Joseph Ecker


Plant Molecular and Cellular Biology Laboratory

Director, Genomic Analysis Laboratory

Howard Hughes Medical Institute Investigator

Salk International Council Chair in Genetics

Salk Institute for Biological Studies - Publications Joe Ecker


Jupe, F., Rivkin, A.C., Michael, T.P., Zander, M., Motley, S.T., Sandoval,J.P., Slotkin, R.K., Chen, H., Castanon, R., Nery, J.R., Ecker, J.R. The complex architecture and epigenomic impact of plant T-DNA insertions. PLOS, 2019 Jan 18.

Luo, C., Lee, Q.Y., Wapinski, O., Castanon, R., Nery, J.R., Mall, M., Kareta, M.S., Cullen, S.M., Goodell, M.A., Chang, H.Y., Wernig, M., Ecker, J.R. Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. eLife, 2019;8:e40197.

Ecker, J.R., Geschwind, D.H., Kriegstein, A.R., Ngai, J., Osten, P., Polioudakis, D., Regev, A., Sestan, N., Wickersham, I.R., Zeng, H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron, 2017 Nov 1;96(3):542-557. doi.10.1016/j.neuron. 2017.10.007. PMID:29096072.

Luo, C., Keown, C.L., Kurihara, L., Zhou, J., He, Y., Castanon, R., Lucero, J., Nery, J.R., Sandoval, J.P., Bui., B., Sejnowski, T.J., Harkins, T.T., Mukamel, E.A., Behrens, M.M., Ecker, J.R. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science, 2017 Aug 11;357(6351):600-604. doi. 10.1126/science.aan3351. PMID:28798132. PMCID: PMC5570439.

Trigg, S.A., Garza, R.M., MacWilliams, A., Nery, J.R., Bartlett, A., Castanon, R., Goubil, A., Feeney, J, O'Malley, R., Huang, S.C., Zhang, ZZ., Galli, M., Ecker, J.R. CrY2H-seq interactome screening. Prot Exchange. 2017 Jun 28. doi: 10.1038/protex.2017.058.

Trigg, S.A., Garza, R.M., MacWilliams, A., Nery, J.R., Bartlett, A., Castanon, R., Goubil, A., Feeney, J, O'Malley, R., Huang, S.C., Zhang, ZZ., Galli, M., Ecker, J.R. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2017 Jun 26. doi: 10.1038/nmeth.4343. [Epub ahead of print] PMID:2865047.

Michael, T., Jupe, F., Bemm, F., Motley, S., Sandoval, J., Loudet, O., Weigel, D., Ecker, J.R. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. bioRxiv, 2017 Jun 14. Doi:10.1101/149997.

Kawakatsu, T., Nery, J.R., Castanon, R., Ecker, J.R. Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biology, 2017 Sep 15;18(1):171. doi: 10.1186/s13059-017-1251-x. PMID: 28911331.

Hsia, M., Malley, R.O., Cartwright, A., Nieu, R., Gordon, S., Kelly, S., Williams, T.G.,Wood, DF., Zhao, Y., Bragg, J., Jordan, M., Pauly,M., Ecker, J.R., Gu, Y., Vogel, J.P. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection, Plant J, 2017 Apr 22. doi: 111/tpj.13582. [Epub ahead of print] PMID: 28432803.

Bartlett, A., O’Malley, R.D., Huang, S-s.C., Galli, M., Nery, J.R., Gallavotti, A., Ecker J.R. Mapping genome-wide transcription factor binding sites using DAP-seq. Nature Protocols, 2017 Aug;12(8):1659-1672. doi: 10.1038/nprot.2017.055. Epub 2017 Jul 20. PMID: 28726847.

He, Y., Gorkin, D.U., Dickel, D.E., Nery, J.R., Castanon, R., Lee, A.Y., Shen, Y., Visel, A., Pennacchio, L.A., Ren, B., Ecker, J.R. (2017) Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc Natl Acad Sci U S A. 28;114(9):E1633-E1640. doi: 10.1073/pnas.1618353114.

Luo, C., Lancaster, M.A., Castanon, R., Nery, J.R., *Knoblich, J.A.,*Ecker, J.R. (2016) Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain, Cell Reports 17: 1-16. EndFragment

Song L., Huang SS., Wise A., Castanon R., Nery J.R., Chen H., Watanabe M., Thomas J., Bar-Joseph Z., Ecker JR. (2016) A transcription factor hierarchy defines an environmental stress response network. Science 354: 598. PMID: 27811239; NIHMSID: 836046;

Kawakatsu T, Huang SS, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O'Neil R, O'Malley RC, Quarless DX; 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR. (2016) Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell 166: 492-505. PMID: 27419873; NIHMSID: 836043;

O'Malley RC, Huang SS, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A,, Ecker JR. (2016) Cistrome and epicistrome features shape the regulatory DNA landscape. Cell 165: 1280-92. PMID: 27203113; PMC4907330.

1001 Genomes Consortium. (2016) 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell. 166: 481-91. PMID: 27293186; PMCID: PMC4949382.

Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. (2016) Unique cell-type-specific patterns of DNA methylation in the root meristem. Nature Plants 2: 16058. PMID: 27243651; PMCID: PMC4855458.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR. (2016) Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A 113: E801-10. PMID: 26787884; PMCID: PMC4760824.

Schultz, MD, He, Y., Whitaker, JW., Hariharan, M., Mukamel, EA, Leung, D., Rajagopal, N., Nery, JR., Urich, MA, Chen, H., Lin, S., Lin, Y., Jung, I., Schmitt, AD., Selvaraj, S., Ren, B., Sejnowski, TD., Wang W., Ecker, JR. (2015) Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2015 Jul 9;523(7559):212-6. doi: 10.1038/nature14465. Epub 2015 Jun 1.

Lister R*, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM*, Ecker JR*. (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341: 1237905. PMID: 23828890;PMCID: PMC3785061.

Schmitz, R.J., Schultz, M.D., Urich, M.A., Nery, J.R., Pelizzola, M., Libiger, O., Alix, A., McCosh, R.B., Chen, H., Schork, N.J. and Ecker, J.R. (2013) Patterns of population epigenomic diversity. Nature. Mar 14;495(7440):193-8. doi: 10.1038/nature11968. Epub 2013 Mar 6. Link

Chang, K.N., Zhong, S., Weirauch, M.T., Hon, G., Pelizzola, M., Li, H., Huang, S.S., Schmitz, R.J., Urich, M.A., Kuo, D., Nery, J.R., Qiao, H., Yang, A., Jamali, A., Chen, H., Ideker, T., Ren, B., Bar-Joseph, Z., Hughes, T.R. and Ecker, J.R. (2013) Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2013 Jun 11;2:e00675. Link

Lister, R., Mukamel, E.A., Nery, J.R., Urich, M., Puddifoot, C.A., Johnson, N.D., Lucero, J., Huang, Y., Dwork, A.J., Schultz, M.D., Yu, M., Tonti-Filippini, J., Heyn, H., Hu, S., Wu, J.C., Rao, A., Esteller, M., He, C., Haghighi, F.G., Sejnowski, T.J., Behrens, M.M. and Ecker, JR. (2013) Global epigenomic reconfiguration during mammalian brain development. Science. 2013 Aug 9;341(6146):1237905. Epub 2013 Jul 4. Link

Qiao, H., Shen, Z., Huang, S.S., Schmitz, RJ., Urich, M.A., Briggs, S.P. and Ecker, J.R. (2012) Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas. Science 338(6105):390-393. Abstract

Lister R., Pelizzola M., Kida Y.S., Hawkins R.D., Nery J.R., Hon G., Antosiewicz-Bourget J., O'Malley R., Castanon R., Klugman S., Downes M., Yu R., Stewart R., Ren B., Thomson J.A., Evans R.M. and Ecker J.R. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature Mar 3;471(7336):68-73. Epub 2011 Feb 2.

Evidence for network evolution in an Arabidopsis interactome map. Arabidopsis Interactome Mapping Consortium. Science. 2011 333(6042):601-7.

Mukhtar, M.S., Carvunis, A.R., Dreze, M., Epple, P., Steinbrenner, J., Moore, J., Tasa,n M., Galli, M., Hao, T., Nishimura, M.T., Pevzner, S.J., Donovan, S.E., Ghamsari, .L, Santhanam, B., Romero, V., Poulin, M.M., Gebreab, F., Gutierrez, B.J., Tam, S., Monachello, D., Boxem, M., Harbort, C.J., McDonald, N., Gai, L., Chen. H., He, Y., European Union Effectoromics Consortium, Vandenhaute, J., Roth, F.P., Hill, D.E., Ecker, J.R., Vidal, M., Beynon, J., Braun, P., Dangl, J.L. (2011) Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science. 333(6042):596-601.

Schmitz, R.J., Schultz, M.D., Lewsey, M.G., O'Malley, R.C., Urich, M.A., Libiger, O., Schork, N.J., Ecker, J.R. (2011) Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants. Science. 334(6054):369-73. Abstract | Download the article

Lister, R., Pelizzola, M., Dowen, R.H, Hawkins, R.D., Hon, G., Tonti-Filippini, J., Nery, J.R., Lee, L., Ye, Z., Ngo, Q-M., Edsall, L., Antosiewicz-Bourget, J., Stewart, R., Ruotti, V., Millar, A.H., Thomson, J.A., Ren, B. and Ecker, J.R. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462:315-322

Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H. and Ecker, J.R. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 133:1-14 | Download the article

Clark, RM, Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T.T., Fu, G., Hinds. D.A. , Chen, H., Frazer, K.A., Huson, D.H., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker. J. R., and Weigel, D. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science. 317(5836):338-42

Alonso, J.M. and J.R. Ecker (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat. Rev. Genet. 7:524-

Olmedo, G., G. Guo, B.D. Gregory, S.D. Nourizadeh, L. Aguilar-Henonin, H. Li, H. An, P. Guzman, and J.R. Ecker (2006) ETHYLENE-INSENSITIVE5 encodes a 5'→3' exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2. Proc Natl Acad Sci U S A, |. 103: 13286-13293

Zhang, X., Yazaki, J., Sundaresan, A. Cokus,S., Chan, S.W.-L., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E., and Ecker, J.R. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell. 126, 1189-1201

Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR. (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics. 85(1):1-15.

Wang, K. L., Yoshida, H., Lurin, C., and Ecker, J. R. (2004). Regulation of ethylene gas biosynthesis by the Arabidopsis ETO1 protein. Nature. 428, 945-950.

Li, H., Johnson, P., Stepanova, A., Alonso, J. M., and Ecker, J. R. (2004). Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. Dev Cell. 7, 193-204.

Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., Stevenson, D.K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C., Heller, C., Jeske, A., Koesema, E., Meyers, C.C., Parker, H., Prednis, L., Ansari, Y., Choy, N., Deen, H., Geralt, M., Hazari, N., Hom, E., Karnes, M., Mulholland, C., Ndubaku, R., Schmidt, I., Guzman, P., Aguilar-Henonin, L., Schmid, M., Weigel, D., Carter, D.E., Marchand, T., Risseeuw, E., Brogden, D., Zeko, A., Crosby, W.L., Berry, C.C. and Ecker. J.R., (2003) Genome-wide Insertional mutagenesis of Arabidopsis thaliana. Science. 301:653-657.

Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, and Ecker JR. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 302:842-846.

Guo, H., and Ecker J.R. (2003) Plant Responses to Ethylene Gas Are Mediated by SCFEBF1/EBF2-dependent Proteolysis of EIN3 transcription factor. Cell. 115: 667-677.

Recent Publications - Pubmed database


BA, Biology/Chemistry, The College of New Jersey, Ewing, N.J.
PhD, Microbiology, Pennsylvania State University College of Medicine
Postdoctoral Fellow, Stanford University School of Medicine

Awards & Honors

  • 2015 American Academy of Arts and Sciences
  • 2012 Elected as AAAS Fellow
  • 2011 Investigator, Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation
  • 2011 George W. Beadle Award, Genetics Society of America
  • 2009 #2 Scientific Discovery of the Year 2009-TIME Magazine
  • 2007 National Academy of Sciences, John J. Carty Award for the Advancement of Science
  • 2006 Elected, National Academy of Sciences
  • 2005 American Society for Plant Biology, Martin Gibbs Medal
  • 2004 Scientific American 50 Research Leader of the Year
  • 2004 International Plant Growth Substances Association Distinguished Research Award
  • 2001 Kumho Science International Award in Plant Molecular Biology
  • President International Society for Plant Molecular Biology