Joseph R Nery

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 21

Top Topics

Dna Methylation

Arabidopsis Thaliana

Top Venues

Science (New York, N.Y.)

Nature genetics

Nature communications

This page only lists publications with an associated author ORCID identifier.

Publications

Nathan R Zemke, Ethan J Armand, Wenliang Wang, Seoyeon Lee, Jingtian Zhou, Yang Eric Li, Hanqing Liu, Wei Tian, Joseph R Nery, Rosa Gomez Castanon, Anna Bartlett, Julia K Osteen, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Lei Chang, Keyi Dong, Hannah S Indralingam, Jonathan A Rink, Yang Xie, Michael Miller, Fenna M Krienen, Qiangge Zhang, Naz Taskin, Jonathan Ting, Guoping Feng, Steven A McCarroll, Edward M Callaway, Ting Wang, Ed S Lein, M Margarita Behrens, Joseph R Ecker, Bing Ren
Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature (2024)
Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa Gomez Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, António Pinto-Duarte, Jasper Lee, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Hongkui Zeng, Chongyuan Luo, Jesse R Dixon, Bing Ren, M Margarita Behrens, Joseph R Ecker
Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. bioRxiv : the preprint server for biology (2023)
Nathan R Zemke, Ethan J Armand, Wenliang Wang, Seoyeon Lee, Jingtian Zhou, Yang Eric Li, Hanqing Liu, Wei Tian, Joseph R Nery, Rosa Gomez Castanon, Anna Bartlett, Julia K Osteen, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Lei Chang, Keyi Dong, Hannah S Indralingam, Jonathan A Rink, Yang Xie, Michael Miller, Fenna M Krienen, Qiangge Zhang, Naz Taskin, Jonathan Ting, Guoping Feng, Steven A McCarroll, Edward M Callaway, Ting Wang, Ed S Lein, M Margarita Behrens, Joseph R Ecker, Bing Ren
Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature 624 (7991) (2023)
Björn C Willige, Mark Zander, Chan Yul Yoo, Amy Phan, Renee M Garza, Shelly A Trigg, Yupeng He, Joseph R Nery, Huaming Chen, Meng Chen, Joseph R Ecker, Joanne Chory
Author Correction: PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. Nature genetics (2023)
Wei Tian, Jingtian Zhou, Anna Bartlett, Qiurui Zeng, Hanqing Liu, Rosa Gomez Castanon, Mia Kenworthy, Jordan Altshul, Cynthia Valadon, Andrew I Aldridge, Joseph R Nery, Huaming Chen, Jiaying Xu, Nicholas D Johnson, Jacinta Lucero, Julia K Osteen, Nora Emerson, Jonathan A Rink, Jasper Lee, Yang Eric Li, Kimberly Siletti, Michelle Liem, Naomi Claffey, Carolyn O'Connor, Anna Marie Yanny, Julie Nyhus, Nick Dee, Tamara Casper, Nadiya V Shapovalova, Daniel Hirschstein, Song-Lin Ding, Rebecca D Hodge, Boaz P Levi, C Dirk Keene, Sten Linnarsson, Ed S Lein, Bing Ren, M Margarita Behrens, Joseph R Ecker
Single-cell DNA methylation and 3D genome architecture in the human brain. Science (New York, N.Y.) 382 (6667) (2023)
Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa Gomez Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, António Pinto-Duarte, Jasper Lee, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Hongkui Zeng, Chongyuan Luo, Jesse R Dixon, Bing Ren, M Margarita Behrens, Joseph R Ecker
Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. bioRxiv : the preprint server for biology (2023)
Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R Nery, Huaming Chen, Rosa Gomez Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K Osteen, António Pinto-Duarte, Jasper Lee, Jonathan A Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zhanghao Wu, Ion Stoica, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Chongyuan Luo, Jesse R Dixon, Hongkui Zeng, Bing Ren, M Margarita Behrens, Joseph R Ecker
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature 624 (7991) (2023)
Jingtian Zhou, Zhuzhu Zhang, May Wu, Hanqing Liu, Yan Pang, Anna Bartlett, Zihao Peng, Wubin Ding, Angeline Rivkin, Will N Lagos, Elora Williams, Cheng-Ta Lee, Paula Assakura Miyazaki, Andrew Aldridge, Qiurui Zeng, J L Angelo Salinda, Naomi Claffey, Michelle Liem, Conor Fitzpatrick, Lara Boggeman, Zizhen Yao, Kimberly A Smith, Bosiljka Tasic, Jordan Altshul, Mia A Kenworthy, Cynthia Valadon, Joseph R Nery, Rosa Gomez Castanon, Neelakshi S Patne, Minh Vu, Mohammad Rashid, Matthew Jacobs, Tony Ito, Julia Osteen, Nora Emerson, Jasper Lee, Silvia Cho, Jonathan A Rink, Hsiang-Hsuan Huang, António Pinto-Duarte, Bertha Dominguez, Jared B Smith, Carolyn O'Connor, Hongkui Zeng, Shengbo Chen, Kuo-Fen Lee, Eran A Mukamel, Xin Jin, M Margarita Behrens, Joseph R Ecker, Edward M Callaway
Brain-wide correspondence of neuronal epigenomics and distant projections. Nature 624 (7991) (2023)
Carl Procko, Travis A Lee, Aleca M Borsuk, Bastiaan O R Bargmann, Tsegaye Dabi, Joseph R Nery, Mark Estelle, Lisa M Baird, Carolyn O'Connor, Craig R Brodersen, Joseph R Ecker, Joanne Chory
Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection. The Plant cell 34 (9) (2022)
Zhuzhu Zhang, Jingtian Zhou, Pengcheng Tan, Yan Pang, Angeline C Rivkin, Megan A Kirchgessner, Elora Williams, Cheng-Ta Lee, Hanqing Liu, Alexis D Franklin, Paula Assakura Miyazaki, Anna Bartlett, Andrew I Aldridge, Minh Vu, Lara Boggeman, Conor Fitzpatrick, Joseph R Nery, Rosa G Castanon, Mohammad Rashid, Matthew W Jacobs, Tony Ito-Cole, Carolyn O'Connor, António Pinto-Duarte, Bertha Dominguez, Jared B Smith, Sheng-Yong Niu, Kuo-Fen Lee, Xin Jin, Eran A Mukamel, M Margarita Behrens, Joseph R Ecker, Edward M Callaway
Epigenomic diversity of cortical projection neurons in the mouse brain. Nature 598 (7879) (2021)
Trygve E Bakken, Nikolas L Jorstad, Qiwen Hu, Blue B Lake, Wei Tian, Brian E Kalmbach, Megan Crow, Rebecca D Hodge, Fenna M Krienen, Staci A Sorensen, Jeroen Eggermont, Zizhen Yao, Brian D Aevermann, Andrew I Aldridge, Anna Bartlett, Darren Bertagnolli, Tamara Casper, Rosa G Castanon, Kirsten Crichton, Tanya L Daigle, Rachel Dalley, Nick Dee, Nikolai C Dembrow, Dinh Diep, Song-Lin Ding, Weixiu Dong, Rongxin Fang, Stephan Fischer, Melissa Goldman, Jeff Goldy, Lucas T Gray, Brian R Herb, Xiaomeng Hou, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Baldur van Lew, Yang Eric Li, Christine S Liu, Hanqing Liu, Jacinta D Lucero, Anup A Mahurkar, Delissa McMillen, Jeremy A Miller, Marmar Moussa, Joseph R Nery, Philip R Nicovich, Sheng-Yong Niu, Joshua Orvis, Julia K Osteen, Scott Owen, Carter R Palmer, Trangthanh H Pham, Nongluk Plongthongkum, Olivier Poirion, Nora M Reed, Christine Rimorin, Angeline Rivkin, William J Romanow, Adriana E Sedeño-Cortés, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Xinxin Wang, Fangming Xie, Anna Marie Yanny, Renee Zhang, Seth A Ament, M Margarita Behrens, Hector Corrada Bravo, Jerold Chun, Alexander Dobin, Jesse Gillis, Ronna Hertzano, Patrick R Hof, Thomas Höllt, Gregory D Horwitz, C Dirk Keene, Peter V Kharchenko, Andrew L Ko, Boudewijn P F Lelieveldt, Chongyuan Luo, Eran A Mukamel, António Pinto-Duarte, Sebastian Preissl, Aviv Regev, Bing Ren, Richard H Scheuermann, Kimberly A Smith, William J Spain, Owen R White, Christof Koch, Michael J Hawrylycz, Bosiljka Tasic, Evan Z Macosko, Steven A McCarroll, Jonathan T Ting, Hongkui Zeng, Kun Zhang, Guoping Feng, Joseph R Ecker, Sten Linnarsson, Ed S Lein
Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 598 (7879) (2021)
Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S Adkins, Andrew I Aldridge, Seth A Ament, Anna Bartlett, M Margarita Behrens, Koen Van den Berge, Darren Bertagnolli, Hector Roux de Bezieux, Tommaso Biancalani, Ali Sina Booeshaghi, Héctor Corrada Bravo, Tamara Casper, Carlo Colantuoni, Jonathan Crabtree, Heather H Creasy, Kirsten Crichton, Megan Crow, Nick Dee, Elizabeth L Dougherty, Wayne I Doyle, Sandrine Dudoit, Rongxin Fang, Victor Felix, Olivia Fong, Michelle G Giglio, Jeff Goldy, Michael J Hawrylycz, Brian R Herb, Ronna Hertzano, Xiaomeng Hou, Qiwen Hu, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Yang Eric Li, Jacinta D Lucero, Chongyuan Luo, Anup A Mahurkar, Delissa McMillen, Naeem M Nadaf, Joseph R Nery, Thuc Nghi Nguyen, Sheng-Yong Niu, Vasilis Ntranos, Joshua Orvis, Julia K Osteen, Trangthanh H Pham, António Pinto-Duarte, Olivier Poirion, Sebastian Preissl, Elizabeth Purdom, Christine Rimorin, Davide Risso, Angeline C Rivkin, Kimberly A Smith, Kelly Street, Josef Sulc, Valentine Svensson, Michael Tieu, Amy Torkelson, Herman Tung, Eeshit Dhaval Vaishnav, Charles R Vanderburg, Cindy T J van Velthoven, Xinxin Wang, Owen R White, Z Josh Huang, Peter V Kharchenko, Lior Pachter, John Ngai, Aviv Regev, Bosiljka Tasic, Joshua D Welch, Jesse Gillis, Evan Z Macosko, Bing Ren, Joseph R Ecker, Hongkui Zeng, Eran A Mukamel
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 598 (7879) (2021)
Alex de Mendoza, Daniel Poppe, Sam Buckberry, Jahnvi Pflueger, Caroline B Albertin, Tasman Daish, Stéphanie Bertrand, Elisa de la Calle-Mustienes, José Luis Gómez-Skarmeta, Joseph R Nery, Joseph R Ecker, Boris Baer, Clifton W Ragsdale, Frank Grützner, Héctor Escrivá, Byrappa Venkatesh, Ozren Bogdanovic, Ryan Lister
The emergence of the brain non-CpG methylation system in vertebrates. Nature ecology & evolution 5 (3) (2021)
Frederique Ruf Zamojski, Zidong Zhang, Michel Zamojski, Gregory R Smith, Natalia Mendelev, Hanqing Liu, German Nudelman, Mika Moriwaki, Hanna Pincas, Rosa Gomez Castanon, Venugopalan D Nair, Nitish Seenarine, Mary Anne S Amper, Xiang Zhou, Luisina Ongaro, Chirine Toufaily, Gauthier Schang, Joseph R Nery, Anna Bartlett, Andrew I Aldridge, Nimisha Jain, Gwen V Childs, Olga G Troyanskaya, Joseph R Ecker, Judith L Turgeon, Corrine K Welt, Daniel J Bernard, Stuart C Sealfon
Single nucleus multi-omics regulatory landscape of the murine pituitary. Nature communications 12 (1) (2021)
Chao Gao, Jialin Liu, April R Kriebel, Sebastian Preissl, Chongyuan Luo, Rosa Castanon, Justin Sandoval, Angeline Rivkin, Joseph R Nery, Margarita M Behrens, Joseph R Ecker, Bing Ren, Joshua D Welch
Iterative single-cell multi-omic integration using online learning. Nature biotechnology 39 (8) (2021)
Björn C Willige, Mark Zander, Chan Yul Yoo, Amy Phan, Renee M Garza, Shelly A Trigg, Yupeng He, Joseph R Nery, Huaming Chen, Meng Chen, Joseph R Ecker, Joanne Chory
PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. Nature genetics 53 (7) (2021)
Hanqing Liu, Jingtian Zhou, Wei Tian, Chongyuan Luo, Anna Bartlett, Andrew I Aldridge, Jacinta Lucero, Julia K Osteen, Joseph R Nery, Huaming Chen, Angeline Rivkin, Rosa G Castanon, Ben Clock, Yang Eric Li, Xiaomeng Hou, Olivier B Poirion, Sebastian Preissl, António Pinto-Duarte, Carolyn O'Connor, Lara Boggeman, Conor Fitzpatrick, Michael Nunn, Eran A Mukamel, Zhuzhu Zhang, Edward M Callaway, Bing Ren, Jesse R Dixon, M Margarita Behrens, Joseph R Ecker
DNA methylation atlas of the mouse brain at single-cell resolution. Nature 598 (7879) (2021)
Mark Zander, Mathew G Lewsey, Natalie M Clark, Lingling Yin, Anna Bartlett, J Paola Saldierna Guzmán, Elizabeth C Hann, Amber E Langford, Bruce Jow, Aaron Wise, Joseph R Nery, Huaming Chen, Ziv Bar-Joseph, Justin W Walley, Roberto Solano, Joseph R Ecker
Integrated multi-omics framework of the plant response to jasmonic acid. Nature plants 6 (3) (2020)
Dong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R Nery, Conor Fitzpatrick, Carolyn O'Connor, Jesse R Dixon, Joseph R Ecker
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nature methods 16 (10) (2019)
Chongyuan Luo, Angeline Rivkin, Jingtian Zhou, Justin P Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Gomez Castanon, Joseph R Nery, António Pinto-Duarte, Brian Bui, Conor Fitzpatrick, Carolyn O'Connor, Seth Ruga, Marc E Van Eden, David A Davis, Deborah C Mash, M Margarita Behrens, Joseph R Ecker
Robust single-cell DNA methylome profiling with snmC-seq2. Nature communications 9 (1) (2018)
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Jun-Hao Li, Rosa Gomez Castanon, Jacinta Lucero, Joseph R Nery, Justin P Sandoval, Brian Bui, Terrence J Sejnowski, Timothy T Harkins, Eran A Mukamel, M Margarita Behrens, Joseph R Ecker
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science (New York, N.Y.) 357 (6351) (2017)