Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
Mo, Alisa, Mukamel, Eran A., Davis, Fred P., Luo, Chongyuan, Henry, Gilbert L., Picard, Serge, Urich, Mark A., Nery, Joseph R., Sejnowski, Terrence J., Lister, Ryan, Eddy, Sean R., Ecker, Joseph R., Nathans, Jeremy
Published in Neuron (Cambridge, Mass.) (17.06.2015)
Published in Neuron (Cambridge, Mass.) (17.06.2015)
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Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
O’Malley, Ronan C., Huang, Shao-shan Carol, Song, Liang, Lewsey, Mathew G., Bartlett, Anna, Nery, Joseph R., Galli, Mary, Gallavotti, Andrea, Ecker, Joseph R.
Published in Cell (19.05.2016)
Published in Cell (19.05.2016)
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Molecular Criteria for Defining the Naive Human Pluripotent State
Theunissen, Thorold W., Friedli, Marc, He, Yupeng, Planet, Evarist, O’Neil, Ryan C., Markoulaki, Styliani, Pontis, Julien, Wang, Haoyi, Iouranova, Alexandra, Imbeault, Michaël, Duc, Julien, Cohen, Malkiel A., Wert, Katherine J., Castanon, Rosa, Zhang, Zhuzhu, Huang, Yanmei, Nery, Joseph R., Drotar, Jesse, Lungjangwa, Tenzin, Trono, Didier, Ecker, Joseph R., Jaenisch, Rudolf
Published in Cell stem cell (06.10.2016)
Published in Cell stem cell (06.10.2016)
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Dynamic DNA methylation reconfiguration during seed development and germination
Kawakatsu, Taiji, Nery, Joseph R, Castanon, Rosa, Ecker, Joseph R
Published in Genome Biology (15.09.2017)
Published in Genome Biology (15.09.2017)
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Integration of omic networks in a developmental atlas of maize
Walley, Justin W., Sartor, Ryan C., Shen, Zhouxin, Schmitz, Robert J., Wu, Kevin J., Urich, Mark A., Nery, Joseph R., Smith, Laurie G., Schnable, James C., Ecker, Joseph R., Briggs, Steven P.
Published in Science (American Association for the Advancement of Science) (19.08.2016)
Published in Science (American Association for the Advancement of Science) (19.08.2016)
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Mapping genome-wide transcription-factor binding sites using DAP-seq
Bartlett, Anna, O'Malley, Ronan C, Huang, Shao-shan Carol, Galli, Mary, Nery, Joseph R, Gallavotti, Andrea, Ecker, Joseph R
Published in Nature protocols (01.08.2017)
Published in Nature protocols (01.08.2017)
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A transcription factor hierarchy defines an environmental stress response network
Song, Liang, Huang, Shao-shan Carol, Wise, Aaron, Castanon, Rosa, Nery, Joseph R., Chen, Huaming, Watanabe, Marina, Thomas, Jerushah, Bar-Joseph, Ziv, Ecker, Joseph R.
Published in Science (American Association for the Advancement of Science) (04.11.2016)
Published in Science (American Association for the Advancement of Science) (04.11.2016)
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Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light
Pedmale, Ullas V., Huang, Shao-shan Carol, Zander, Mark, Cole, Benjamin J., Hetzel, Jonathan, Ljung, Karin, Reis, Pedro A.B., Sridevi, Priya, Nito, Kazumasa, Nery, Joseph R., Ecker, Joseph R., Chory, Joanne
Published in Cell (14.01.2016)
Published in Cell (14.01.2016)
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MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing
Urich, Mark A, Nery, Joseph R, Lister, Ryan, Schmitz, Robert J, Ecker, Joseph R
Published in Nature protocols (01.03.2015)
Published in Nature protocols (01.03.2015)
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Widespread dynamic DNA methylation in response to biotic stress
Dowen, Robert H, Pelizzola, Mattia, Schmitz, Robert J, Lister, Ryan, Dowen, Jill M, Nery, Joseph R, Dixon, Jack E, Ecker, Joseph R
Published in Proceedings of the National Academy of Sciences - PNAS (07.08.2012)
Published in Proceedings of the National Academy of Sciences - PNAS (07.08.2012)
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Journal Article
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex
Luo, Chongyuan, Keown, Christopher L., Kurihara, Laurie, Zhou, Jingtian, He, Yupeng, Li, Junhao, Castanon, Rosa, Lucero, Jacinta, Nery, Joseph R., Sandoval, Justin P., Bui, Brian, Sejnowski, Terrence J., Harkins, Timothy T., Mukamel, Eran A., Behrens, M. Margarita, Ecker, Joseph R.
Published in Science (American Association for the Advancement of Science) (11.08.2017)
Published in Science (American Association for the Advancement of Science) (11.08.2017)
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Journal Article
Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain
Luo, Chongyuan, Lancaster, Madeline A., Castanon, Rosa, Nery, Joseph R., Knoblich, Juergen A., Ecker, Joseph R.
Published in Cell reports (Cambridge) (20.12.2016)
Published in Cell reports (Cambridge) (20.12.2016)
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Journal Article
Dynamic DNA methylation: In the right place at the right time
Luo, Chongyuan, Hajkova, Petra, Ecker, Joseph R
Published in Science (American Association for the Advancement of Science) (28.09.2018)
Published in Science (American Association for the Advancement of Science) (28.09.2018)
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Global Epigenomic Reconfiguration During Mammalian Brain Development
Lister, Ryan, Mukamel, Eran A., Nery, Joseph R., Urich, Mark, Puddifoot, Clare A., Johnson, Nicholas D., Lucero, Jacinta, Huang, Yun, Dwork, Andrew J., Schultz, Matthew D., Yu, Miao, Tonti-Filippini, Julian, Heyn, Holger, Hu, Shijun, Wu, Joseph C., Rao, Anjana, Esteller, Manel, He, Chuan, Haghighi, Fatemeh G., Sejnowski, Terrence J., Behrens, M. Margarita, Ecker, Joseph R.
Published in Science (American Association for the Advancement of Science) (09.08.2013)
Published in Science (American Association for the Advancement of Science) (09.08.2013)
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Patterns of population epigenomic diversity
Schmitz, Robert J., Schultz, Matthew D., Urich, Mark A., Nery, Joseph R., Pelizzola, Mattia, Libiger, Ondrej, Alix, Andrew, McCosh, Richard B., Chen, Huaming, Schork, Nicholas J., Ecker, Joseph R.
Published in Nature (London) (14.03.2013)
Published in Nature (London) (14.03.2013)
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Journal Article
Mobile small RNAs regulate genome-wide DNA methylation
Lewsey, Mathew G., Hardcastle, Thomas J., Melnyk, Charles W., Molnar, Attila, Valli, Adrián, Urich, Mark A., Nery, Joseph R., Baulcombe, David C., Ecker, Joseph R.
Published in Proceedings of the National Academy of Sciences - PNAS (09.02.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (09.02.2016)
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Journal Article
The Developmental Potential of iPSCs Is Greatly Influenced by Reprogramming Factor Selection
Buganim, Yosef, Markoulaki, Styliani, van Wietmarschen, Niek, Hoke, Heather, Wu, Tao, Ganz, Kibibi, Akhtar-Zaidi, Batool, He, Yupeng, Abraham, Brian J., Porubsky, David, Kulenkampff, Elisabeth, Faddah, Dina A., Shi, Linyu, Gao, Qing, Sarkar, Sovan, Cohen, Malkiel, Goldmann, Johanna, Nery, Joseph R., Schultz, Matthew D., Ecker, Joseph R., Xiao, Andrew, Young, Richard A., Lansdorp, Peter M., Jaenisch, Rudolf
Published in Cell stem cell (04.09.2014)
Published in Cell stem cell (04.09.2014)
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