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Items: 31


Excess Light Priming in Arabidopsis thaliana Genotypes with Altered DNA Methylomes.

Ganguly DR, Stone BAB, Bowerman AF, Eichten SR, Pogson BJ.

G3 (Bethesda). 2019 Nov 5;9(11):3611-3621. doi: 10.1534/g3.119.400659.


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.


RNA Polymerase II Read-Through Promotes Expression of Neighboring Genes in SAL1-PAP-XRN Retrograde Signaling.

Crisp PA, Smith AB, Ganguly DR, Murray KD, Eichten SR, Millar AA, Pogson BJ.

Plant Physiol. 2018 Dec;178(4):1614-1630. doi: 10.1104/pp.18.00758. Epub 2018 Oct 9.


Correction to: Genome-wide discovery and characterization of maize long non-coding RNAs.

Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MMS, Scanlon MJ, Yu J, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ.

Genome Biol. 2018 Aug 23;19(1):122. doi: 10.1186/s13059-018-1508-z.


Maintenance of pre-existing DNA methylation states through recurring excess-light stress.

Ganguly DR, Crisp PA, Eichten SR, Pogson BJ.

Plant Cell Environ. 2018 Jul;41(7):1657-1672. doi: 10.1111/pce.13324. Epub 2018 May 16.


The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress.

Ganguly DR, Crisp PA, Eichten SR, Pogson BJ.

Plant Physiol. 2017 Dec;175(4):1893-1912. doi: 10.1104/pp.17.00744. Epub 2017 Oct 6.


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.


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.


Twenty-four-nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids.

Greaves IK, Eichten SR, Groszmann M, Wang A, Ying H, Peacock WJ, Dennis ES.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):E6895-E6902. Epub 2016 Oct 17.


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.


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.


Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress.

Eichten SR, Springer NM.

Front Plant Sci. 2015 May 6;6:308. doi: 10.3389/fpls.2015.00308. eCollection 2015.


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

Li Q, Song J, West PT, Zynda G, Eichten SR, Vaughn MW, Springer NM.

Plant Physiol. 2015 Aug;168(4):1262-74. doi: 10.1104/pp.15.00052. Epub 2015 Apr 13.


Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.

Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM.

Nucleic Acids Res. 2015 Jul 13;43(12):e81. doi: 10.1093/nar/gkv244. Epub 2015 Mar 26.


Genetic perturbation of the maize methylome.

Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess DL, Richmond TA, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Kaeppler SM, Jeddeloh JA, Springer NM.

Plant Cell. 2014 Dec;26(12):4602-16. doi: 10.1105/tpc.114.133140. Epub 2014 Dec 19.


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

West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer NM.

PLoS One. 2014 Aug 14;9(8):e105267. doi: 10.1371/journal.pone.0105267. eCollection 2014.


Insights into the effects of long-term artificial selection on seed size in maize.

Hirsch CN, Flint-Garcia SA, Beissinger TM, Eichten SR, Deshpande S, Barry K, McMullen MD, Holland JB, Buckler ES, Springer N, Buell CR, de Leon N, Kaeppler SM.

Genetics. 2014 Sep;198(1):409-21. doi: 10.1534/genetics.114.167155. Epub 2014 Jul 17.


Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize.

Stelpflug SC, Eichten SR, Hermanson PJ, Springer NM, Kaeppler SM.

Genetics. 2014 Sep;198(1):209-18. doi: 10.1534/genetics.114.165480. Epub 2014 Jul 14.


Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation.

Eichten SR, Schmitz RJ, Springer NM.

Plant Physiol. 2014 Jul;165(3):933-947. Epub 2014 May 28. Review.


Genome-wide discovery and characterization of maize long non-coding RNAs.

Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MM, Scanlon MJ, Yu J, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ.

Genome Biol. 2014 Feb 27;15(2):R40. doi: 10.1186/gb-2014-15-2-r40. Erratum in: Genome Biol. 2018 Aug 23;19(1):122.


Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines.

Li Q, Eichten SR, Hermanson PJ, Springer NM.

Genetics. 2014 Mar;196(3):667-76. doi: 10.1534/genetics.113.158980. Epub 2013 Dec 20.


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

Waters AJ, Bilinski P, Eichten SR, Vaughn MW, Ross-Ibarra J, Gehring M, Springer NM.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19639-44. doi: 10.1073/pnas.1309182110. Epub 2013 Nov 11.


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

Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM.

Plant Cell. 2013 Aug;25(8):2783-97. doi: 10.1105/tpc.113.114793. Epub 2013 Aug 6.


Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome.

Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KF, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N.

Genome Biol. 2013 Jun 12;14(6):R58. doi: 10.1186/gb-2013-14-6-r58.


Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27.

Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM.

Plant Cell. 2013 Mar;25(3):780-93. doi: 10.1105/tpc.112.106427. Epub 2013 Mar 5.


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

Eichten SR, Ellis NA, Makarevitch I, Yeh CT, Gent JI, Guo L, McGinnis KM, Zhang X, Schnable PS, Vaughn MW, Dawe RK, Springer NM.

PLoS Genet. 2012;8(12):e1003127. doi: 10.1371/journal.pgen.1003127. Epub 2012 Dec 13.


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

Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM.

Plant Cell. 2011 Dec;23(12):4221-33. doi: 10.1105/tpc.111.092668. Epub 2011 Dec 23.


Heritable epigenetic variation among maize inbreds.

Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM.

PLoS Genet. 2011 Nov;7(11):e1002372. doi: 10.1371/journal.pgen.1002372. Epub 2011 Nov 17.


B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize.

Eichten SR, Foerster JM, de Leon N, Kai Y, Yeh CT, Liu S, Jeddeloh JA, Schnable PS, Kaeppler SM, Springer NM.

Plant Physiol. 2011 Aug;156(4):1679-90. doi: 10.1104/pp.111.174748. Epub 2011 Jun 24.


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

Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM.

Genome Res. 2010 Dec;20(12):1689-99. doi: 10.1101/gr.109165.110. Epub 2010 Oct 29.

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