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M. Y. Kim et al., “DNA demethylation by ROa in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.

K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019.

J. M. Frost et al., “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” Proceedings of the National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences, pp. 20–29, 2018.

D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.

D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.

J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.

K. Park et al., “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” Proceedings of the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.

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J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.

M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.

J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.

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X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.

C. A. Ibarra et al., “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.

D. Coleman-Derr and D. Zilberman, “DNA methylation, A.Z, and the regulation of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.

S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EM and PR cooperate to repress key regulators of Arabidopsis development,” PLoS Genetics, vol. 8, no. 3. Public Library of Science, 2012.

D. Coleman-Derr and D. Zilberman, “Deposition of histone variant A.Z within gene bodies regulates responsive genes,” PLoS Genetics, vol. 8, no. 10. Public Library of Science, 2012.

J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” Current Opinion in Genetics and Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.

T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis endosperm,” Proceedings of the National Academy of Sciences, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011.

D. Zilberman, Balancing parental contributions in plant embryonic gene activation, vol. 20, no. 6. Elsevier, 2011, pp. 735–736.

A. Zemach et al., “Local DNA hypomethylation activates genes in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.

A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp. 0–5, 2010.

A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” Science, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010.

T.-F. Hsieh et al., “Genome-wide demethylation of Arabidopsis endosperm,” Science, vol. 324, no. 5933. American Association for the Advancement of Science, pp. 1451–1454, 2009.

D. Zilberman, “The evolving functions of DNA methylation,” Current Opinion in Plant Biology, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.

D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone A.Z and DNA methylation are mutually antagonistic chromatin marks,” Nature, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.

J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer, “DNA demethylation in the Arabidopsis genome,” Proceedings of the National Academy of Sciences, vol. 104, no. 16. National Academy of Sciences, pp. 6752–6757, 2007.

D. Zilberman, The human promoter methylome, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.

D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,” Development, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965, 2007.

D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription,” Nature Genetics, vol. 39, no. 1. Nature Publishing Group, pp. 61–69, 2006.

R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes,” Current Biology, vol. 15, no. 2. Elsevier, pp. 154–159, 2005.

R. K. Tran et al., “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis,” Genome Biology, vol. 6, no. 11. Springer Nature, 2005.

D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective silence,” Current Opinion in Genetics and Development, vol. 15, no. 5. Elsevier, pp. 557–562, 2005.

D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUT in RNA-directed DNA methylation triggered by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004.

Z. Xie et al., “Genetic and functional diversification of small RNA pathways in plants,” PLoS Biology, vol. 2, no. 5. Public Library of Science, pp. 0642–0652, 2004.

D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes: kick them when they’re down,” Genome Biology, vol. 5, no. 12. Springer Nature, 2004.

S. W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J. C. Carrington, and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” Science, vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336, 2004.

X. Cao et al., “Role of the DRM and CM methyltransferases in RNA-directed DNA methylation,” Current Biology, vol. 13, no. 24. Elsevier, pp. 2212–2217, 2003.

D. Zilberman,  Xiaofeng Cao, and S. E. Jacobsen, “ARGONAUT control of locus-specific siRNA accumulation and DNA and histone methylation,” Science, vol. 299, no. 5607. American Association for the Advancement of Science, pp. 716–719, 2003.

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