Works by Nery, Joseph R.

Results: 20

Arabidopsis transcriptome responses to low water potential using highthroughput plate assays.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.84747

By:

Gonzalez, Stephen;
Swift, Joseph;
Yaaran, Adi;
Jiaying Xu;
Miller, Charlotte;
Illouz-Eliaz, Natanella;
Nery, Joseph R.;
Busch, Wolfgang;
Zait, Yotam;
Ecker, Joseph R.

Publication type:

Article

Mapping genome-wide transcription-factor binding sites using DAP-seq.

Published in:

Nature Protocols, 2017, v. 12, n. 8, p. 1659, doi. 10.1038/nprot.2017.055

By:

Bartlett, Anna;
O'Malley, Ronan C;
Huang, Shao-shan Carol;
Galli, Mary;
Nery, Joseph R;
Gallavotti, Andrea;
Ecker, Joseph R

Publication type:

Article

The complex architecture and epigenomic impact of plant T-DNA insertions.

Published in:

PLoS Genetics, 2019, v. 15, n. 1, p. 1, doi. 10.1371/journal.pgen.1007819

By:

Jupe, Florian;
Rivkin, Angeline C.;
Sandoval, Justin P.;
Chen, Huaming;
Castanon, Rosa;
Nery, Joseph R.;
Zander, Mark;
Ecker, Joseph R.;
Michael, Todd P.;
Motley, S. Timothy;
Slotkin, R. Keith

Publication type:

Article

Robust single-cell DNA methylome profiling with snmC-seq2.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06355-2

By:

Luo, Chongyuan;
Rivkin, Angeline;
Zhou, Jingtian;
Sandoval, Justin P.;
Kurihara, Laurie;
Lucero, Jacinta;
Castanon, Rosa;
Nery, Joseph R.;
Pinto-Duarte, António;
Bui, Brian;
Fitzpatrick, Conor;
O’Connor, Carolyn;
Ruga, Seth;
Van Eden, Marc E.;
Davis, David A.;
Mash, Deborah C.;
Behrens, M. Margarita;
Ecker, Joseph R.

Publication type:

Article

Patterns of population epigenomic diversity.

Published in:

Nature, 2013, v. 495, n. 7440, p. 193, doi. 10.1038/nature11968

By:

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.

Publication type:

Article

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.

Published in:

Nature, 2011, v. 471, n. 7336, p. 68, doi. 10.1038/nature09798

By:

Lister, Ryan;
Pelizzola, Mattia;
Kida, Yasuyuki S.;
Hawkins, R. David;
Nery, Joseph R.;
Hon, Gary;
Antosiewicz-Bourget, Jessica;
O'Malley, Ronan;
Castanon, Rosa;
Klugman, Sarit;
Downes, Michael;
Yu, Ruth;
Stewart, Ron;
Ren, Bing;
Thomson, James A.;
Evans, Ronald M.;
Ecker, Joseph R.

Publication type:

Article

Human DNA methylomes at base resolution show widespread epigenomic differences.

Published in:

Nature, 2009, v. 462, n. 7271, p. 315, doi. 10.1038/nature08514

By:

Lister, Ryan;
Pelizzola, Mattia;
Dowen, Robert H.;
Hawkins, R. David;
Hon, Gary;
Tonti-Filippini, Julian;
Nery, Joseph R.;
Lee, Leonard;
Zhen Ye;
Que-Minh Ngo;
Edsall, Lee;
Antosiewicz-Bourget, Jessica;
Stewart, Ron;
Ruotti, Victor;
Millar, A. Harvey;
Thomson, James A.;
Ren, Bing;
Ecker, Joseph R.

Publication type:

Article

Dynamic DNA methylation reconfiguration during seed development and germination.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1251-x

By:

Taiji Kawakatsu;
Nery, Joseph R.;
Castanon, Rosa;
Ecker, Joseph R.

Publication type:

Article

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.

Published in:

Nature Protocols, 2015, v. 10, n. 3, p. 475, doi. 10.1038/nprot.2014.114

By:

Urich, Mark A.;
Nery, Joseph R.;
Lister, Ryan;
Schmitz, Robert J.;
Ecker, Joseph R.

Publication type:

Article

Human body epigenome maps reveal noncanonical DNA methylation variation.

Published in:

Nature, 2015, v. 523, n. 7559, p. 212, doi. 10.1038/nature14465

By:

Schultz, Matthew D.;
He, Yupeng;
Whitaker, John W.;
Hariharan, Manoj;
Mukamel, Eran A.;
Leung, Danny;
Rajagopal, Nisha;
Nery, Joseph R.;
Urich, Mark A.;
Chen, Huaming;
Lin, Shin;
Lin, Yiing;
Jung, Inkyung;
Schmitt, Anthony D.;
Selvaraj, Siddarth;
Ren, Bing;
Sejnowski, Terrence J.;
Wang, Wei;
Ecker, Joseph R.

Publication type:

Article

An alternative pluripotent state confers interspecies chimaeric competency.

Published in:

Nature, 2015, v. 521, n. 7552, p. 316, doi. 10.1038/nature14413

By:

Wu, Jun;
Okamura, Daiji;
Li, Mo;
Suzuki, Keiichiro;
Luo, Chongyuan;
Ma, Li;
He, Yupeng;
Li, Zhongwei;
Benner, Chris;
Tamura, Isao;
Krause, Marie N.;
Nery, Joseph R.;
Du, Tingting;
Zhang, Zhuzhu;
Hishida, Tomoaki;
Takahashi, Yuta;
Aizawa, Emi;
Kim, Na Young;
Lajara, Jeronimo;
Guillen, Pedro

Publication type:

Article

Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.

Published in:

Nature, 2014, v. 514, n. 7520, p. 126, doi. 10.1038/nature13843

By:

Lister, Ryan;
Pelizzola, Mattia;
Kida, Yasuyuki S.;
Hawkins, R. David;
Nery, Joseph R.;
Hon, Gary;
Antosiewicz-Bourget, Jessica;
O'Malley, Ronan;
Castanon, Rosa;
Klugman, Sarit;
Downes, Michael;
Yu, Ruth;
Stewart, Ron;
Ren, Bing;
Thomson, James A.;
Evans, Ronald M.;
Ecker, Joseph R.

Publication type:

Article

Abnormalities in human pluripotent cells due to reprogramming mechanisms.

Published in:

Nature, 2014, v. 511, n. 7508, p. 177, doi. 10.1038/nature13551

By:

Ma, Hong;
Morey, Robert;
O'Neil, Ryan C.;
He, Yupeng;
Daughtry, Brittany;
Schultz, Matthew D.;
Hariharan, Manoj;
Nery, Joseph R.;
Castanon, Rosa;
Sabatini, Karen;
Thiagarajan, Rathi D.;
Tachibana, Masahito;
Kang, Eunju;
Tippner-Hedges, Rebecca;
Ahmed, Riffat;
Gutierrez, Nuria Marti;
Van Dyken, Crystal;
Polat, Alim;
Sugawara, Atsushi;
Sparman, Michelle

Publication type:

Article

Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3.

Published in:

eLife, 2022, p. 1, doi. 10.7554/eLife.66909

By:

Junhao Li;
Pinto-Duarte, Antonio;
Zander, Mark;
Cuoco, Michael S.;
Chi-Yu Lai;
Osteen, Julia;
Linjing Fang;
Chongyuan Luo;
Lucero, Jacinta D.;
Gomez-Castanon, Rosa;
Nery, Joseph R.;
Silva-Garcia, Isai;
Yan Pang;
Sejnowski, Terrence J.;
Powell, Susan B.;
Ecker, Joseph R.;
Mukamel, Eran A.;
Behrens, M. Margarita

Publication type:

Article

Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3.

Published in:

eLife, 2022, p. 1, doi. 10.7554/eLife.66909

By:

Junhao Li;
Pinto-Duarte, Antonio;
Zander, Mark;
Cuoco, Michael S.;
Chi-Yu Lai;
Osteen, Julia;
Linjing Fang;
Chongyuan Luo;
Lucero, Jacinta D.;
Gomez-Castanon, Rosa;
Nery, Joseph R.;
Silva-Garcia, Isai;
Yan Pang;
Sejnowski, Terrence J.;
Powell, Susan B.;
Ecker, Joseph R.;
Mukamel, Eran A.;
Behrens, M. Margarita

Publication type:

Article

Iterative single-cell multi-omic integration using online learning.

Published in:

Nature Biotechnology, 2021, v. 39, n. 8, p. 1000, doi. 10.1038/s41587-021-00867-x

By:

Gao, Chao;
Liu, Jialin;
Kriebel, April R.;
Preissl, Sebastian;
Luo, Chongyuan;
Castanon, Rosa;
Sandoval, Justin;
Rivkin, Angeline;
Nery, Joseph R.;
Behrens, Margarita M.;
Ecker, Joseph R.;
Ren, Bing;
Welch, Joshua D.

Publication type:

Article

Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection.

Published in:

Plant Cell, 2022, v. 34, n. 9, p. 3261, doi. 10.1093/plcell/koac167

By:

Procko, 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

Publication type:

Article

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons.

Published in:

eLife, 2019, p. 1, doi. 10.7554/eLife.40197

By:

Chongyuan Luo;
Qian Yi Lee;
Wapinski, Orly;
Castanon, Rosa;
Nery, Joseph R.;
Mall, Moritz;
Kareta, Michael S.;
Cullen, Sean M.;
Goodell, Margaret A.;
Chang, Howard Y.;
Wernig, Marius;
Ecker, Joseph R.

Publication type:

Article

Epigenomic landscapes of retinal rods and cones.

Published in:

eLife, 2016, p. 1, doi. 10.7554/eLife.11613

By:

Mo, Alisa;
Chongyuan Luo;
Davis, Fred P.;
Mukamel, Eran A.;
Henry, Gilbert L.;
Nery, Joseph R.;
Urich, Mark A.;
Picard, Serge;
Lister, Ryan;
Eddy, Sean R.;
Beer, Michael A.;
Ecker, Joseph R.;
Nathans, Jeremy

Publication type:

Article

Single nucleus multi-omics regulatory landscape of the murine pituitary.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-22859-w

By:

Ruf-Zamojski, Frederique;
Zhang, Zidong;
Zamojski, Michel;
Smith, Gregory R.;
Mendelev, Natalia;
Liu, Hanqing;
Nudelman, German;
Moriwaki, Mika;
Pincas, Hanna;
Castanon, Rosa Gomez;
Nair, Venugopalan D.;
Seenarine, Nitish;
Amper, Mary Anne S.;
Zhou, Xiang;
Ongaro, Luisina;
Toufaily, Chirine;
Schang, Gauthier;
Nery, Joseph R.;
Bartlett, Anna;
Aldridge, Andrew

Publication type:

Article