Publications by authors named "Justin O Borevitz"

73Publications

Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra.

Mol Ecol 2020 Sep 3. Epub 2020 Sep 3.

Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia.

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http://dx.doi.org/10.1111/mec.15614DOI Listing
September 2020

Genomic evidence of introgression and adaptation in a model subtropical tree species, Eucalyptus grandis.

Mol Ecol 2020 Sep 2. Epub 2020 Sep 2.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.

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http://dx.doi.org/10.1111/mec.15615DOI Listing
September 2020

Extending the Genotype in by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits.

G3 (Bethesda) 2020 May 4;10(5):1629-1637. Epub 2020 May 4.

Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Acton, Australian Capital Territory 2601, Australia

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http://dx.doi.org/10.1534/g3.120.401189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7202021PMC
May 2020

Landscape drivers of genomic diversity and divergence in woodland Eucalyptus.

Mol Ecol 2019 12 17;28(24):5232-5247. Epub 2019 Nov 17.

Australian National University, Canberra, ACT, Australia.

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http://dx.doi.org/10.1111/mec.15287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7065176PMC
December 2019

A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in .

Plant Direct 2019 May 23;3(5):e00138. Epub 2019 May 23.

ARC Centre of Excellence for Plant Energy Biology Australian National University Canberra Australian Capital Territory Australia.

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http://dx.doi.org/10.1002/pld3.138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6603398PMC
May 2019

HOME: a histogram based machine learning approach for effective identification of differentially methylated regions.

BMC Bioinformatics 2019 May 16;20(1):253. Epub 2019 May 16.

ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.

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http://dx.doi.org/10.1186/s12859-019-2845-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521357PMC
May 2019

Deep phenotyping: deep learning for temporal phenotype/genotype classification.

Plant Methods 2018 4;14:66. Epub 2018 Aug 4.

1Research School of Biology, Australian National University, Canberra, Australia.

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http://dx.doi.org/10.1186/s13007-018-0333-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076396PMC
August 2018

Axe: rapid, competitive sequence read demultiplexing using a trie.

Bioinformatics 2018 11;34(22):3924-3925

ARC Centre of Excellence in Plant Energy Biology, Department of Plant Science, Research School of Biology, ANU, Canberra, Australia.

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http://dx.doi.org/10.1093/bioinformatics/bty432DOI Listing
November 2018

Adaptation genomics: The angel is in the details.

Plant Cell Environ 2018 10 8;41(10):2244-2246. Epub 2018 Jun 8.

ARC Centre of Excellence for Plant Energy Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia.

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http://dx.doi.org/10.1111/pce.13344DOI Listing
October 2018

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis.

Plant Cell 2017 Aug 13;29(8):1836-1863. Epub 2017 Jul 13.

Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia

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http://dx.doi.org/10.1105/tpc.16.00828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590493PMC
August 2017

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation.

Elife 2016 12 2;5. Epub 2016 Dec 2.

ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.

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http://dx.doi.org/10.7554/eLife.20777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167521PMC
December 2016

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity.

Genome Res 2016 11 9;26(11):1520-1531. Epub 2016 Sep 9.

ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia, 2601.

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http://dx.doi.org/10.1101/gr.205468.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5088594PMC
November 2016

Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems.

Glob Change Biol Bioenergy 2016 Sep 10;8(5):1000-1014. Epub 2016 Jan 10.

Biosciences Division Argonne National Laboratory Argonne IL 60439 USA.

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http://dx.doi.org/10.1111/gcbb.12309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5019262PMC
September 2016

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics.

Sci Adv 2016 Feb 19;2(2):e1501340. Epub 2016 Feb 19.

Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia.

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http://dx.doi.org/10.1126/sciadv.1501340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4788475PMC
February 2016

Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium.

Mol Ecol 2016 May 11;25(9):2000-14. Epub 2016 May 11.

Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia.

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http://dx.doi.org/10.1111/mec.13584DOI Listing
May 2016

Genomic variation across landscapes: insights and applications.

New Phytol 2015 Sep 22;207(4):953-67. Epub 2015 Apr 22.

Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, ACT, 0200, Australia.

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http://dx.doi.org/10.1111/nph.13410DOI Listing
September 2015

A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation.

Front Plant Sci 2014 21;5:533. Epub 2014 Oct 21.

Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University Canberra, ACT, Australia.

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http://dx.doi.org/10.3389/fpls.2014.00533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4204441PMC
November 2014

Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass.

Mol Ecol 2014 Aug 21;23(16):4059-73. Epub 2014 Jul 21.

U.S. Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA; Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1111/mec.12845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142443PMC
August 2014

TraitCapture: genomic and environment modelling of plant phenomic data.

Curr Opin Plant Biol 2014 Apr 16;18:73-9. Epub 2014 Mar 16.

Division of Plant Sciences, Research School of Biology, Australian National University, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.pbi.2014.02.002DOI Listing
April 2014

Genetic variation for life history sensitivity to seasonal warming in Arabidopsis thaliana.

Genetics 2014 Feb 26;196(2):569-77. Epub 2013 Nov 26.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637.

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http://dx.doi.org/10.1534/genetics.113.157628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914627PMC
February 2014

C(m)CGG methylation-independent parent-of-origin effects on genome-wide transcript levels in isogenic reciprocal F1 triploid plants.

DNA Res 2014 7;21(2):141-51. Epub 2013 Nov 7.

1Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Aras de Brun, National University of Ireland,  Galway (NUI Galway), Ireland.

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http://dx.doi.org/10.1093/dnares/dst046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989486PMC
April 2015

Widespread interspecific divergence in cis-regulation of transposable elements in the Arabidopsis genus.

Mol Biol Evol 2012 Mar 15;29(3):1081-91. Epub 2011 Nov 15.

Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

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http://dx.doi.org/10.1093/molbev/msr281DOI Listing
March 2012

Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape.

Mol Ecol 2011 Dec 8;20(23):4938-52. Epub 2011 Nov 8.

Department of Ecology and Evolution, University of Chicago, 1101 East 57th St., Chicago, IL 60637, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2011.05335.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383086PMC
December 2011

Genome-wide association studies in plants: the missing heritability is in the field.

Genome Biol 2011 Oct 28;12(10):232. Epub 2011 Oct 28.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1186/gb-2011-12-10-232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333769PMC
October 2011

Source verification of mis-identified Arabidopsis thaliana accessions.

Plant J 2011 Aug 16;67(3):554-66. Epub 2011 Jun 16.

Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

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http://doi.wiley.com/10.1111/j.1365-313X.2011.04606.x
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http://dx.doi.org/10.1111/j.1365-313X.2011.04606.xDOI Listing
August 2011

Genetic architecture of regulatory variation in Arabidopsis thaliana.

Genome Res 2011 May 5;21(5):725-33. Epub 2011 Apr 5.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.115337.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083089PMC
May 2011

A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1.

PLoS Genet 2010 Nov 11;6(11):e1001193. Epub 2010 Nov 11.

United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Donald Danforth Plant Sciences Center, St. Louis, Missouri, United States of America.

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http://aura.abdn.ac.uk/bitstream/2164/3483/1/A_coastal_cline
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http://dx.plos.org/10.1371/journal.pgen.1001193
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http://dx.doi.org/10.1371/journal.pgen.1001193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978683PMC
November 2010

Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana.

Proc Natl Acad Sci U S A 2010 Dec 15;107(49):21199-204. Epub 2010 Nov 15.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1073/pnas.1007431107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000268PMC
December 2010

Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis.

PLoS One 2010 Mar 23;5(3):e9735. Epub 2010 Mar 23.

Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009735PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2843724PMC
March 2010

Global analysis of allele-specific expression in Arabidopsis thaliana.

Genetics 2009 Aug 27;182(4):943-54. Epub 2009 May 27.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1534/genetics.109.103499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728882PMC
August 2009

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.

Genome Biol 2009 Feb 11;10(2):R17. Epub 2009 Feb 11.

Section of Cell and Developmental Biology, University of California San Diego, Gilman Drive, La Jolla, CA 92093-0130, USA.

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http://dx.doi.org/10.1186/gb-2009-10-2-r17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688271PMC
February 2009

Whole genome transcriptome polymorphisms in Arabidopsis thaliana.

Genome Biol 2008 24;9(11):R165. Epub 2008 Nov 24.

Department of Ecology and Evolution, University of Chicago, 1101 E, 57th Street, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1186/gb-2008-9-11-r165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614497PMC
February 2009

Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster.

Science 2008 Jun 5;320(5883):1629-31. Epub 2008 Jun 5.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1158078
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http://dx.doi.org/10.1126/science.1158078DOI Listing
June 2008

Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays.

PLoS Genet 2008 Mar 21;4(3):e1000032. Epub 2008 Mar 21.

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265482PMC
March 2008

Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light.

Proc Natl Acad Sci U S A 2008 Feb 14;105(8):3157-62. Epub 2008 Feb 14.

Section of Plant Biology, College of Biological Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0712174105
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http://dx.doi.org/10.1073/pnas.0712174105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268601PMC
February 2008

Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins.

PLoS Genet 2007 Oct 24;3(10):1848-61. Epub 2007 Aug 24.

Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1371/journal.pgen.0030171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2014789PMC
October 2007

Redundancy in genotyping arrays.

PLoS One 2007 Mar 14;2(3):e287. Epub 2007 Mar 14.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0000287PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805688PMC
March 2007

Genetic and epigenetic dissection of cis regulatory variation.

Curr Opin Plant Biol 2007 Apr 14;10(2):142-8. Epub 2007 Feb 14.

Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1016/j.pbi.2007.02.002DOI Listing
April 2007

Mapping a plant's chemical vocabulary.

Nat Genet 2006 Jul;38(7):737-8

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http://dx.doi.org/10.1038/ng0706-737DOI Listing
July 2006

Inferring population parameters from single-feature polymorphism data.

Genetics 2006 Aug 15;173(4):2257-67. Epub 2006 May 15.

Molecular and Computational Biology Program, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles 90089, USA.

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http://dx.doi.org/10.1534/genetics.105.047472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569697PMC
August 2006

Association mapping with single-feature polymorphisms.

Genetics 2006 Jun 1;173(2):1125-33. Epub 2006 Mar 1.

Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1534/genetics.105.052720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526505PMC
June 2006

LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms.

Proc Natl Acad Sci U S A 2005 Jul 8;102(29):10387-92. Epub 2005 Jul 8.

Department of Cell Biology and Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.0503029102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1177380PMC
July 2005

FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions.

Genetics 2005 Jul 23;170(3):1197-207. Epub 2005 May 23.

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1534/genetics.104.036533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1451178PMC
July 2005

Rapid array mapping of circadian clock and developmental mutations in Arabidopsis.

Plant Physiol 2005 Jun 20;138(2):990-7. Epub 2005 May 20.

Department of Cell Biology and Institute for Childhood and Neglected Diseases, Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1104/pp.105.061408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150413PMC
June 2005

Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation.

Proc Natl Acad Sci U S A 2005 Feb 4;102(7):2460-5. Epub 2005 Feb 4.

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.0409474102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548991PMC
February 2005

Plant genomics: the third wave.

Annu Rev Genomics Hum Genet 2004 ;5:443-77

Genomic Analysis Laboratory, Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1146/annurev.genom.5.061903.180017DOI Listing
November 2004

Genomics tools for QTL analysis and gene discovery.

Curr Opin Plant Biol 2004 Apr;7(2):132-6

Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S136952660400014
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http://dx.doi.org/10.1016/j.pbi.2004.01.011DOI Listing
April 2004

The impact of genomics on the study of natural variation in Arabidopsis.

Plant Physiol 2003 Jun;132(2):718-25

Plant Biology, Salk Institute, 10010 North Torrey Pines Rd, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1104/pp.103.023549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC523862PMC
June 2003

Large-scale identification of single-feature polymorphisms in complex genomes.

Genome Res 2003 Mar;13(3):513-23

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1101/gr.541303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430246PMC
March 2003

The extent of linkage disequilibrium in Arabidopsis thaliana.

Nat Genet 2002 Feb 7;30(2):190-3. Epub 2002 Jan 7.

Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.

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http://dx.doi.org/10.1038/ng813DOI Listing
February 2002