Daniel Zilberman

Zilberman Group

48 Publications

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[48]
2023 | Published | Journal Article | IST-REx-ID: 12672 | OA
Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.
[Published Version] View | Files available | DOI | WoS
 
[47]
2023 | Journal Article | IST-REx-ID: 13965 | OA
Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[46]
2023 | Published | Journal Article | IST-REx-ID: 14551 | OA
Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[45]
2021 | Published | Journal Article | IST-REx-ID: 9877 | OA
Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[44]
2021 | Published | Journal Article | IST-REx-ID: 10533 | OA
Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[43]
2020 | Published | Journal Article | IST-REx-ID: 9526 | OA
Choi, Jaemyung, David B. Lyons, M. Yvonne Kim, Jonathan D. Moore, and Daniel Zilberman. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.” Molecular Cell. Elsevier, 2020. https://doi.org/10.1016/j.molcel.2019.10.011.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[42]
2019 | Published | Journal Article | IST-REx-ID: 9460 | OA
Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[41]
2019 | Published | Journal Article | IST-REx-ID: 9530 | OA
Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf 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. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[40]
2018 | Published | Journal Article | IST-REx-ID: 9471 | OA
Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[39]
2017 | Published | Journal Article | IST-REx-ID: 9445 | OA
Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[38]
2017 | Published | Journal Article | IST-REx-ID: 9506 | OA
Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[37]
2016 | Published | Journal Article | IST-REx-ID: 9456 | OA
Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature , 2016. https://doi.org/10.1038/nature20110.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[36]
2016 | Published | Journal Article | IST-REx-ID: 9473 | OA
Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619074114.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[35]
2016 | Published | Journal Article | IST-REx-ID: 9477 | OA
Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[34]
2015 | Published | Journal Article | IST-REx-ID: 9532 | OA
Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[33]
2014 | Published | Journal Article | IST-REx-ID: 9458 | OA
Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.01.029.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[32]
2014 | Published | Journal Article | IST-REx-ID: 9479 | OA
Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[31]
2014 | Published | Journal Article | IST-REx-ID: 9519
Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
View | DOI | PubMed | Europe PMC
 
[30]
2013 | Published | Journal Article | IST-REx-ID: 9459 | OA
Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[29]
2013 | Published | Journal Article | IST-REx-ID: 9481 | OA
Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[28]
2013 | Published | Journal Article | IST-REx-ID: 9520 | OA
Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier, 2013. https://doi.org/10.1016/j.devcel.2013.01.014.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[27]
2012 | Published | Journal Article | IST-REx-ID: 9451 | OA
Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[26]
2012 | Published | Journal Article | IST-REx-ID: 9497 | OA
Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[25]
2012 | Published | Journal Article | IST-REx-ID: 9499 | OA
Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[24]
2012 | Published | Journal Article | IST-REx-ID: 9528
Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.
View | DOI | PubMed | Europe PMC
 
[23]
2012 | Published | Journal Article | IST-REx-ID: 9535 | OA
Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[22]
2011 | Published | Journal Article | IST-REx-ID: 9483 | OA
Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[21]
2011 | Published | Other Publication | IST-REx-ID: 9522 | OA
Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011. https://doi.org/10.1016/j.devcel.2011.05.018.
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[20]
2010 | Published | Journal Article | IST-REx-ID: 9452
Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” Science. American Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1186366.
View | DOI | PubMed | Europe PMC
 
[19]
2010 | Published | Journal Article | IST-REx-ID: 9485 | OA
Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[18]
2010 | Published | Journal Article | IST-REx-ID: 9489 | OA
Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[17]
2009 | Published | Journal Article | IST-REx-ID: 9453 | OA
Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis Endosperm.” Science. American Association for the Advancement of Science, 2009. https://doi.org/10.1126/science.1172417.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[16]
2008 | Published | Journal Article | IST-REx-ID: 9457 | OA
Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” Nature. Springer Nature, 2008. https://doi.org/10.1038/nature07324.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[15]
2008 | Published | Journal Article | IST-REx-ID: 9537
Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current Opinion in Plant Biology. Elsevier , 2008. https://doi.org/10.1016/j.pbi.2008.07.004.
View | DOI | PubMed | Europe PMC
 
[14]
2007 | Published | Journal Article | IST-REx-ID: 9487 | OA
Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0701861104.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[13]
2007 | Published | Other Publication | IST-REx-ID: 9504
Zilberman, Daniel. The Human Promoter Methylome. Nature Genetics. Vol. 39. Nature Publishing Group, 2007. https://doi.org/10.1038/ng0407-442.
View | DOI | PubMed | Europe PMC
 
[12]
2007 | Published | Journal Article | IST-REx-ID: 9524 | OA
Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” Development. The Company of Biologists, 2007. https://doi.org/10.1242/dev.001131.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[11]
2006 | Published | Journal Article | IST-REx-ID: 9505
Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” Nature Genetics. Nature Publishing Group, 2006. https://doi.org/10.1038/ng1929.
View | DOI | PubMed | Europe PMC
 
[10]
2005 | Published | Journal Article | IST-REx-ID: 9491 | OA
Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.01.008.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[9]
2005 | Published | Journal Article | IST-REx-ID: 9514 | OA
Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology. Springer Nature, 2005. https://doi.org/10.1186/gb-2005-6-11-r90.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[8]
2005 | Published | Journal Article | IST-REx-ID: 9529
Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” Current Opinion in Genetics and Development. Elsevier, 2005. https://doi.org/10.1016/j.gde.2005.07.002.
View | DOI | PubMed | Europe PMC
 
[7]
2004 | Published | Journal Article | IST-REx-ID: 9454
Chan, Simon W.-L., Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.” Science. American Association for the Advancement of Science, 2004. https://doi.org/10.1126/science.1095989.
View | DOI | PubMed | Europe PMC
 
[6]
2004 | Published | Journal Article | IST-REx-ID: 9493 | OA
Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier, 2004. https://doi.org/10.1016/j.cub.2004.06.055.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[5]
2004 | Published | Journal Article | IST-REx-ID: 9511 | OA
Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” Genome Biology. Springer Nature, 2004. https://doi.org/10.1186/gb-2004-5-12-249.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[4]
2004 | Published | Journal Article | IST-REx-ID: 9517 | OA
Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS Biology. Public Library of Science, 2004. https://doi.org/10.1371/journal.pbio.0020104.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[3]
2003 | Published | Journal Article | IST-REx-ID: 9455
Zilberman, Daniel, Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” Science. American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1079695.
View | DOI | PubMed | Europe PMC
 
[2]
2003 | Published | Journal Article | IST-REx-ID: 9495 | OA
Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation.” Current Biology. Elsevier, 2003. https://doi.org/10.1016/j.cub.2003.11.052.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[1]
2001 | Published | Journal Article | IST-REx-ID: 9444
Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation.” Science. American Association for the Advancement of Science, 2001. https://doi.org/10.1126/science.1059745.
View | DOI | PubMed | Europe PMC
 
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48 Publications

Mark all

[48]
2023 | Published | Journal Article | IST-REx-ID: 12672 | OA
Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.
[Published Version] View | Files available | DOI | WoS
 
[47]
2023 | Journal Article | IST-REx-ID: 13965 | OA
Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[46]
2023 | Published | Journal Article | IST-REx-ID: 14551 | OA
Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[45]
2021 | Published | Journal Article | IST-REx-ID: 9877 | OA
Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[44]
2021 | Published | Journal Article | IST-REx-ID: 10533 | OA
Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676.
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[43]
2020 | Published | Journal Article | IST-REx-ID: 9526 | OA
Choi, Jaemyung, David B. Lyons, M. Yvonne Kim, Jonathan D. Moore, and Daniel Zilberman. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.” Molecular Cell. Elsevier, 2020. https://doi.org/10.1016/j.molcel.2019.10.011.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[42]
2019 | Published | Journal Article | IST-REx-ID: 9460 | OA
Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[41]
2019 | Published | Journal Article | IST-REx-ID: 9530 | OA
Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf 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. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[40]
2018 | Published | Journal Article | IST-REx-ID: 9471 | OA
Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[39]
2017 | Published | Journal Article | IST-REx-ID: 9445 | OA
Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[38]
2017 | Published | Journal Article | IST-REx-ID: 9506 | OA
Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[37]
2016 | Published | Journal Article | IST-REx-ID: 9456 | OA
Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature , 2016. https://doi.org/10.1038/nature20110.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[36]
2016 | Published | Journal Article | IST-REx-ID: 9473 | OA
Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619074114.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[35]
2016 | Published | Journal Article | IST-REx-ID: 9477 | OA
Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[34]
2015 | Published | Journal Article | IST-REx-ID: 9532 | OA
Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[33]
2014 | Published | Journal Article | IST-REx-ID: 9458 | OA
Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.01.029.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[32]
2014 | Published | Journal Article | IST-REx-ID: 9479 | OA
Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[31]
2014 | Published | Journal Article | IST-REx-ID: 9519
Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
View | DOI | PubMed | Europe PMC
 
[30]
2013 | Published | Journal Article | IST-REx-ID: 9459 | OA
Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[29]
2013 | Published | Journal Article | IST-REx-ID: 9481 | OA
Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[28]
2013 | Published | Journal Article | IST-REx-ID: 9520 | OA
Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier, 2013. https://doi.org/10.1016/j.devcel.2013.01.014.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[27]
2012 | Published | Journal Article | IST-REx-ID: 9451 | OA
Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[26]
2012 | Published | Journal Article | IST-REx-ID: 9497 | OA
Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002988.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[25]
2012 | Published | Journal Article | IST-REx-ID: 9499 | OA
Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[24]
2012 | Published | Journal Article | IST-REx-ID: 9528
Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.
View | DOI | PubMed | Europe PMC
 
[23]
2012 | Published | Journal Article | IST-REx-ID: 9535 | OA
Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[22]
2011 | Published | Journal Article | IST-REx-ID: 9483 | OA
Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[21]
2011 | Published | Other Publication | IST-REx-ID: 9522 | OA
Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011. https://doi.org/10.1016/j.devcel.2011.05.018.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[20]
2010 | Published | Journal Article | IST-REx-ID: 9452
Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” Science. American Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1186366.
View | DOI | PubMed | Europe PMC
 
[19]
2010 | Published | Journal Article | IST-REx-ID: 9485 | OA
Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[18]
2010 | Published | Journal Article | IST-REx-ID: 9489 | OA
Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[17]
2009 | Published | Journal Article | IST-REx-ID: 9453 | OA
Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis Endosperm.” Science. American Association for the Advancement of Science, 2009. https://doi.org/10.1126/science.1172417.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[16]
2008 | Published | Journal Article | IST-REx-ID: 9457 | OA
Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” Nature. Springer Nature, 2008. https://doi.org/10.1038/nature07324.
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[15]
2008 | Published | Journal Article | IST-REx-ID: 9537
Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current Opinion in Plant Biology. Elsevier , 2008. https://doi.org/10.1016/j.pbi.2008.07.004.
View | DOI | PubMed | Europe PMC
 
[14]
2007 | Published | Journal Article | IST-REx-ID: 9487 | OA
Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0701861104.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[13]
2007 | Published | Other Publication | IST-REx-ID: 9504
Zilberman, Daniel. The Human Promoter Methylome. Nature Genetics. Vol. 39. Nature Publishing Group, 2007. https://doi.org/10.1038/ng0407-442.
View | DOI | PubMed | Europe PMC
 
[12]
2007 | Published | Journal Article | IST-REx-ID: 9524 | OA
Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” Development. The Company of Biologists, 2007. https://doi.org/10.1242/dev.001131.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[11]
2006 | Published | Journal Article | IST-REx-ID: 9505
Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” Nature Genetics. Nature Publishing Group, 2006. https://doi.org/10.1038/ng1929.
View | DOI | PubMed | Europe PMC
 
[10]
2005 | Published | Journal Article | IST-REx-ID: 9491 | OA
Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.01.008.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[9]
2005 | Published | Journal Article | IST-REx-ID: 9514 | OA
Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology. Springer Nature, 2005. https://doi.org/10.1186/gb-2005-6-11-r90.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[8]
2005 | Published | Journal Article | IST-REx-ID: 9529
Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” Current Opinion in Genetics and Development. Elsevier, 2005. https://doi.org/10.1016/j.gde.2005.07.002.
View | DOI | PubMed | Europe PMC
 
[7]
2004 | Published | Journal Article | IST-REx-ID: 9454
Chan, Simon W.-L., Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.” Science. American Association for the Advancement of Science, 2004. https://doi.org/10.1126/science.1095989.
View | DOI | PubMed | Europe PMC
 
[6]
2004 | Published | Journal Article | IST-REx-ID: 9493 | OA
Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier, 2004. https://doi.org/10.1016/j.cub.2004.06.055.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[5]
2004 | Published | Journal Article | IST-REx-ID: 9511 | OA
Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” Genome Biology. Springer Nature, 2004. https://doi.org/10.1186/gb-2004-5-12-249.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[4]
2004 | Published | Journal Article | IST-REx-ID: 9517 | OA
Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS Biology. Public Library of Science, 2004. https://doi.org/10.1371/journal.pbio.0020104.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[3]
2003 | Published | Journal Article | IST-REx-ID: 9455
Zilberman, Daniel, Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” Science. American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1079695.
View | DOI | PubMed | Europe PMC
 
[2]
2003 | Published | Journal Article | IST-REx-ID: 9495 | OA
Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation.” Current Biology. Elsevier, 2003. https://doi.org/10.1016/j.cub.2003.11.052.
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[1]
2001 | Published | Journal Article | IST-REx-ID: 9444
Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation.” Science. American Association for the Advancement of Science, 2001. https://doi.org/10.1126/science.1059745.
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