Joshua C Stein

Joshua C Stein

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Joshua C Stein

Joshua C Stein

Publications by authors named "Joshua C Stein"

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Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.

Nat Genet 2018 09 30;50(9):1289-1295. Epub 2018 Jul 30.

State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.

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http://dx.doi.org/10.1038/s41588-018-0182-0DOI Listing
September 2018

Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure.

Curr Protoc Bioinformatics 2018 09 31;63(1):e53. Epub 2018 Aug 31.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

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http://doi.wiley.com/10.1002/cpbi.53
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http://dx.doi.org/10.1002/cpbi.53DOI Listing
September 2018

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.

Nat Commun 2016 06 24;7:11708. Epub 2016 Jun 24.

Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/ncomms11708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931018PMC
June 2016

Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

Plant Physiol 2015 Jan 10;167(1):25-39. Epub 2014 Nov 10.

The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)

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http://dx.doi.org/10.1104/pp.114.245027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280997PMC
January 2015

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

Syst Biol 2014 Sep 9;63(5):645-59. Epub 2014 Apr 9.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/sysbio/syu027DOI Listing
September 2014

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor.

Genome Res 2010 Dec 29;20(12):1689-99. Epub 2010 Oct 29.

Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA.

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http://dx.doi.org/10.1101/gr.109165.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989995PMC
December 2010

A genome-wide characterization of microRNA genes in maize.

PLoS Genet 2009 Nov 20;5(11):e1000716. Epub 2009 Nov 20.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773440PMC
November 2009

The B73 maize genome: complexity, diversity, and dynamics.

Authors:
Patrick S Schnable Doreen Ware Robert S Fulton Joshua C Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda Fulton Tina A Graves Patrick Minx Amy Denise Reily Laura Courtney Scott S Kruchowski Chad Tomlinson Cindy Strong Kim Delehaunty Catrina Fronick Bill Courtney Susan M Rock Eddie Belter Feiyu Du Kyung Kim Rachel M Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie M Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna Kanchi Thynn Thane Adam Scimone Nay Thane Jessica Henke Tom Wang Jessica Ruppert Neha Shah Kelsi Rotter Jennifer Hodges Elizabeth Ingenthron Matt Cordes Sara Kohlberg Jennifer Sgro Brandon Delgado Kelly Mead Asif Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Ruifeng He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Lopez David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser HyeRan Kim Seunghee Lee Jinke Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth Miller Claude Ambroise Stephanie Muller Will Spooner Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J Levy Linda McMahan Peter Van Buren Matthew W Vaughn Kai Ying Cheng-Ting Yeh Scott J Emrich Yi Jia Ananth Kalyanaraman An-Ping Hsia W Brad Barbazuk Regina S Baucom Thomas P Brutnell Nicholas C Carpita Cristian Chaparro Jer-Ming Chia Jean-Marc Deragon James C Estill Yan Fu Jeffrey A Jeddeloh Yujun Han Hyeran Lee Pinghua Li Damon R Lisch Sanzhen Liu Zhijie Liu Dawn Holligan Nagel Maureen C McCann Phillip SanMiguel Alan M Myers Dan Nettleton John Nguyen Bryan W Penning Lalit Ponnala Kevin L Schneider David C Schwartz Anupma Sharma Carol Soderlund Nathan M Springer Qi Sun Hao Wang Michael Waterman Richard Westerman Thomas K Wolfgruber Lixing Yang Yeisoo Yu Lifang Zhang Shiguo Zhou Qihui Zhu Jeffrey L Bennetzen R Kelly Dawe Jiming Jiang Ning Jiang Gernot G Presting Susan R Wessler Srinivas Aluru Robert A Martienssen Sandra W Clifton W Richard McCombie Rod A Wing Richard K Wilson

Science 2009 Nov;326(5956):1112-5

Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.

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http://www.dawelab.org/wp-content/uploads/2011/03/schnable-2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1178534
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http://dx.doi.org/10.1126/science.1178534DOI Listing
November 2009

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.

BMC Genomics 2008 Oct 31;9:517. Epub 2008 Oct 31.

Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.

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http://dx.doi.org/10.1186/1471-2164-9-517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613927PMC
October 2008