Joseph R Ecker

Scopus Author ID ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 63

Top Venues

Nature

eLife

bioRxiv : the preprint server for biology

Science (New York, N.Y.)

University of Pennsylvania

The Pennsylvania State University College of Medicine (PHD)

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

Affiliation History

University of Pennsylvania

United States

Assistant, Associate, Full Professor :: Biology

Education History

The Pennsylvania State University College of Medicine Aug 15 1978 - May 15 1982

United States

PHD :: Microbiology

Publications

Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature 625 (7996) (2024)
Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature 625 (7996) (2024)
Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature 625 (7996) (2024)
Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature (2024)
Stephen Gonzalez, Joseph Swift, Adi Yaaran, Jiaying Xu, Charlotte Miller, Natanella Illouz-Eliaz, Joseph R Nery, Wolfgang Busch, Yotam Zait, Joseph R Ecker
Arabidopsis transcriptome responses to low water potential using high-throughput plate assays. eLife 12 (2024)
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)
Stephen Gonzalez, Joseph Swift, Adi Yaaran, Jiaying Xu, Charlotte Miller, Natanella Illouz-Eliaz, Joseph R Nery, Wolfgang Busch, Yotam Zait, Joseph R Ecker
Arabidopsis transcriptome responses to low water potential using high-throughput plate assays. eLife 12 (2024)
Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature 625 (7996) (2024)
Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature 625 (7996) (2024)
Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature 625 (7996) (2024)
Nelson J Johansen, Niklas Kempynck, Nathan R Zemke, Saroja Somasundaram, Seppe De Winter, Marcus J Hooper, Deepanjali Dwivedi, Ruchi Lohia, Fabien Wehbe, Bocheng Li, Darina Abaffyová, Ethan J Armand, Julie De Man, Eren Can Eksi, Nikolai Hecker, Gert Hulselmans, Vasileios Konstantakos, David Mauduit, John K Mich, Gabriele Partel, Tanya L Daigle, Boaz P Levi, Kai Zhang, Yoshiaki Tanaka, Jonathan M Werner, Jonathan T Ting, Yoav Ben-Simon, Jeremy A Miller, Joseph R Ecker, Bing Ren, Stein Aerts, Ed S Lein, Bosiljka Tasic, Trygve E Bakken
Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex. bioRxiv : the preprint server for biology (2024)
Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature 625 (7996) (2024)
Wei Tian, Wubin Ding, Jiawei Shen, Daofeng Li, Ting Wang, Joseph R Ecker
BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data. Bioinformatics (Oxford, England) 40 (7) (2024)
Stephen Gonzalez, Joseph Swift, Adi Yaaran, Jiaying Xu, Charlotte Miller, Natanella Illouz-Eliaz, Joseph R Nery, Wolfgang Busch, Yotam Zait, Joseph R Ecker
Arabidopsis transcriptome responses to low water potential using high-throughput plate assays. eLife 12 (2024)
Wei Tian, Wubin Ding, Jiawei Shen, Daofeng Li, Ting Wang, Joseph R Ecker
BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data. Bioinformatics (Oxford, England) 40 (7) (2024)
Min Cao, Matthieu Pierre Platre, Huei-Hsuan Tsai, Ling Zhang, Tatsuya Nobori, Laia Armengot, Yintong Chen, Wenrong He, Lukas Brent, Nuria S Coll, Joseph R Ecker, Niko Geldner, Wolfgang Busch
Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. 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)
Tatsuya Nobori, Marina Oliva, Ryan Lister, Joseph R Ecker
Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap. Nature plants (2023)
Songpeng Zu, Yang Eric Li, Kangli Wang, Ethan J Armand, Sainath Mamde, Maria Luisa Amaral, Yuelai Wang, Andre Chu, Yang Xie, Michael Miller, Jie Xu, Zhaoning Wang, Kai Zhang, Bojing Jia, Xiaomeng Hou, Lin Lin, Qian Yang, Seoyeon Lee, Bin Li, Samantha Kuan, Hanqing Liu, Jingtian Zhou, António Pinto-Duarte, Jacinta Lucero, Julia Osteen, Michael Nunn, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Zihan Wang, Jingbo Shang, M Margarita Behrens, Joseph R Ecker, Allen Wang, Sebastian Preissl, Bing Ren
Single-cell analysis of chromatin accessibility in the adult mouse brain. 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)
Yang Eric Li, Sebastian Preissl, Michael Miller, Nicholas D Johnson, Zihan Wang, Henry Jiao, Chenxu Zhu, Zhaoning Wang, Yang Xie, Olivier B Poirion, Colin Kern, António Pinto-Duarte, Wei Tian, Kimberly Siletti, Nora Emerson, Julia Osteen, Jacinta Lucero, Lin Lin, Qian Yang, Quan Zhu, Nathan R Zemke, Sarah Espinoza, Anna Marie Yanny, Julie Nyhus, Nick Dee, Tamara Casper, Nadiya V Shapovalova, Daniel Hirschstein, Rebecca D Hodge, Sten Linnarsson, Trygve E Bakken, Boaz P Levi, C Dirk Keene, Jingbo Shang, Ed S Lein, Allen Wang, M Margarita Behrens, Joseph R Ecker, Bing Ren
A comparative atlas of single-cell chromatin accessibility in the human brain. Science (New York, N.Y.) 382 (6667) (2023)
Wenliang Wang, Manoj Hariharan, Anna Bartlett, Cesar Barragan, Rosa Castanon, Vince Rothenberg, Haili Song, Joseph Nery, Andrew Aldridge, Jordan Altshul, Mia Kenworthy, Wubin Ding, Hanqing Liu, Wei Tian, Jingtian Zhou, Huaming Chen, Bei Wei, Irem B Gündüz, Todd Norell, Timothy J Broderick, Micah T McClain, Lisa L Satterwhite, Thomas W Burke, Elizabeth A Petzold, Xiling Shen, Christopher W Woods, Vance G Fowler, Felicia Ruffin, Parinya Panuwet, Dana B Barr, Jennifer L Beare, Anthony K Smith, Rachel R Spurbeck, Sindhu Vangeti, Irene Ramos, German Nudelman, Stuart C Sealfon, Flora Castellino, Anna Maria Walley, Thomas Evans, Fabian Müller, William J Greenleaf, Joseph R Ecker
Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures. bioRxiv : the preprint server for biology (2023)
Natasha Raikhel, Joseph R Ecker, Gloria M Coruzzi
Remembering Philip N. Benfey: A visionary pioneer in plant biology and mentor extraordinaire. Proceedings of the National Academy of Sciences of the United States of America 120 (45) (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)
Bianca Castro Gouveia-Mageste, Laura Gonçalves Costa Martins, Maximiller Dal-Bianco, João Paulo Batista Machado, José Cleydson Ferreira da Silva, Alice Y Kim, Junshi Yazaki, Anésia Aparecida Dos Santos, Joseph R Ecker, Elizabeth Pacheco Batista Fontes
A plant-specific syntaxin-6 protein contributes to the intracytoplasmic route for the begomovirus CabLCV. Plant physiology 187 (1) (2022)
Magdalena E Potok, Zhenhui Zhong, Colette L Picard, Qikun Liu, Truman Do, Cassidy E Jacobsen, Ocean Sakr, Bilguudei Naranbaatar, Ruwan Thilakaratne, Zhanna Khnkoyan, Megan Purl, Harrison Cheng, Helena Vervaet, Suhua Feng, Shima Rayatpisheh, James A Wohlschlegel, Ronan C O'Malley, Joseph R Ecker, Steven E Jacobsen
The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis . Proceedings of the National Academy of Sciences of the United States of America 119 (3) (2022)
Jun-Hao Li, António Pinto-Duarte, Mark Zander, Michael S Cuoco, Chi-Yu Lai, Julia K Osteen, Lingjing Fang, Chongyuan Luo, Jacinta D Lucero, Rosa Gomez-Castanon, Joseph R Nery, Isai Silva-Garcia, Yan Pang, Terrence J Sejnowski, Susan B Powell, Joseph R Ecker, Eran A Mukamel, M Margarita Behrens
Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. eLife 11 (2022)
Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K Shiau, Xinzhu Zhou, Fangming Xie, Eran A Mukamel, Kai Zhang, Yanxiao Zhang, M Margarita Behrens, Joseph R Ecker, Bing Ren
Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nature communications 12 (1) (2021)
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)
Isabella Farhy-Tselnicker, Matthew M Boisvert, Hanqing Liu, Cari Dowling, Galina A Erikson, Elena Blanco-Suarez, Chen Farhy, Maxim Nikolaievich Shokhirev, Joseph R Ecker, Nicola J Allen
Activity-dependent modulation of synapse-regulating genes in astrocytes. eLife 10 (2021)
Yang Eric Li, Sebastian Preissl, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Yunjiang Qiu, Olivier B Poirion, Bin Li, Joshua Chiou, Hanqing Liu, António Pinto-Duarte, Naoki Kubo, Xiaoyu Yang, Rongxin Fang, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Michael Miller, Samantha Kuan, David Gorkin, Kyle J Gaulton, Yin Shen, Michael Nunn, Eran A Mukamel, M Margarita Behrens, Joseph R Ecker, Bing Ren
An atlas of gene regulatory elements in adult mouse cerebrum. Nature 598 (7879) (2021)
Joseph Swift, Kathleen Greenham, Joseph R Ecker, Gloria M Coruzzi, C Robertson McClung
The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues. The Plant journal : for cell and molecular biology (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)
Yupeng He, Manoj Hariharan, David U Gorkin, Diane E Dickel, Chongyuan Luo, Rosa G Castanon, Joseph R Nery, Ah Young Lee, Yuan Zhao, Hui Huang, Brian A Williams, Diane Trout, Henry Amrhein, Rongxin Fang, Huaming Chen, Bin Li, Axel Visel, Len A Pennacchio, Bing Ren, Joseph R Ecker
Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature 583 (7818) (2020)
Shayne D Wierbowski, Tommy V Vo, Pascal Falter-Braun, Timothy O Jobe, Lars H Kruse, Xiaomu Wei, Jin Liang, Michael J Meyer, Nurten Akturk, Christen A Rivera-Erick, Nicolas A Cordero, Mauricio I Paramo, Elnur E Shayhidin, Marta Bertolotti, Nathaniel D Tippens, Kazi Akther, Rita Sharma, Yuichi Katayose, Kourosh Salehi-Ashtiani, Tong Hao, Pamela C Ronald, Joseph R Ecker, Peter A Schweitzer, Shoshi Kikuchi, Hiroshi Mizuno, David E Hill, Marc Vidal, Gaurav D Moghe, Susan R McCouch, Haiyuan Yu
A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proceedings of the National Academy of Sciences of the United States of America 117 (21) (2020)
Laura A Lavery, Kerstin Ure, Ying-Wooi Wan, Chongyuan Luo, Alexander J Trostle, Wei Wang, Haijing Jin, Joanna Lopez, Jacinta Lucero, Mark A Durham, Rosa Castanon, Joseph R Nery, Zhandong Liu, Margaret A Goodell, Joseph R Ecker, M Margarita Behrens, Huda Yaya Zoghbi
Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome. eLife 9 (2020)
Yogev Burko, Adam Seluzicki, Mark Zander, Ullas V Pedmale, Joseph R Ecker, Joanne Chory
Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism. The Plant cell 32 (4) (2020)
null null, Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L Van Nostrand, Peter Freese, David U Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A Williams, Ali Mortazavi, Cheryl A Keller, Xiao-Ou Zhang, Shaimae I Elhajjajy, Jack Huey, Diane E Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B Chhetri, Jialing Zhang, Alec Victorsen, Kevin P White, Axel Visel, Gene W Yeo, Christopher B Burge, Eric Lécuyer, David M Gilbert, Job Dekker, John L Rinn, Eric M Mendenhall, Joseph R Ecker, Manolis Kellis, Robert J Klein, William S Noble, Anshul Kundaje, Roderic Guigó, Peggy J Farnham, J Michael Cherry, Richard M Myers, Bing Ren, Brenton R Graveley, Mark B Gerstein, Len A Pennacchio, Michael Paul Snyder, Bradley E Bernstein, Barbara Wold, Ross Cameron Hardison, Thomas R Gingeras, John A Stamatoyannopoulos, Nishigandha Phalke
Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583 (7818) (2020)
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)
Todd P Michael, Evan Ernst, Nolan Hartwick, Philomena Chu, Douglas Bryant, Sarah Gilbert, Stefan Ortleb, Erin L Baggs, K Sowjanya Sree, Klaus-Juergen Appenroth, Joerg Fuchs, Florian Jupe, Justin P Sandoval, Ksenia V Krasileva, Ljudmilla Borisjuk, Todd C Mockler, Joseph R Ecker, Robert A Martienssen, Eric Lam
Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome research (2020)
Mark Zander, Björn Christopher Willige, Yupeng He, Thu A Nguyen, Amber E Langford, Ramlah Nehring, Elizabeth Howell, Robert McGrath, Anna Bartlett, Rosa Castanon, Joseph R Nery, Huaming Chen, Zhuzhu Zhang, Florian Jupe, Anna Stepanova, Robert J Schmitz, Mathew G Lewsey, Joanne Chory, Joseph R Ecker
Epigenetic silencing of a multifunctional plant stress regulator. eLife 8 (2019)
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)
Eriko Sasaki, Taiji Kawakatsu, Joseph R Ecker, Magnus Nordborg
Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana. PLoS genetics 15 (12) (2019)
Florian Jupe, Angeline C Rivkin, Todd P Michael, Mark Zander, S Timothy Motley, Justin P Sandoval, R Keith Slotkin, Huaming Chen, Rosa Gomez Castanon, Joseph R Nery, Joseph R Ecker
The complex architecture and epigenomic impact of plant T-DNA insertions. PLoS genetics 15 (1) (2019)
Chongyuan Luo, Qian Yi Lee, Orly Wapinski, Rosa Castanon, Joseph R Nery, Moritz Mall, Michael S Kareta, Sean M Cullen, Margaret A Goodell, Howard Y Chang, Marius Wernig, Joseph R Ecker
Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. eLife 8 (2019)
Mohammad Salehin, Baohua Li, Michelle Tang, Ella Katz, Liang Song, Joseph R Ecker, Daniel J Kliebenstein, Mark Estelle
Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels. Nature communications 10 (1) (2019)
Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa G Castanon, Joseph R Nery, Amir Rattner, Christopher A Walsh, Joseph R Ecker, Jeremy Nathans
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. eLife 7 (2018)
Joel Hrit, Leeanne Goodrich, Cheng Li, Bang-An Wang, Ji Nie, Xiaolong Cui, Elizabeth Allene Martin, Eric Simental, Jenna Fernandez, Monica Yun Liu, Joseph R Nery, Rosa Castanon, Rahul M Kohli, Natalia Y Tretyakova, Chuan He, Joseph R Ecker, Mary G Goll, Barbara Panning
OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. eLife 7 (2018)
Chongyuan Luo, Petra Hajkova, Joseph R Ecker
Dynamic DNA methylation: In the right place at the right time. Science (New York, N.Y.) 361 (6409) (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)
Joy Bergelson, Edward S Buckler, Joseph R Ecker, Magnus Nordborg, Detlef Weigel
A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants. The Plant cell 28 (3) (2016)
Alisa Mo, Chongyuan Luo, Fred P Davis, Eran A Mukamel, Gilbert L Henry, Joseph R Nery, Mark A Urich, Serge Picard, Ryan Lister, Sean R Eddy, Michael A Beer, Joseph R Ecker, Jeremy Nathans
Epigenomic landscapes of retinal rods and cones. eLife 5 (2016)

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Joseph R Ecker