Publications by authors named "Jeremy Schmutz"

100Publications

Environmentally responsive QTL controlling surface wax load in switchgrass.

Theor Appl Genet 2020 Nov 14;133(11):3119-3137. Epub 2020 Aug 14.

Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA.

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http://dx.doi.org/10.1007/s00122-020-03659-0DOI Listing
November 2020

Sequencing and Analysis of the Sex Determination Region of .

Genes (Basel) 2020 Jul 24;11(8). Epub 2020 Jul 24.

Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA.

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http://dx.doi.org/10.3390/genes11080843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465354PMC
July 2020

Network Modeling of Complex Data Sets.

Methods Mol Biol 2020 ;2096:197-215

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

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http://dx.doi.org/10.1007/978-1-0716-0195-2_15DOI Listing
January 2020

Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway.

Mol Phylogenet Evol 2020 Oct 6;151:106904. Epub 2020 Jul 6.

Department of Biology, Duke University, Durham, NC 27708, United States.

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http://dx.doi.org/10.1016/j.ympev.2020.106904DOI Listing
October 2020

SoyCSN: Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data.

Plant Direct 2019 Sep 17;3(9):e00167. Epub 2019 Sep 17.

Christopher S. Bond Life Sciences Center University of Missouri St. Louis MO USA.

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http://dx.doi.org/10.1002/pld3.167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747016PMC
September 2019

High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome.

Sci Rep 2019 08 21;9(1):12183. Epub 2019 Aug 21.

Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), University of Georgia, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1038/s41598-019-48257-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6704178PMC
August 2019

Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.

Front Genet 2019 31;10:487. Epub 2019 May 31.

The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.

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http://dx.doi.org/10.3389/fgene.2019.00487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6554479PMC
May 2019

Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium).

Theor Appl Genet 2019 Aug 6;132(8):2325-2351. Epub 2019 Jun 6.

United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT, 84322, USA.

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http://dx.doi.org/10.1007/s00122-019-03357-6DOI Listing
August 2019

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.

Dev Biol 2019 08 10;452(1):8-20. Epub 2019 Apr 10.

University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition, Berkeley, CA 94720-3200, USA; Joint Genome Institute, 2800 Mitchell Dr # 100, Walnut Creek, CA 94598, USA; Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 9040495, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2019.03.015DOI Listing
August 2019

Enhancing microRNA167A expression in seed decreases the α-linolenic acid content and increases seed size in Camelina sativa.

Plant J 2019 04 14;98(2):346-358. Epub 2019 Feb 14.

Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.

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http://dx.doi.org/10.1111/tpj.14223DOI Listing
April 2019

Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae).

BMC Genomics 2018 Nov 1;19(1):792. Epub 2018 Nov 1.

Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.

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http://dx.doi.org/10.1186/s12864-018-5179-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211516PMC
November 2018

Characterization of a large sex determination region in Salix purpurea L. (Salicaceae).

Mol Genet Genomics 2018 Dec 18;293(6):1437-1452. Epub 2018 Jul 18.

Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA.

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http://dx.doi.org/10.1007/s00438-018-1473-yDOI Listing
December 2018

Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

Gene 2018 Jul 12;663:165-177. Epub 2018 Apr 12.

Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA; Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2018.04.024DOI Listing
July 2018

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.

Genes (Basel) 2018 Mar 28;9(4). Epub 2018 Mar 28.

Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia.

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http://dx.doi.org/10.3390/genes9040185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924527PMC
March 2018

Amplification and adaptation of centromeric repeats in polyploid switchgrass species.

New Phytol 2018 06 25;218(4):1645-1657. Epub 2018 Mar 25.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1111/nph.15098DOI Listing
June 2018

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.

Sci Rep 2017 11 10;7(1):15274. Epub 2017 Nov 10.

Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA.

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http://dx.doi.org/10.1038/s41598-017-14885-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681701PMC
November 2017

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

Authors:
John L Bowman Takayuki Kohchi Katsuyuki T Yamato Jerry Jenkins Shengqiang Shu Kimitsune Ishizaki Shohei Yamaoka Ryuichi Nishihama Yasukazu Nakamura Frédéric Berger Catherine Adam Shiori Sugamata Aki Felix Althoff Takashi Araki Mario A Arteaga-Vazquez Sureshkumar Balasubrmanian Kerrie Barry Diane Bauer Christian R Boehm Liam Briginshaw Juan Caballero-Perez Bruno Catarino Feng Chen Shota Chiyoda Mansi Chovatia Kevin M Davies Mihails Delmans Taku Demura Tom Dierschke Liam Dolan Ana E Dorantes-Acosta D Magnus Eklund Stevie N Florent Eduardo Flores-Sandoval Asao Fujiyama Hideya Fukuzawa Bence Galik Daniel Grimanelli Jane Grimwood Ueli Grossniklaus Takahiro Hamada Jim Haseloff Alexander J Hetherington Asuka Higo Yuki Hirakawa Hope N Hundley Yoko Ikeda Keisuke Inoue Shin-Ichiro Inoue Sakiko Ishida Qidong Jia Mitsuru Kakita Takehiko Kanazawa Yosuke Kawai Tomokazu Kawashima Megan Kennedy Keita Kinose Toshinori Kinoshita Yuji Kohara Eri Koide Kenji Komatsu Sarah Kopischke Minoru Kubo Junko Kyozuka Ulf Lagercrantz Shih-Shun Lin Erika Lindquist Anna M Lipzen Chia-Wei Lu Efraín De Luna Robert A Martienssen Naoki Minamino Masaharu Mizutani Miya Mizutani Nobuyoshi Mochizuki Isabel Monte Rebecca Mosher Hideki Nagasaki Hirofumi Nakagami Satoshi Naramoto Kazuhiko Nishitani Misato Ohtani Takashi Okamoto Masaki Okumura Jeremy Phillips Bernardo Pollak Anke Reinders Moritz Rövekamp Ryosuke Sano Shinichiro Sawa Marc W Schmid Makoto Shirakawa Roberto Solano Alexander Spunde Noriyuki Suetsugu Sumio Sugano Akifumi Sugiyama Rui Sun Yutaka Suzuki Mizuki Takenaka Daisuke Takezawa Hirokazu Tomogane Masayuki Tsuzuki Takashi Ueda Masaaki Umeda John M Ward Yuichiro Watanabe Kazufumi Yazaki Ryusuke Yokoyama Yoshihiro Yoshitake Izumi Yotsui Sabine Zachgo Jeremy Schmutz

Cell 2017 Oct;171(2):287-304.e15

Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.

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http://dx.doi.org/10.1016/j.cell.2017.09.030DOI Listing
October 2017

Sparse panicle1 is required for inflorescence development in Setaria viridis and maize.

Nat Plants 2017 04 18;3:17054. Epub 2017 Apr 18.

Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, Missouri 63132, USA.

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http://dx.doi.org/10.1038/nplants.2017.54DOI Listing
April 2017

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

New Phytol 2017 Apr 20;214(2):808-819. Epub 2017 Jan 20.

Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.

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http://dx.doi.org/10.1111/nph.14421DOI Listing
April 2017

Empty Niches after Extinctions Increase Population Sizes of Modern Corals.

Curr Biol 2016 12 17;26(23):3190-3194. Epub 2016 Nov 17.

Department of Biology, The Pennsylvania State University, 208 Mueller Lab, State College, PA 16802, USA; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10(th) and Constitution Avenue, NW Washington, DC 20560-0163, USA; Smithsonian Tropical Research Institute, Smithsonian Institution, 9100 Panama City PL, Washington, DC 20521, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2016.09.039DOI Listing
December 2016

Genome evolution in the allotetraploid frog Xenopus laevis.

Nature 2016 10;538(7625):336-343

University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.

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http://dx.doi.org/10.1038/nature19840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313049PMC
October 2016

Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis.

Dev Biol 2017 06 5;426(2):236-244. Epub 2016 Oct 5.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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http://dx.doi.org/10.1016/j.ydbio.2016.04.014DOI Listing
June 2017

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.

Curr Biol 2016 06 26;26(12):1577-1584. Epub 2016 May 26.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089372PMC
http://dx.doi.org/10.1016/j.cub.2016.04.038DOI Listing
June 2016

Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation.

Mol Plant 2016 07 24;9(7):1078-81. Epub 2016 Mar 24.

Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA; Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2016.03.009DOI Listing
July 2016

Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins.

Cell 2016 Jan 7;164(1-2):45-56. Epub 2016 Jan 7.

Howard Hughes Medical Institute; Stanford University School of Medicine, Department of Developmental Biology, 279 Campus Drive, Beckman Center B300, Stanford, CA 94305, USA. Electronic address:

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http://www.cell.com/cell/pdf/S0092-8674(15)01631-1.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S009286741501631
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http://dx.doi.org/10.1016/j.cell.2015.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759241PMC
January 2016