin J Peterson Angelika Böttger Patrick Tischler Alexander Wolf Takashi Gojobori Karin A Remington Robert L Strausberg J Craig Venter Ulrich Technau Bert Hobmayer Thomas C G Bosch Thomas W Holstein Toshitaka Fujisawa Hans R Bode Charles N David Daniel S Rokhsar Robert E Steele

Nature 2010 Mar 14;464(7288):592-6. Epub 2010 Mar 14.

US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature08830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479502PMC
March 2010

Genome sequence of the palaeopolyploid soybean.

Authors:
Jeremy Schmutz Steven B Cannon Jessica Schlueter Jianxin Ma Therese Mitros William Nelson David L Hyten Qijian Song Jay J Thelen Jianlin Cheng Dong Xu Uffe Hellsten Gregory D May Yeisoo Yu Tetsuya Sakurai Taishi Umezawa Madan K Bhattacharyya Devinder Sandhu Babu Valliyodan Erika Lindquist Myron Peto David Grant Shengqiang Shu David Goodstein Kerrie Barry Montona Futrell-Griggs Brian Abernathy Jianchang Du Zhixi Tian Liucun Zhu Navdeep Gill Trupti Joshi Marc Libault Anand Sethuraman Xue-Cheng Zhang Kazuo Shinozaki Henry T Nguyen Rod A Wing Perry Cregan James Specht Jane Grimwood Dan Rokhsar Gary Stacey Randy C Shoemaker Scott A Jackson

Nature 2010 Jan;463(7278):178-83

HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA.

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http://dx.doi.org/10.1038/nature08670DOI Listing
January 2010

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.

Authors:
Nicole King M Jody Westbrook Susan L Young Alan Kuo Monika Abedin Jarrod Chapman Stephen Fairclough Uffe Hellsten Yoh Isogai Ivica Letunic Michael Marr David Pincus Nicholas Putnam Antonis Rokas Kevin J Wright Richard Zuzow William Dirks Matthew Good David Goodstein Derek Lemons Wanqing Li Jessica B Lyons Andrea Morris Scott Nichols Daniel J Richter Asaf Salamov J G I Sequencing Peer Bork Wendell A Lim Gerard Manning W Todd Miller William McGinnis Harris Shapiro Robert Tjian Igor V Grigoriev Daniel Rokhsar

Nature 2008 Feb;451(7180):783-8

Department of Molecular and Cell Biology and the Center for Integrative Genomics, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/nature06617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562698PMC
February 2008

The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Authors:
Sabeeha S Merchant Simon E Prochnik Olivier Vallon Elizabeth H Harris Steven J Karpowicz George B Witman Astrid Terry Asaf Salamov Lillian K Fritz-Laylin Laurence Maréchal-Drouard Wallace F Marshall Liang-Hu Qu David R Nelson Anton A Sanderfoot Martin H Spalding Vladimir V Kapitonov Qinghu Ren Patrick Ferris Erika Lindquist Harris Shapiro Susan M Lucas Jane Grimwood Jeremy Schmutz Pierre Cardol Heriberto Cerutti Guillaume Chanfreau Chun-Long Chen Valérie Cognat Martin T Croft Rachel Dent Susan Dutcher Emilio Fernández Hideya Fukuzawa David González-Ballester Diego González-Halphen Armin Hallmann Marc Hanikenne Michael Hippler William Inwood Kamel Jabbari Ming Kalanon Richard Kuras Paul A Lefebvre Stéphane D Lemaire Alexey V Lobanov Martin Lohr Andrea Manuell Iris Meier Laurens Mets Maria Mittag Telsa Mittelmeier James V Moroney Jeffrey Moseley Carolyn Napoli Aurora M Nedelcu Krishna Niyogi Sergey V Novoselov Ian T Paulsen Greg Pazour Saul Purton Jean-Philippe Ral Diego Mauricio Riaño-Pachón Wayne Riekhof Linda Rymarquis Michael Schroda David Stern James Umen Robert Willows Nedra Wilson Sara Lana Zimmer Jens Allmer Janneke Balk Katerina Bisova Chong-Jian Chen Marek Elias Karla Gendler Charles Hauser Mary Rose Lamb Heidi Ledford Joanne C Long Jun Minagawa M Dudley Page Junmin Pan Wirulda Pootakham Sanja Roje Annkatrin Rose Eric Stahlberg Aimee M Terauchi Pinfen Yang Steven Ball Chris Bowler Carol L Dieckmann Vadim N Gladyshev Pamela Green Richard Jorgensen Stephen Mayfield Bernd Mueller-Roeber Sathish Rajamani Richard T Sayre Peter Brokstein Inna Dubchak David Goodstein Leila Hornick Y Wayne Huang Jinal Jhaveri Yigong Luo Diego Martínez Wing Chi Abby Ngau Bobby Otillar Alexander Poliakov Aaron Porter Lukasz Szajkowski Gregory Werner Kemin Zhou Igor V Grigoriev Daniel S Rokhsar Arthur R Grossman

Science 2007 Oct;318(5848):245-50

Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1126/science.1143609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087PMC
October 2007

The sequence and analysis of duplication-rich human chromosome 16.

Authors:
Joel Martin Cliff Han Laurie A Gordon Astrid Terry Shyam Prabhakar Xinwei She Gary Xie Uffe Hellsten Yee Man Chan Michael Altherr Olivier Couronne Andrea Aerts Eva Bajorek Stacey Black Heather Blumer Elbert Branscomb Nancy C Brown William J Bruno Judith M Buckingham David F Callen Connie S Campbell Mary L Campbell Evelyn W Campbell Chenier Caoile Jean F Challacombe Leslie A Chasteen Olga Chertkov Han C Chi Mari Christensen Lynn M Clark Judith D Cohn Mirian Denys John C Detter Mark Dickson Mira Dimitrijevic-Bussod Julio Escobar Joseph J Fawcett Dave Flowers Dea Fotopulos Tijana Glavina Maria Gomez Eidelyn Gonzales David Goodstein Lynne A Goodwin Deborah L Grady Igor Grigoriev Matthew Groza Nancy Hammon Trevor Hawkins Lauren Haydu Carl E Hildebrand Wayne Huang Sanjay Israni Jamie Jett Phillip B Jewett Kristen Kadner Heather Kimball Arthur Kobayashi Marie-Claude Krawczyk Tina Leyba Jonathan L Longmire Frederick Lopez Yunian Lou Steve Lowry Thom Ludeman Chitra F Manohar Graham A Mark Kimberly L McMurray Linda J Meincke Jenna Morgan Robert K Moyzis Mark O Mundt A Christine Munk Richard D Nandkeshwar Sam Pitluck Martin Pollard Paul Predki Beverly Parson-Quintana Lucia Ramirez Sam Rash James Retterer Darryl O Ricke Donna L Robinson Alex Rodriguez Asaf Salamov Elizabeth H Saunders Duncan Scott Timothy Shough Raymond L Stallings Malinda Stalvey Robert D Sutherland Roxanne Tapia Judith G Tesmer Nina Thayer Linda S Thompson Hope Tice David C Torney Mary Tran-Gyamfi Ming Tsai Levy E Ulanovsky Anna Ustaszewska Nu Vo P Scott White Albert L Williams Patricia L Wills Jung-Rung Wu Kevin Wu Joan Yang Pieter Dejong David Bruce Norman A Doggett Larry Deaven Jeremy Schmutz Jane Grimwood Paul Richardson Daniel S Rokhsar Evan E Eichler Paul Gilna Susan M Lucas Richard M Myers Edward M Rubin Len A Pennacchio

Nature 2004 Dec;432(7020):988-94

DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature03187DOI Listing
December 2004

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.

Authors:
E Virginia Armbrust John A Berges Chris Bowler Beverley R Green Diego Martinez Nicholas H Putnam Shiguo Zhou Andrew E Allen Kirk E Apt Michael Bechner Mark A Brzezinski Balbir K Chaal Anthony Chiovitti Aubrey K Davis Mark S Demarest J Chris Detter Tijana Glavina David Goodstein Masood Z Hadi Uffe Hellsten Mark Hildebrand Bethany D Jenkins Jerzy Jurka Vladimir V Kapitonov Nils Kröger Winnie W Y Lau Todd W Lane Frank W Larimer J Casey Lippmeier Susan Lucas Mónica Medina Anton Montsant Miroslav Obornik Micaela Schnitzler Parker Brian Palenik Gregory J Pazour Paul M Richardson Tatiana A Rynearson Mak A Saito David C Schwartz Kimberlee Thamatrakoln Klaus Valentin Assaf Vardi Frances P Wilkerson Daniel S Rokhsar

Science 2004 Oct;306(5693):79-86

School of Oceanography, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1126/science.1101156DOI Listing
October 2004

The DNA sequence and comparative analysis of human chromosome 5.

Authors:
Jeremy Schmutz Joel Martin Astrid Terry Olivier Couronne Jane Grimwood Steve Lowry Laurie A Gordon Duncan Scott Gary Xie Wayne Huang Uffe Hellsten Mary Tran-Gyamfi Xinwei She Shyam Prabhakar Andrea Aerts Michael Altherr Eva Bajorek Stacey Black Elbert Branscomb Chenier Caoile Jean F Challacombe Yee Man Chan Mirian Denys John C Detter Julio Escobar Dave Flowers Dea Fotopulos Tijana Glavina Maria Gomez Eidelyn Gonzales David Goodstein Igor Grigoriev Matthew Groza Nancy Hammon Trevor Hawkins Lauren Haydu Sanjay Israni Jamie Jett Kristen Kadner Heather Kimball Arthur Kobayashi Frederick Lopez Yunian Lou Diego Martinez Catherine Medina Jenna Morgan Richard Nandkeshwar James P Noonan Sam Pitluck Martin Pollard Paul Predki James Priest Lucia Ramirez James Retterer Alex Rodriguez Stephanie Rogers Asaf Salamov Angelica Salazar Nina Thayer Hope Tice Ming Tsai Anna Ustaszewska Nu Vo Jeremy Wheeler Kevin Wu Joan Yang Mark Dickson Jan-Fang Cheng Evan E Eichler Anne Olsen Len A Pennacchio Daniel S Rokhsar Paul Richardson Susan M Lucas Richard M Myers Edward M Rubin

Nature 2004 Sep;431(7006):268-74

Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Ave, Palo Alto, California 94304, USA.

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http://dx.doi.org/10.1038/nature02919DOI Listing
September 2004

The DNA sequence and biology of human chromosome 19.

Authors:
Jane Grimwood Laurie A Gordon Anne Olsen Astrid Terry Jeremy Schmutz Jane Lamerdin Uffe Hellsten David Goodstein Olivier Couronne Mary Tran-Gyamfi Andrea Aerts Michael Altherr Linda Ashworth Eva Bajorek Stacey Black Elbert Branscomb Sean Caenepeel Anthony Carrano Chenier Caoile Yee Man Chan Mari Christensen Catherine A Cleland Alex Copeland Eileen Dalin Paramvir Dehal Mirian Denys John C Detter Julio Escobar Dave Flowers Dea Fotopulos Carmen Garcia Anca M Georgescu Tijana Glavina Maria Gomez Eidelyn Gonzales Matthew Groza Nancy Hammon Trevor Hawkins Lauren Haydu Isaac Ho Wayne Huang Sanjay Israni Jamie Jett Kristen Kadner Heather Kimball Arthur Kobayashi Vladimer Larionov Sun-Hee Leem Frederick Lopez Yunian Lou Steve Lowry Stephanie Malfatti Diego Martinez Paula McCready Catherine Medina Jenna Morgan Kathryn Nelson Matt Nolan Ivan Ovcharenko Sam Pitluck Martin Pollard Anthony P Popkie Paul Predki Glenda Quan Lucia Ramirez Sam Rash James Retterer Alex Rodriguez Stephanine Rogers Asaf Salamov Angelica Salazar Xinwei She Doug Smith Tom Slezak Victor Solovyev Nina Thayer Hope Tice Ming Tsai Anna Ustaszewska Nu Vo Mark Wagner Jeremy Wheeler Kevin Wu Gary Xie Joan Yang Inna Dubchak Terrence S Furey Pieter DeJong Mark Dickson David Gordon Evan E Eichler Len A Pennacchio Paul Richardson Lisa Stubbs Daniel S Rokhsar Richard M Myers Edward M Rubin Susan M Lucas

Nature 2004 Apr;428(6982):529-35

Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, California 94304, USA.

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http://dx.doi.org/10.1038/nature02399DOI Listing
April 2004

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.

Authors:
Paramvir Dehal Yutaka Satou Robert K Campbell Jarrod Chapman Bernard Degnan Anthony De Tomaso Brad Davidson Anna Di Gregorio Maarten Gelpke David M Goodstein Naoe Harafuji Kenneth E M Hastings Isaac Ho Kohji Hotta Wayne Huang Takeshi Kawashima Patrick Lemaire Diego Martinez Ian A Meinertzhagen Simona Necula Masaru Nonaka Nik Putnam Sam Rash Hidetoshi Saiga Masanobu Satake Astrid Terry Lixy Yamada Hong-Gang Wang Satoko Awazu Kaoru Azumi Jeffrey Boore Margherita Branno Stephen Chin-Bow Rosaria DeSantis Sharon Doyle Pilar Francino David N Keys Shinobu Haga Hiroko Hayashi Kyosuke Hino Kaoru S Imai Kazuo Inaba Shungo Kano Kenji Kobayashi Mari Kobayashi Byung-In Lee Kazuhiro W Makabe Chitra Manohar Giorgio Matassi Monica Medina Yasuaki Mochizuki Steve Mount Tomomi Morishita Sachiko Miura Akie Nakayama Satoko Nishizaka Hisayo Nomoto Fumiko Ohta Kazuko Oishi Isidore Rigoutsos Masako Sano Akane Sasaki Yasunori Sasakura Eiichi Shoguchi Tadasu Shin-i Antoinetta Spagnuolo Didier Stainier Miho M Suzuki Olivier Tassy Naohito Takatori Miki Tokuoka Kasumi Yagi Fumiko Yoshizaki Shuichi Wada Cindy Zhang P Douglas Hyatt Frank Larimer Chris Detter Norman Doggett Tijana Glavina Trevor Hawkins Paul Richardson Susan Lucas Yuji Kohara Michael Levine Nori Satoh Daniel S Rokhsar

Science 2002 Dec;298(5601):2157-67

U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1126/science.1080049DOI Listing
December 2002