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

Eichten SR, Srivastava A, Reddiex AJ, Ganguly DR, Heussler A, Streich JC, Wilson PB, Borevitz JO.

G3 (Bethesda). 2020 Mar 4. pii: g3.401189.2020. doi: 10.1534/g3.120.401189. [Epub ahead of print]


Landscape drivers of genomic diversity and divergence in woodland Eucalyptus.

Murray KD, Janes JK, Jones A, Bothwell HM, Andrew RL, Borevitz JO.

Mol Ecol. 2019 Dec;28(24):5232-5247. doi: 10.1111/mec.15287. Epub 2019 Nov 17.


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

Rungrat T, Almonte AA, Cheng R, Gollan PJ, Stuart T, Aro EM, Borevitz JO, Pogson B, Wilson PB.

Plant Direct. 2019 May 23;3(5):e00138. doi: 10.1002/pld3.138. eCollection 2019 May.


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

Srivastava A, Karpievitch YV, Eichten SR, Borevitz JO, Lister R.

BMC Bioinformatics. 2019 May 16;20(1):253. doi: 10.1186/s12859-019-2845-y.


Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate.

Wilson PB, Streich JC, Murray KD, Eichten SR, Cheng R, Aitken NC, Spokas K, Warthmann N, Gordon SP; Accession Contributors, Vogel JP, Borevitz JO.

Genetics. 2019 Jan;211(1):317-331. doi: 10.1534/genetics.118.301589. Epub 2018 Nov 16.


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

Taghavi Namin S, Esmaeilzadeh M, Najafi M, Brown TB, Borevitz JO.

Plant Methods. 2018 Aug 4;14:66. doi: 10.1186/s13007-018-0333-4. eCollection 2018.


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

Murray KD, Borevitz JO.

Bioinformatics. 2018 Nov 15;34(22):3924-3925. doi: 10.1093/bioinformatics/bty432.


Adaptation genomics: The angel is in the details.

Almonte AA, Borevitz JO.

Plant Cell Environ. 2018 Oct;41(10):2244-2246. doi: 10.1111/pce.13344. Epub 2018 Jun 8.


Landscape genomic prediction for restoration of a Eucalyptus foundation species under climate change.

Supple MA, Bragg JG, Broadhurst LM, Nicotra AB, Byrne M, Andrew RL, Widdup A, Aitken NC, Borevitz JO.

Elife. 2018 Apr 24;7. pii: e31835. doi: 10.7554/eLife.31835.


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

Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ.

Plant Cell. 2017 Aug;29(8):1836-1863. doi: 10.1105/tpc.16.00828. Epub 2017 Jul 13.


Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain.

Ahrens CW, Supple MA, Aitken NC, Cantrill DJ, Borevitz JO, James EA.

Ann Bot. 2017 Jun 1;119(8):1267-1277. doi: 10.1093/aob/mcx022.


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

Stuart T, Eichten SR, Cahn J, Karpievitch YV, Borevitz JO, Lister R.

Elife. 2016 Dec 2;5. pii: e20777. doi: 10.7554/eLife.20777.


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

Eichten SR, Stuart T, Srivastava A, Lister R, Borevitz JO.

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


Using Phenomic Analysis of Photosynthetic Function for Abiotic Stress Response Gene Discovery.

Rungrat T, Awlia M, Brown T, Cheng R, Sirault X, Fajkus J, Trtilek M, Furbank B, Badger M, Tester M, Pogson BJ, Borevitz JO, Wilson P.

Arabidopsis Book. 2016 Sep 9;14:e0185. eCollection 2016.


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

Morris GP, Hu Z, Grabowski PP, Borevitz JO, de Graaff MA, Miller RM, Jastrow JD.

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


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

Crisp PA, Ganguly D, Eichten SR, Borevitz JO, Pogson BJ.

Sci Adv. 2016 Feb 19;2(2):e1501340. doi: 10.1126/sciadv.1501340. eCollection 2016 Feb. Review.


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

Nicotra AB, Chong C, Bragg JG, Ong CR, Aitken NC, Chuah A, Lepschi B, Borevitz JO.

Mol Ecol. 2016 May;25(9):2000-14. doi: 10.1111/mec.13584. Epub 2016 May 11.


Genomic variation across landscapes: insights and applications.

Bragg JG, Supple MA, Andrew RL, Borevitz JO.

New Phytol. 2015 Sep;207(4):953-67. doi: 10.1111/nph.13410. Epub 2015 Apr 22. Review.


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

Cazzonelli CI, Nisar N, Roberts AC, Murray KD, Borevitz JO, Pogson BJ.

Front Plant Sci. 2014 Oct 21;5:533. doi: 10.3389/fpls.2014.00533. eCollection 2014.


Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.

Noutsos C, Borevitz JO, Hodges SA.

Mol Ecol. 2014 Nov;23(22):5589-98. doi: 10.1111/mec.12962. Epub 2014 Nov 10.


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

Grabowski PP, Morris GP, Casler MD, Borevitz JO.

Mol Ecol. 2014 Aug;23(16):4059-73. doi: 10.1111/mec.12845. Epub 2014 Jul 21.


TraitCapture: genomic and environment modelling of plant phenomic data.

Brown TB, Cheng R, Sirault XR, Rungrat T, Murray KD, Trtilek M, Furbank RT, Badger M, Pogson BJ, Borevitz JO.

Curr Opin Plant Biol. 2014 Apr;18:73-9. doi: 10.1016/j.pbi.2014.02.002. Epub 2014 Mar 16. Review.


New Arabidopsis advanced intercross recombinant inbred lines reveal female control of nonrandom mating.

Fitz Gerald JN, Carlson AL, Smith E, Maloof JN, Weigel D, Chory J, Borevitz JO, Swanson RJ.

Plant Physiol. 2014 May;165(1):175-85. doi: 10.1104/pp.113.233213. Epub 2014 Mar 12.


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

Li Y, Cheng R, Spokas KA, Palmer AA, Borevitz JO.

Genetics. 2014 Feb;196(2):569-77. doi: 10.1534/genetics.113.157628. Epub 2013 Nov 26.


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

Donoghue MT, Fort A, Clifton R, Zhang X, McKeown PC, Voigt-Zielinksi ML, Borevitz JO, Spillane C.

DNA Res. 2014;21(2):141-51. doi: 10.1093/dnares/dst046. Epub 2013 Nov 7.


Natural Genetic Variation for Growth and Development Revealed by High-Throughput Phenotyping in Arabidopsis thaliana.

Zhang X, Hause RJ Jr, Borevitz JO.

G3 (Bethesda). 2012 Jan;2(1):29-34. doi: 10.1534/g3.111.001487. Epub 2012 Jan 1.


Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel.

Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjálmsson BJ, Nordborg M, Borevitz JO, Bergelson J.

Nat Genet. 2012 Jan 8;44(2):212-6. doi: 10.1038/ng.1042.


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

He F, Zhang X, Hu JY, Turck F, Dong X, Goebel U, Borevitz JO, de Meaux J.

Mol Biol Evol. 2012 Mar;29(3):1081-91. doi: 10.1093/molbev/msr281. Epub 2011 Nov 15.


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

Morris GP, Grabowski PP, Borevitz JO.

Mol Ecol. 2011 Dec;20(23):4938-52. doi: 10.1111/j.1365-294X.2011.05335.x. Epub 2011 Nov 8.


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

Brachi B, Morris GP, Borevitz JO.

Genome Biol. 2011 Oct 28;12(10):232. doi: 10.1186/gb-2011-12-10-232. Review.


Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.

Huang YS, Horton M, Vilhjálmsson BJ, Seren U, Meng D, Meyer C, Ali Amer M, Borevitz JO, Bergelson J, Nordborg M.

Database (Oxford). 2011 May 23;2011:bar014. doi: 10.1093/database/bar014. Print 2011.


Source verification of mis-identified Arabidopsis thaliana accessions.

Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J.

Plant J. 2011 Aug;67(3):554-66. doi: 10.1111/j.1365-313X.2011.04606.x. Epub 2011 Jun 16.


Genetic architecture of regulatory variation in Arabidopsis thaliana.

Zhang X, Cal AJ, Borevitz JO.

Genome Res. 2011 May;21(5):725-33. doi: 10.1101/gr.115337.110. Epub 2011 Apr 5.


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

Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, Li Y, Bergelson J, Borevitz JO, Nordborg M, Vitek O, Salt DE.

PLoS Genet. 2010 Nov 11;6(11):e1001193. doi: 10.1371/journal.pgen.1001193.


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

Li Y, Huang Y, Bergelson J, Nordborg M, Borevitz JO.

Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):21199-204. doi: 10.1073/pnas.1007431107. Epub 2010 Nov 15.


A methyl transferase links the circadian clock to the regulation of alternative splicing.

Sanchez SE, Petrillo E, Beckwith EJ, Zhang X, Rugnone ML, Hernando CE, Cuevas JC, Godoy Herz MA, Depetris-Chauvin A, Simpson CG, Brown JW, Cerdán PD, Borevitz JO, Mas P, Ceriani MF, Kornblihtt AR, Yanovsky MJ.

Nature. 2010 Nov 4;468(7320):112-6. doi: 10.1038/nature09470. Epub 2010 Oct 20.


Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana.

Todesco M, Balasubramanian S, Hu TT, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, Laitinen RA, Huang Y, Chory J, Lipka V, Borevitz JO, Dangl JL, Bergelson J, Nordborg M, Weigel D.

Nature. 2010 Jun 3;465(7298):632-6. doi: 10.1038/nature09083.


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

Voelckel C, Borevitz JO, Kramer EM, Hodges SA.

PLoS One. 2010 Mar 23;5(3):e9735. doi: 10.1371/journal.pone.0009735.


Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M.

Nature. 2010 Jun 3;465(7298):627-31. doi: 10.1038/nature08800. Epub 2010 Mar 24.


The scale of population structure in Arabidopsis thaliana.

Platt A, Horton M, Huang YS, Li Y, Anastasio AE, Mulyati NW, Agren J, Bossdorf O, Byers D, Donohue K, Dunning M, Holub EB, Hudson A, Le Corre V, Loudet O, Roux F, Warthmann N, Weigel D, Rivero L, Scholl R, Nordborg M, Bergelson J, Borevitz JO.

PLoS Genet. 2010 Feb 12;6(2):e1000843. doi: 10.1371/journal.pgen.1000843.


Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arabidopsis thaliana.

Schwartz C, Balasubramanian S, Warthmann N, Michael TP, Lempe J, Sureshkumar S, Kobayashi Y, Maloof JN, Borevitz JO, Chory J, Weigel D.

Genetics. 2009 Oct;183(2):723-32, 1SI-7SI. doi: 10.1534/genetics.109.104984. Epub 2009 Aug 3.


Global analysis of allele-specific expression in Arabidopsis thaliana.

Zhang X, Borevitz JO.

Genetics. 2009 Aug;182(4):943-54. doi: 10.1534/genetics.109.103499. Epub 2009 May 27.


Root suberin forms an extracellular barrier that affects water relations and mineral nutrition in Arabidopsis.

Baxter I, Hosmani PS, Rus A, Lahner B, Borevitz JO, Muthukumar B, Mickelbart MV, Schreiber L, Franke RB, Salt DE.

PLoS Genet. 2009 May;5(5):e1000492. doi: 10.1371/journal.pgen.1000492. Epub 2009 May 22.


A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior.

Williams R 4th, Lim JE, Harr B, Wing C, Walters R, Distler MG, Teschke M, Wu C, Wiltshire T, Su AI, Sokoloff G, Tarantino LM, Borevitz JO, Palmer AA.

PLoS One. 2009;4(3):e4649. doi: 10.1371/journal.pone.0004649. Epub 2009 Mar 6.


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

Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA.

Genome Biol. 2009 Feb 11;10(2):R17. doi: 10.1186/gb-2009-10-2-r17.


QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines.

Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, Maloof JN, Loudet O, Trainer GT, Dabi T, Borevitz JO, Chory J, Weigel D.

PLoS One. 2009;4(2):e4318. doi: 10.1371/journal.pone.0004318. Epub 2009 Feb 2.


Whole genome transcriptome polymorphisms in Arabidopsis thaliana.

Zhang X, Byrnes JK, Gal TS, Li WH, Borevitz JO.

Genome Biol. 2008;9(11):R165. doi: 10.1186/gb-2008-9-11-r165. Epub 2008 Nov 24.


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

Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M.

Science. 2008 Jun 20;320(5883):1629-31. doi: 10.1126/science.1158078. Epub 2008 Jun 5.


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

Zhang X, Shiu SH, Cal A, Borevitz JO.

PLoS Genet. 2008 Mar 21;4(3):e1000032. doi: 10.1371/journal.pgen.1000032. Erratum in: PLoS Genet. 2008 Jun;4(6). doi: 10.1371/annotation/e21d3565-fec6-44d9-8fab-83da49c7c0b8. Shiu, Shinhan [corrected to Shiu, Shin-Han].


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

Filiault DL, Wessinger CA, Dinneny JR, Lutes J, Borevitz JO, Weigel D, Chory J, Maloof JN.

Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3157-62. doi: 10.1073/pnas.0712174105. Epub 2008 Feb 14. Erratum in: Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8482.

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