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J

Joseph R. Ecker

the salk institute for biological studies

168H-index
535Paper Count
13.1WCitation Count
Published Papers 146
Publication Date
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Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina
errScience Advances
IF12.5
err2026-07-23
err0
errOAAI
errYing Yuan; Pooja Biswas; Nathan R. Zemke; Kelsey Dang; Yue Wu; Matteo D’Antonio; Yang Xie; Qian Yang; Keyi Dong; Pik Ki Lau; Daofeng Li; Chanrung Seng; Weronika Bartosik; Justin Buchanan; Lin Lin; Ryan Lancione; Kangli Wang; Seoyeon Lee; Zane Gibbs; Bing Yang; Joseph R. Ecker; Kelly Frazer; Ting Wang; Sebastian Preissl; Allen Wang; Radha Ayyagari; Bing Ren
errShare
errSave
Human body single-cell atlas of three-dimensional genome organization and DNA methylation
errScience
IF45.8
err2026-07-23
err0
PREAI
errJingtian Zhou; Yue Wu; Hanqing Liu; Wei Tian; Rosa G. Castanon; Anna Bartlett; Zuolong Zhang; Guocong Yao; Dengxiaoyu Shi; Ben Clock; Samantha Marcotte; Joseph R. Nery; Michelle Liem; Naomi Claffey; Lara Boggeman; Cesar Barragan; Rafael Arrojo e Drigo; Annika K. Weimer; Minyi Shi; Johnathan Cooper-Knock; Sai Zhang; Michael P. Snyder; Sebastian Preissl; Bing Ren; Carolyn O’Connor; Shengbo Chen; Chongyuan Luo; Jesse R. Dixon; Joseph R. Ecker
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errSave
Epigenetic and 3D genome reprogramming during the aging of the human hippocampus
errScience
IF45.8
err2026-07-23
err0
PREAI
errNathan R. Zemke; Seoyeon Lee; Sainath Mamde; Bing Yang; Nicole Berchtold; B. Maximiliano Garduño; Hannah S. Indralingam; Weronika M. Bartosik; Pik Ki Lau; Keyi Dong; Emily Hsu; Amanda Yang; Yasmine Tani; Chumo Chen; Qiurui Zeng; Varun Ajith; Liqi Tong; Chanrung Seng; Daofeng Li; Ting Wang; Jingtian Zhou; Joseph R. Ecker; Christopher K. Glass; Carl W. Cotman; Xiangmin Xu; Bing Ren
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errSave
Probabilistic modelling of single-cell bisulfite sequencing data with MethylVI
errNature Machine Intelligence
IF23.9
err2026-04-28
err0
PREAI
errEthan Weinberger; Wei Qiu; Wei Tian; Qiurui Zeng; Can Ergen; Ori Kronfeld; Martin Kim; Nir Yosef; Joseph R. Ecker; Su-In Lee
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errSave
Stress drives plasticity in leaf ageing transcriptional dynamics in Arabidopsis thaliana
errNature Plants
IF13.6
err2026-03-19
err0
errOAAI
errJoseph Swift; Xuelin Wu; Jiaying Xu; Carl Procko; Tanvi Jain; Natanella Illouz-Eliaz; Joseph R. Nery; Joanne Chory; Joseph R. Ecker
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errSave
Alternative oxidase and ethylene form a positive feed-forward loop in mitochondrial retrograde signalling
errPlant Communications
IF11.6
err2026-01-29
err0
errOAAI
errCunman He; Reena Narsai; Lim Chee Liew; Yan Zhang; Lingling Yin; Juan Xu; Mingtang Xie; Huixia Shou; Joseph R. Ecker; Mathew G. Lewsey; Yong Wang; Oliver Berkowitz; James Whelan
errShare
errSave
Innate immune molecular landscape following controlled human influenza virus infection
errCell Reports
IF6.9
err2025-09-16
err0
PREAI
errWilliam Thistlethwaite; Sindhu Vangeti; Wan-Sze Cheng; Pankaj Agarwal; Antonio Cappuccio; Wenliang Wang; Bei Wei; Rachel Myers; Aliza B. Rubenstein; Daniel Chawla; Manoj Hariharan; Micah T. McClain; Thomas W. Burke; Steven H. Kleinstein; Joseph R. Ecker; Christopher W. Woods; William J. Greenleaf; Xi Chen; Irene Ramos; Elena Zaslavsky; Thomas G. Evans; Olga G. Troyanskaya; Stuart C. Sealfon
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errSave
Cell-type-specific enrichment of somatic aneuploidy in the mammalian brain
errNeuron
IF15
err2025-09-03
err0
errOAAI
errEran A. Mukamel; Hanqing Liu; M. Margarita Behrens; Joseph R. Ecker
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errSave
Cell-type-specific effects of age and sex on human cortical neurons
errNEURON
IF15
err2024-08-01
err4
errOAAI
errChien, Jo-Fan; Liu, Hanqing; Wang, Bang-An; Luo, Chongyuan; Bartlett, Anna; Castanon, Rosa; Johnson, Nicholas D.; Nery, Joseph R.; Osteen, Julia; Li, Junhao; Altshul, Jordan; Kenworthy, Mia; Valadon, Cynthia; Liem, Michelle; Claffey, Naomi; O'Connor, Carolyn; Seeker, Luise A.; Ecker, Joseph R.; Behrens, M. Margarita; Mukamel, Eran A.
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errSave
Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
errGENOME RESEARCH
IF5.5
err2024-07-01
err1
errOAAI
errDenyer, Tom; Wu, Pin-Jou; Colt, Kelly; Abramson, Bradley W.; Pang, Zhili; Solansky, Pavel; Mamerto, Allen; Nobori, Tatsuya; Ecker, Joseph R.; Lam, Eric; Michael, Todd P.; Timmermans, Marja C. P.
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errSave
Arabidopsis transcriptome responses to low water potential using high-throughput plate assays
errELIFE
IF0
err2024-06-21
err1
errOAAI
errGonzalez, Stephen; Swift, Joseph; Yaaran, Adi; Xu, Jiaying; Miller, Charlotte; Illouz-Eliaz, Natanella; Nery, Joseph R.; Busch, Wolfgang; Zait, Yotam; Ecker, Joseph R.
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errSave
Remembering Philip N. Benfey: A visionary pioneer in plant biology and mentor extraordinaire
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2023-10-30
err0
errOAAI
errRaikhel, Natasha; Ecker, Joseph R.; Coruzzi, Gloria
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errSave
A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development (vol 9, 1604, 2018)
errNATURE COMMUNICATIONS
IF15.7
err2023-09-26
err0
errOAAI
errXie, Mingtang; Chen, Hongyu; Huang, Ling; O'Neil, Ryan C.; Shokhirev, Maxim N.; Ecker, Joseph R.
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errSave
Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes
errCELL GENOMICS
IF9
err2023-07-01
err4
errOAAI
errXie, Fangming; Armand, Ethan J.; Yao, Zizhen; Liu, Hanqing; Bartlett, Anna; Behrens, M. Margarita; Li, Yang Eric; Lucero, Jacinta D.; Luo, Chongyuan; Nery, Joseph R.; Pinto-Duarte, Antonio; Poirion, Olivier B.; Preissl, Sebastian; Rivkin, Angeline C.; Tasic, Bosiljka; Zeng, Hongkui; Ren, Bing; Ecker, Joseph R.; Mukamel, Eran A.
errShare
errSave
Yet uninfected? Resolving cell states of plants under pathogen attack
errCELL REPORTS METHODS
IF4.5
err2023-07-01
err3
errOAAI
errNobori, Tatsuya; Ecker, Joseph R.
errShare
errSave
Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap
errNATURE PLANTS
IF13.6
err2023-06-12
err35
errOAAI
errNobori, Tatsuya; Oliva, Marina; Lister, Ryan; Ecker, Joseph R.
errShare
errSave
PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants (vol 53, 955, 2021)
errNATURE GENETICS
IF31.8
err2023-01-23
err1
errOAAI
errWillige, Bjorn C.; Zander, Mark; Yoo, Chan Yul; Phan, Amy; Garza, Renee M. M.; Wanamaker, Shelly A. A.; He, Yupeng; Nery, Joseph R. R.; Chen, Huaming; Chen, Meng; Ecker, Joseph R. R.; Chory, Joanne
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errSave
CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping (vol 14, pg 819, 2017)
errNATURE METHODS
IF32.1
err2023-01-23
err0
errOAAI
errWanamaker, Shelly A.; Garza, Renee M.; MacWilliams, Andrew; Nery, Joseph R.; Bartlett, Anna; Castanon, Rosa; Goubil, Adeline; Feeney, Joseph; O'Malley, Ronan; Huang, Shao-shan C.; Zhang, Zhuzhu Z.; Galli, Mary; Ecker, Joseph R.
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errSave
Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection
errPLANT CELL
IF11.6
err2022-06-06
err32
errOAAI
errProcko, Carl; Lee, Travis; Borsuk, Aleca; Bargmann, Bastiaan O. R.; Dabi, Tsegaye; Nery, Joseph R.; Estelle, Mark; Baird, Lisa; O'Connor, Carolyn; Brodersen, Craig; Ecker, Joseph R.; Chory, Joanne
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errSave
Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3
errELIFE
IF0
err2022-05-23
err10
errOAAI
errLi, Junhao; Pinto-Duarte, Antonio; Zander, Mark; Cuoco, Michael S.; Lai, Chi-Yu; Osteen, Julia; Fang, Linjing; Luo, Chongyuan; Lucero, Jacinta D.; Gomez-Castanon, Rosa; Nery, Joseph R.; Silva-Garcia, Isai; Pang, Yan; Sejnowski, Terrence J.; Powell, Susan B.; Ecker, Joseph R.; Mukamel, Eran A.; Behrens, M. Margarita
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errSave

Research Directions

No research directions
Co-authors
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A
Aviv Regev
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