Works by Ecker, Joseph R.

Results: 98

Response to perspective.

Published in:

Plant Signaling & Behavior, 2013, v. 8, n. 8, p. 1, doi. 10.4161/psb.25037

By:

Hong Qiao;
Zhouxin Shen;
Shao-shan Carol Huang;
Schmitz, Robert J.;
Urich, Mark A.;
Briggs, Steven P.;
Ecker, Joseph R.

Publication type:

Article

STAR: an integrated solution to management and visualization of sequencing data.

Published in:

Bioinformatics, 2013, v. 29, n. 24, p. 3204, doi. 10.1093/bioinformatics/btt558

By:

Wang, Tao;
Liu, Jie;
Shen, Li;
Tonti-Filippini, Julian;
Zhu, Yun;
Jia, Haiyang;
Lister, Ryan;
Whitaker, John W.;
Ecker, Joseph R.;
Millar, A. Harvey;
Ren, Bing;
Wang, Wei

Publication type:

Article

Detection of allele-specific methylation through a generalized heterogeneous epigenome model.

Published in:

Bioinformatics, 2012, v. 28, n. 12, p. i163, doi. 10.1093/bioinformatics/bts231

By:

Peng, Qian;
Ecker, Joseph R.

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

Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism[OPEN].

Published in:

Plant Cell, 2020, v. 32, n. 4, p. 967, doi. 10.1105/tpc.19.00772

By:

Burko, Yogev;
Seluzicki, Adam;
Zander, Mark;
Pedmale, Ullas V.;
Ecker, Joseph R.;
2, Joanne Chory

Publication type:

Article

Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants.

Published in:

Plant Cell, 2016, v. 28, n. 3, p. 606, doi. 10.1105/tpc.15.00502

By:

Bergelson, Joy;
Buckler, Edward S.;
Ecker, Joseph R.;
Nordborg, Magnus;
Weigel, Detlef

Publication type:

Article

Arabidopsis 14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation.

Published in:

Plant Cell, 2014, v. 26, n. 8, p. 3326, doi. 10.1105/tpc.114.127605

By:

Catalá, Rafael;
López-Cobollo, Rosa;
Castellano, M. Mar;
Angosto, Trinidad;
Alonso, José M.;
Ecker, Joseph R.;
Salinas, Julio

Publication type:

Article

Arabidopsis Basic Helix-Loop-Helix Transcription Factors MYC2, MYC3, and MYC4 Regulate Glucosinolate Biosynthesis, Insect Performance, and Feeding Behavior.

Published in:

Plant Cell, 2013, v. 25, n. 8, p. 3117, doi. 10.1105/tpc.113.115139

By:

Schweizer, Fabian;
Fernández-Calvo, Patricia;
Zander, Mark;
Diez-Diaz, Monica;
Fonseca, Sandra;
Glauser, Gaétan;
Lewsey, Mathew G.;
Ecker, Joseph R.;
Solano, Roberto;
Reymond, Philippe

Publication type:

Article

Ethylene-Induced Stabilization of ETHYLENE INSENSITIVE3 and EIN3-LIKE1 Is Mediated by Proteasomal Degradation of EIN3 Binding F-Box 1 and 2 That Requires EIN2 in Arabidopsis.

Published in:

Plant Cell, 2010, v. 22, n. 7, p. 2384, doi. 10.1105/tpc.110.076588

By:

An, Fengying;
Zhao, Qiong;
Ji, Yusi;
Li, Wenyang;
Jiang, Zhiqiang;
Yu, Xiangchun;
Zhang, Chen;
Han, Ying;
He, Wenrong;
Liu, Yidong;
Zhang, Shuqun;
Ecker, Joseph R.;
Guo, Hongwei

Publication type:

Article

The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues.

Published in:

Plant Journal, 2022, v. 109, n. 4, p. 764, doi. 10.1111/tpj.15589

By:

Swift, Joseph;
Greenham, Kathleen;
Ecker, Joseph R.;
Coruzzi, Gloria M.;
Robertson McClung, C.

Publication type:

Article

The JA‐pathway MYC transcription factors regulate photomorphogenic responses by targeting HY5 gene expression.

Published in:

Plant Journal, 2020, v. 102, n. 1, p. 138, doi. 10.1111/tpj.14618

By:

Ortigosa, Andrés;
Fonseca, Sandra;
Franco‐Zorrilla, José M.;
Fernández‐Calvo, Patricia;
Zander, Mark;
Lewsey, Mathew G.;
García‐Casado, Gloria;
Fernández‐Barbero, Gemma;
Ecker, Joseph R.;
Solano, Roberto

Publication type:

Article

Variation in the Structure of Varicella-Zoster Virus DNA.

Published in:

Intervirology, 1984, v. 21, n. 1, p. 25, doi. 10.1159/000149500

By:

Ecker, Joseph R.;
Kudler, Linda;
Hyman, Richard W.

Publication type:

Article

A role for LEDGF/p75 in targeting HIV DNA integration.

Published in:

Nature Medicine, 2005, v. 11, n. 12, p. 1287, doi. 10.1038/nm1329

By:

Ciuffi, Angela;
Llano, Manuel;
Poeschla, Eric;
Hoffmann, Christian;
Leipzig, Jeremy;
Shinn, Paul;
Ecker, Joseph R.;
Bushman, Frederic

Publication type:

Article

Recombination and linkage disequilibrium in Arabidopsis thaliana.

Published in:

Nature Genetics, 2007, v. 39, n. 9, p. 1151, doi. 10.1038/ng2115

By:

Kim, Sung;
Plagnol, Vincent;
Hu, Tina T.;
Toomajian, Christopher;
Clark, Richard M.;
Ossowski, Stephan;
Ecker, Joseph R.;
Weigel, Detlef;
Nordborg, Magnus

Publication type:

Article

A complete BAC-based physical map of the Arabidopsis thaliana genome.

Published in:

Nature Genetics, 1999, v. 22, n. 3, p. 271, doi. 10.1038/10334

By:

Mozo, Teresa;
Dewar, Ken;
Dunn, Pat;
Ecker, Joseph R.;
Fischer, Sabine;
Kloska, Sebastian;
Lehrach, Hans;
Marra, Marco;
Martienssen, Robert;
Meier-Ewert, Sebastian;
Altmann, Thomas

Publication type:

Article

Two Plant Viral Suppressors of Silencing Require the Ethylene-Inducible Host Transcription Factor RAV2 to Block RNA Silencing.

Published in:

PLoS Pathogens, 2010, v. 6, n. 1, p. 1, doi. 10.1371/journal.ppat.1000729

By:

Endres, Matthew W.;
Gregory, Brian D.;
Zhihuan Gao;
Foreman, Amy Wahba;
Mlotshwa, Sizolwenkosi;
Xin Ge;
Pruss, Gail J.;
Ecker, Joseph R.;
Bowman, Lewis H.;
Vance, Vicki

Publication type:

Article

Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection.

Published in:

PLoS Pathogens, 2006, v. 2, n. 6, p. e60, doi. 10.1371/journal.ppat.0020060

By:

Lewinski, Mary K.;
Yamashita, Masahiro;
Emerman, Michael;
Ciuffi, Angela;
Marshall, Heather;
Crawford, Gregory;
Collins, Francis;
Shinn, Paul;
Leipzig, Jeremy;
Hannenhalli, Sridhar;
Berry, Charles C.;
Ecker, Joseph R.;
Bushman, Frederic D.;
Malim, Michael

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

The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease.

Published in:

Journal of Cell Biology, 2007, v. 178, n. 3, p. 477, doi. 10.1083/jcb.200704094

By:

Gentry, Matthew S.;
Worby, Carolyn A.;
Dixon, Jack E.;
Dowen III, Robert H.;
Mattoo, Seema;
Ecker, Joseph R.

Publication type:

Article

Activity-dependent modulation of synapse-regulating genes in astrocytes.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.70514

By:

Farhy-Tselnicker, Isabella;
Boisvert, Matthew M.;
Hanqing Liu;
Dowling, Cari;
Erikson, Galina A.;
Blanco-Suarez, Elena;
Farhy, Chen;
Shokhirev, Maxim N.;
Ecker, Joseph R.;
Allen, Nicola J.

Publication type:

Article

Genotypic variation of gene expression during the soybean innate immunity response.

Published in:

Plant Genetic Resources: Characterisation & Utilisation, 2014, v. 12, n. S1, p. S27, doi. 10.1017/S1479262114000197

By:

Valdés-López, Oswaldo;
Khan, Saad M.;
Schmitz, Robert J.;
Cui, Shiqi;
Qiu, Jing;
Joshi, Trupti;
Xu, Dong;
Diers, Brian;
Ecker, Joseph R.;
Stacey, Gary

Publication type:

Article

ABA-Activated SnRK2 Protein Kinase is Required for Dehydration Stress Signaling in Arabidopsis.

Published in:

Plant & Cell Physiology, 2002, v. 43, n. 12, p. 1473, doi. 10.1093/pcp/pcf188

By:

Yoshida, Riichiro;
Hobo, Tokunori;
Ichimura, Kazuya;
Mizoguchi, Tsuyoshi;
Takahashi, Fuminori;
Aronso, Jose;
Ecker, Joseph R.;
Shinozaki, Kazuo

Publication type:

Article

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0742-6

By:

Kishore, Kamal;
de Pretis, Stefano;
Lister, Ryan;
Morelli, Marco J.;
Bianchi, Valerio;
Amati, Bruno;
Ecker, Joseph R.;
Pelizzola, Mattia

Publication type:

Article

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0742-6

By:

Kishore, Kamal;
de Pretis, Stefano;
Lister, Ryan;
Morelli, Marco J.;
Bianchi, Valerio;
Amati, Bruno;
Ecker, Joseph R.;
Pelizzola, Mattia

Publication type:

Article

ISPMB Will Disband in 2006 After 8th International Congress of Plant Molecular Biology.

Published in:

Plant Molecular Biology Reporter, 2005, v. 23, n. 1, p. 1, doi. 10.1007/BF02772639

By:

Ecker, Joseph R.

Publication type:

Article

A Combinatorial Interplay Among the 1-Aminocyclopropane-1-Carboxylate Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana.

Published in:

Genetics, 2009, v. 183, n. 3, p. 979, doi. 10.1534/genetics.109.107102

By:

Tsuchisaka, Atsunari;
Guixia Yu;
Hailing Jin;
ALonso, Jose M.;
Ecker, Joseph R.;
Xiaoming Zhang;
Shang Gao;
Theologis, Athanasios

Publication type:

Article

FRIGIDA-Independent Variation in flowering Time of Natural Arabidopsis thaliana Accessions.

Published in:

Genetics, 2005, v. 170, n. 3, p. 1197, doi. 10.1534/genetics.104.036533

By:

Werner, Jonathan D.;
Borevitz, Justin O.;
Uhlenhaut, N. Henriette;
Ecker, Joseph R.;
Chory, Joanne;
Weigel, Detlef;
Sundaresan, V.

Publication type:

Article

Light-Response Quantitative Trait Loci Identified with Composite Interval and eXtreme Array Mapping in Arabidopsis thaliana.

Published in:

Genetics, 2004, v. 167, n. 2, p. 907, doi. 10.1534/genetics.103.024810

By:

Wolyn, David J.;
Borevitz, Justin O.;
Loudet, Olivier;
Schwartz, Chris;
Maloof, Julin;
Ecker, Joseph R.;
Berry, Charles C.;
Chory, Joanne

Publication type:

Article

Three Redundant Brassinosteroid Early Response Genes Encode Putative bHLH Transcription Factors Required for Normal Growth.

Published in:

Genetics, 2002, v. 162, n. 3, p. 1445, doi. 10.1093/genetics/162.3.1445

By:

Friedrichsen, Danielle M.;
Nemhauser, Jennifer;
Muramitsu, Takamichi;
Maloof, Julin N.;
Alonso, José;
Ecker, Joseph R.;
Furuya, Masaki;
Chory, Joanne

Publication type:

Article

An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling.

Published in:

Scientific Reports, 2016, p. 28941, doi. 10.1038/srep28941

By:

Aleman, Fernando;
Yazaki, Junshi;
Lee, Melissa;
Takahashi, Yohei;
Kim, Alice Y.;
Li, Zixing;
Kinoshita, Toshinori;
Ecker, Joseph R.;
Schroeder, Julian I.

Publication type:

Article

Sequencing and functional validation of the JGI Brachypodium distachyon T- DNA collection.

Published in:

Plant Journal, 2017, v. 91, n. 3, p. 361, doi. 10.1111/tpj.13582

By:

Hsia, Mon Mandy;
O'Malley, Ronan;
Cartwright, Amy;
Nieu, Rita;
Gordon, Sean P.;
Kelly, Sandra;
Williams, Tina G.;
Wood, Delilah F.;
Zhao, Yunjun;
Bragg, Jennifer;
Jordan, Mark;
Pauly, Markus;
Ecker, Joseph R.;
Gu, Yong;
Vogel, John P.

Publication type:

Article

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice ( Oryza sativa) coleoptiles under anoxia and re-oxygenation.

Published in:

Plant Journal, 2017, v. 89, n. 4, p. 805, doi. 10.1111/tpj.13418

By:

Narsai, Reena;
Secco, David;
Schultz, Matthew D.;
Ecker, Joseph R.;
Lister, Ryan;
Whelan, James

Publication type:

Article

Sigma factor-mediated plastid retrograde signals control nuclear gene expression.

Published in:

Plant Journal, 2013, v. 73, n. 1, p. 1, doi. 10.1111/tpj.12011

By:

Woodson, Jesse D.;
Perez‐Ruiz, Juan M.;
Schmitz, Robert J.;
Ecker, Joseph R.;
Chory, Joanne

Publication type:

Article

Linking genotype to phenotype using the Arabidopsis unimutant collection.

Published in:

Plant Journal, 2010, v. 61, n. 6, p. 928, doi. 10.1111/j.1365-313X.2010.04119.x

By:

O’Malley, Ronan C.;
Ecker, Joseph R.

Publication type:

Article

Utilizing tiling microarrays for whole-genome analysis in plants.

Published in:

Plant Journal, 2008, v. 53, n. 4, p. 636, doi. 10.1111/j.1365-313X.2007.03320.x

By:

Gregory, Brian D.;
Yazaki, Junshi;
Ecker, Joseph R.

Publication type:

Article

The Arabidopsis heavy metal P-type ATPase HMA5 interacts with metallochaperones and functions in copper detoxification of roots.

Published in:

Plant Journal, 2006, v. 45, n. 2, p. 225, doi. 10.1111/j.1365-313X.2005.02601.x

By:

Andrés-Colás, Nuria;
Sancenón, Vicente;
Rodríguez-Navarro, Susana;
Mayo, Sonia;
Thiele, Dennis J.;
Ecker, Joseph R.;
Puig, Sergi;
Peñarrubia, Lola

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

Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-04514-z

By:

Mingtang Xie;
Hongyu Chen;
Ling Huang;
O’Neil, Ryan C.;
Shokhirev, Maxim N.;
Ecker, Joseph R.

Publication type:

Article

A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03921-6

By:

Mingtang Xie;
Hongyu Chen;
Ling Huang;
O’Neil, Ryan C.;
Shokhirev, Maxim N.;
Ecker, Joseph R.

Publication type:

Article

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03016-2

By:

Michael, Todd P.;
Jupe, Florian;
Bemm, Felix;
Motley, S. Timothy;
Sandoval, Justin P.;
Lanz, Christa;
Loudet, Olivier;
Weigel, Detlef;
Ecker, Joseph R.

Publication type:

Article

The NIH Roadmap Epigenomics Mapping Consortium.

Published in:

Nature Biotechnology, 2010, v. 28, n. 10, p. 1045, doi. 10.1038/nbt1010-1045

By:

Bernstein, Bradley E.;
Stamatoyannopoulos, John A.;
Costello, Joseph F.;
Ren, Bing;
Milosavljevic, Aleksandar;
Meissner, Alexander;
Kellis, Manolis;
Marra, Marco A.;
Beaudet, Arthur L.;
Ecker, Joseph R.;
Farnham, Peggy J.;
Hirst, Martin;
Lander, Eric S.;
Mikkelsen, Tarjei S.;
Thomson, James A.

Publication type:

Article

Divergent perspectives on GM food.

Published in:

Nature Biotechnology, 2002, v. 20, n. 12, p. 1195, doi. 10.1038/nbt1202-1195

By:

Beachy, Roger;
Bennetzen, Jeffrey L.;
Chassy, Bruce M.;
Chrispeels, Maarten;
Chory, Joanne;
Ecker, Joseph R.;
Noel, Joseph P.;
Kay, Steve A.;
Dean, Caroline;
Lamb, Chris;
Jones, Jonathan;
Santerre, Charles R.;
Schroeder, Julian I.;
Umen, Jim;
Yanofsky, Martin;
Wessler, Susan;
Zhao, Yunde;
Parrott, Wayne

Publication type:

Article

CDPKs CPK6 and CPK3 Function in ABA Regulation of Guard Cell S-Type Anion- and Ca<sup>2+</sup>- Permeable Channels and Stomatal Closure.

Published in:

PLoS Biology, 2006, v. 4, n. 10, p. 1749, doi. 10.1371/journal.pbio.0040327

By:

Mori, Izumi C.;
Yoshiyuki Murata;
Yingzhen Yang;
Shintaro Munemasa;
Yong-Fei Wang;
Shannon Andreoli;
Hervé Tiriac;
Alonso, Jose M.;
Harper, Jeffery F.;
Ecker, Joseph R.;
Kwak, June M.;
Schroeder, Julian I.

Publication type:

Article

Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences.

Published in:

PLoS Biology, 2004, v. 2, n. 8, p. 1, doi. 10.1371/journal.pbio.0020234

By:

Mitchell, Rick S;
Beitzel, Brett F;
Schroder, Astrid R. W;
Shinn, Paul;
Chen, Huaming;
Berry, Charles C;
Ecker, Joseph R;
Bushman, Frederic D

Publication type:

Article

Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences.

Published in:

PLoS Biology, 2004, v. 2, n. 8, p. 0, doi. 10.1371/journal.pbio.0020234

By:

Mitchell, Rick S.;
Beitzel, Brett F.;
Schroder, Astrid R. W.;
Shinn, Paul;
Chen, Huaming;
Berry, Charles C.;
Ecker, Joseph R.;
Bushman, Frederic D.

Publication type:

Article

Genes blossom from a weed.

Published in:

Nature, 1998, v. 391, n. 6666, p. 438, doi. 10.1038/35030

By:

Ecker, Joseph R.

Publication type:

Article

Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis.

Published in:

Nature Reviews Genetics, 2006, v. 7, n. 7, p. 524, doi. 10.1038/nrg1893

By:

Alonso, Jose M.;
Ecker, Joseph R.

Publication type:

Article

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

Published in:

New Phytologist, 2017, v. 214, n. 2, p. 808, doi. 10.1111/nph.14421

By:

Hossain, Md Shakhawat;
Kawakatsu, Taiji;
Kim, Kyung Do;
Zhang, Ning;
Nguyen, Cuong T.;
Khan, Saad M.;
Batek, Josef M.;
Joshi, Trupti;
Schmutz, Jeremy;
Grimwood, Jane;
Schmitz, Robert J.;
Xu, Dong;
Jackson, Scott A.;
Ecker, Joseph R.;
Stacey, Gary

Publication type:

Article

JAZ2 controls stomata dynamics during bacterial invasion.

Published in:

New Phytologist, 2017, v. 213, n. 3, p. 1378, doi. 10.1111/nph.14354

By:

Gimenez‐Ibanez, Selena;
Boter, Marta;
Ortigosa, Andrés;
García‐Casado, Gloria;
Chini, Andrea;
Lewsey, Mathew G.;
Ecker, Joseph R.;
Ntoukakis, Vardis;
Solano, Roberto

Publication type:

Article

Comprehensive analysis of single cell ATAC-seq data with SnapATAC.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21583-9

By:

Fang, Rongxin;
Preissl, Sebastian;
Li, Yang;
Hou, Xiaomeng;
Lucero, Jacinta;
Wang, Xinxin;
Motamedi, Amir;
Shiau, Andrew K.;
Zhou, Xinzhu;
Xie, Fangming;
Mukamel, Eran A.;
Zhang, Kai;
Zhang, Yanxiao;
Behrens, M. Margarita;
Ecker, Joseph R.;
Ren, Bing

Publication type:

Article