Matthew W Vaughn

Matthew W Vaughn

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Matthew W Vaughn

Matthew W Vaughn

Publications by authors named "Matthew W Vaughn"

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Genome-Wide Analysis of the Arabidopsis Replication Timing Program.

Plant Physiol 2018 03 4;176(3):2166-2185. Epub 2018 Jan 4.

Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695

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http://dx.doi.org/10.1104/pp.17.01537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841712PMC
March 2018

Repliscan: a tool for classifying replication timing regions.

BMC Bioinformatics 2017 Aug 7;18(1):362. Epub 2017 Aug 7.

Texas Advanced Computing Center, University of Texas at Austin, 10100 Burnet Road, Austin, 78758-4497, TX, USA.

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http://dx.doi.org/10.1186/s12859-017-1774-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5547489PMC
August 2017

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.

Plant Cell Physiol 2017 01;58(1):e4

Plant Genomics, J. Craig Venter Institute, Medical Center Dr, Rockville, MD, USA.

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http://dx.doi.org/10.1093/pcp/pcw200DOI Listing
January 2017

Genomic distribution of H3K9me2 and DNA methylation in a maize genome.

PLoS One 2014 14;9(8):e105267. Epub 2014 Aug 14.

Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105267PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133378PMC
November 2015

Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize.

Plant Physiol 2015 Aug 13;168(4):1262-74. Epub 2015 Apr 13.

Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108 (Q.L., P.T.W., S.R.E., N.M.S.); andTexas Advanced Computing Center, University of Texas, Austin, Texas 78758 (J.S., G.Z., M.W.V.)

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http://dx.doi.org/10.1104/pp.15.00052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528731PMC
August 2015

Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species.

Proc Natl Acad Sci U S A 2013 Nov 11;110(48):19639-44. Epub 2013 Nov 11.

Microbial and Plant Genomics Institute and Department of Plant Biology, University of Minnesota, St. Paul, MN 55108.

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http://dx.doi.org/10.1073/pnas.1309182110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845156PMC
November 2013

Epigenetic and genetic influences on DNA methylation variation in maize populations.

Plant Cell 2013 Aug 6;25(8):2783-97. Epub 2013 Aug 6.

Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minesota, Saint Paul, Minesota 55108.

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http://dx.doi.org/10.1105/tpc.113.114793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784580PMC
August 2013

Spreading of heterochromatin is limited to specific families of maize retrotransposons.

PLoS Genet 2012 13;8(12):e1003127. Epub 2012 Dec 13.

Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521669PMC
May 2013

Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm.

Plant Cell 2011 Dec 23;23(12):4221-33. Epub 2011 Dec 23.

Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minesota, Saint Paul, Minesota 55108, USA.

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http://www.plantcell.org/cgi/doi/10.1105/tpc.111.092668
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http://dx.doi.org/10.1105/tpc.111.092668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269861PMC
December 2011

Heritable epigenetic variation among maize inbreds.

PLoS Genet 2011 Nov 17;7(11):e1002372. Epub 2011 Nov 17.

Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219600PMC
November 2011

CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR.

Nature 2011 Jan 12;469(7328):112-5. Epub 2010 Dec 12.

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nature09608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057531PMC
January 2011

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

Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin.

Cell 2008 Oct;135(2):272-83

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.cell.2008.08.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614271PMC
October 2008

The fission yeast Jmj2 reverses histone H3 Lysine 4 trimethylation.

J Biol Chem 2007 Jul 5;282(30):21662-70. Epub 2007 Jun 5.

Department of Pathology, Harvard Medical School, Boston, MA 02115, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M703897200
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http://dx.doi.org/10.1074/jbc.M703897200DOI Listing
July 2007

Argonaute slicing is required for heterochromatic silencing and spreading.

Science 2006 Aug;313(5790):1134-7

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1126/science.1128813DOI Listing
August 2006

Replication, repair, and reactivation.

Dev Cell 2005 Dec;9(6):724-5

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1016/j.devcel.2005.11.011DOI Listing
December 2005

It's a small RNA world, after all.

Science 2005 Sep;309(5740):1525-6

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1126/science.1117805DOI Listing
September 2005

Finding the right template: RNA Pol IV, a plant-specific RNA polymerase.

Mol Cell 2005 Mar;17(6):754-6

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1016/j.molcel.2005.03.003DOI Listing
March 2005

Protein phosphorylation plays a key role in sucrose-mediated transcriptional regulation of a phloem-specific proton-sucrose symporter.

Planta 2003 Jul 14;217(3):483-9. Epub 2003 Mar 14.

Department of Plant Biology, 190 E.R. Madigan Laboratory, University of Illinois at Urbana-Champaign, IL 61801, USA.

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http://dx.doi.org/10.1007/s00425-003-1011-xDOI Listing
July 2003

Sucrose-mediated transcriptional regulation of sucrose symporter activity in the phloem.

Proc Natl Acad Sci U S A 2002 Aug 29;99(16):10876-80. Epub 2002 Jul 29.

Program in Physiological and Molecular Plant Biology, University of Illinois at Urbana-Champaign, Urbana IL, 61801, USA.

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http://dx.doi.org/10.1073/pnas.172198599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC125066PMC
August 2002