Joseph Ecker

Professor

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

all Publications


Brigidi, G.S., Hayes, M.G.B., Delos Santos, N.P., Hartzell, A.L., Texari, L., Lin, P.A., Bartlett, A., Ecker, J.R., Benner, C., Heinz, S., Bloodgood, B.L. Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers. (2019) Cell. 179(2):373-391.e27. DOI: 10.1016/j.cell.2019.09.004

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Salehin, M., Li, B., Tang, M., Katz, E., Song, L., Ecker, J.R., Kliebenstein, D.J., Estelle, M. Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels. (2019) Nature Communications. 10(1):4021. DOI: 10.1038/s41467-019-12002-1

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Lee, D.S., Luo, C., Zhou, J., Chandran, S., Rivkin, A., Bartlett, A., Nery, J.R., Fitzpatrick, C., O'Connor, C., Dixon, J.R., Ecker, J.R. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. (2019) Nature Methods. DOI: 10.1038/s41592-019-0547-z

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Zander, M., Willige, B.C., He, Y., Nguyen, T.A., Langford, A.E., Nehring, R., Howell, E., McGrath, R., Bartlett, A., Castanon, R., Nery, J.R., Chen, H., Zhang, Z., Jupe, F., Stepanova, A., Schmitz, R.J., Lewsey, M., Chory, J., Ecker, J.R. Epigenetic silencing of a multifunctional plant stress regulator. (2019) Elife. 8. DOI: 10.7554/eLife.47835

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Zhou, J., Ma, J., Chen, Y., Cheng, C., Bao, B., Peng, J., Sejnowski, T.J., Dixon, J.R., Ecker, J.R. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. (2019) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1901423116

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Kawakatsu, T., Ecker, J.R. Diversity and dynamics of DNA methylation: epigenomic resources and tools for crop breeding. (2019) Breeding Science. 69(2):191-204. DOI: 10.1270/jsbbs.19005

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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. (2019) Elife. 8. DOI: 10.7554/eLife.40197

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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. (2019) PLOS Genetics. 15(1):e1007819. DOI: 10.1371/journal.pgen.1007819

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Hrit, J., Goodrich, L., Li, C., Wang, B.A., Nie, J., Cui, X., Martin, E.A., Simental, E., Fernandez, J., Liu, M.Y., Nery, J.R., Castanon, R., Kohli, R.M., Tretyakova, N., He, C., Ecker, J.R., Goll, M., Panning, B. OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. (2018) Elife. 7. DOI: 10.7554/eLife.34870

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Luo, C., Hajkova, P., Ecker, J.R. Dynamic DNA methylation: In the right place at the right time. (2018) Science. 361(6409):1336-1340. DOI: 10.1126/science.aat6806

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Sabbagh, M.F., Heng, J.S., Luo, C., Castanon, R.G., Nery, J.R., Rattner, A., Goff, L.A., Ecker, J.R., Nathans, J. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. (2018) Elife. 7. DOI: 10.7554/eLife.36187

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Luo, C., Rivkin, A., Zhou, J., Sandoval, J.P., Kurihara, L., Lucero, J., Castanon, R., Nery, J.R., Pinto-Duarte, A., Bui, B., Fitzpatrick, C., O'Connor, C., Ruga, S., Van Eden, M.E., Davis, D.A., Mash, D.C., Behrens, M.M., Ecker, J.R. Robust single-cell DNA methylome profiling with snmC-seq2. (2018) Nature Communications. 9(1):3824. DOI: 10.1038/s41467-018-06355-2

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Yazaki, J., Galli, M., Kim, A.Y., Ecker, J.R. Profiling Interactome Networks with the HaloTag-NAPPA In Situ Protein Array. (2018) Current Protocols in Plant Biology.:e20071 DOI: 10.1002/cppb.20071

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Xie, M., Chen, H., Huang, L., O'Neil, R.C., Shokhirev, M.N., Ecker, J.R. Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. (2018) Nature Communications. 9(1):2075. DOI: 10.1038/s41467-018-04514-z

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Xie, M., Chen, H., Huang, L., O'Neil, R.C., Shokhirev, M.N., Ecker, J.R. A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. (2018) Nature Communications. 9(1):1604. DOI: 10.1038/s41467-018-03921-6

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Michael, T.P., Jupe, F., Bemm, F., Motley, S.T., Sandoval, J.P., Lanz, C., Loudet, O., Weigel, D., Ecker, J.R. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. (2018) Nature Communications. 9(1):541. DOI: 10.1038/s41467-018-03016-2

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Carter, A.C., Chang, H.Y., Church, G., Dombkowski, A., Ecker, J.R., Gil, E., Giresi, P.G., Greely, H., Greenleaf, W.J., Hacohen, N., He, C., Hill, D., Ko, J., Kohane, I., Kundaje, A., Palmer, M., Snyder, M.P., Tung, J., Urban, A., Vidal, M., Wong, W. Challenges and recommendations for epigenomics in precision health. (2017) Nature Biotechnology. 35(12):1128-1132. DOI: 10.1038/nbt.4030


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. (2017) Neuron. 96(3):542-557. DOI: 10.1016/j.neuron.2017.10.007

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Huang, S.C., Ecker, J.R. Piecing together cis-regulatory networks: insights from epigenomics studies in plants. (2017) Wiley Interdisciplinary Reviews. Systems biology and Medicine. DOI: 10.1002/wsbm.1411

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

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Luo, C., Keown, C.L., Kurihara, L., Zhou, J., He, Y., Li, J., 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. (2017) Science. 357(6351):600-604. DOI: 10.1126/science.aan3351

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Bartlett, A., O'Malley, R.C., Huang, S.C., Galli, M., Nery, J.R., Gallavotti, A., Ecker, J.R. Mapping genome-wide transcription-factor binding sites using DAP-seq. (2017) Nature Protocols. 12(8):1659-1672. DOI: 10.1038/nprot.2017.055

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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, Z.Z., Galli, M., Ecker, J.R. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. (2017) Nature Methods. 14(8):819-825. DOI: 10.1038/nmeth.4343

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Hsia, M.M., O'Malley, R., Cartwright, A., Nieu, R., Gordon, S.P., Kelly, S., Williams, T.G., Wood, D.F., 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. (2017) Plant Journal. 91(3):361-370. DOI: 10.1111/tpj.13582

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Keown, C.L., Berletch, J.B., Castanon, R., Nery, J.R., Disteche, C.M., Ecker, J.R., Mukamel, E.A. Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain. (2017) Proceedings of the National Academy of Sciences of the United States of America. 114(14):E2882-E2890. DOI: 10.1073/pnas.1611905114

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Hossain, M.S., Kawakatsu, T., Kim, K.D., Zhang, N., Nguyen, C.T., Khan, S.M., Batek, J.M., Joshi, T., Schmutz, J., Grimwood, J., Schmitz, R.J., Xu, D., Jackson, S.A., Ecker, J.R., Stacey, G. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. (2017) New Phytol. 214(2):808-819. DOI: 10.1111/nph.14421

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He, Y., Gorkin, D.U., Dickel, D.E., Nery, J.R., Castanon, R.G., Lee, A.Y., Shen, Y., Visel, A., Pennacchio, L.A., Ren, B., Ecker, J.R. Improved regulatory element prediction based on tissue-specific local epigenomic signatures. (2017) Proceedings of the National Academy of Sciences of the United States of America. 114(9):E1633-E1640. DOI: 10.1073/pnas.1618353114

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Shani, E., Salehin, M., Zhang, Y., Sanchez, S.E., Doherty, C., Wang, R., Mangado, C.C., Song, L., Tal, I., Pisanty, O., Ecker, J.R., Kay, S.A., Pruneda-Paz, J., Estelle, M. Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. (2017) Current Biology. 27(3):437-444. DOI: 10.1016/j.cub.2016.12.016

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Gimenez-Ibanez, S., Boter, M., Ortigosa, A., García-Casado, G., Chini, A., Lewsey, M.G., Ecker, J.R., Ntoukakis, V., Solano, R. JAZ2 controls stomata dynamics during bacterial invasion. (2017) New Phytol. 213(3):1378-1392. DOI: 10.1111/nph.14354

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Narsai, R., Secco, D., Schultz, M.D., Ecker, J.R., Lister, R., Whelan, J. Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. (2017) Plant Journal. 89(4):805-824. DOI: 10.1111/tpj.13418

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Ma, H., O'Neil, R.C., Marti Gutierrez, N., Hariharan, M., Zhang, Z.Z., He, Y., Cinnioglu, C., Kayali, R., Kang, E., Lee, Y., Hayama, T., Koski, A., Nery, J., Castanon, R., Tippner-Hedges, R., Ahmed, R., Van Dyken, C., Li, Y., Olson, S., Battaglia, D., Lee, D.M., Wu, D.H., Amato, P., Wolf, D.P., Ecker, J.R., Mitalipov, S. Functional Human Oocytes Generated by Transfer of Polar Body Genomes. (2017) Cell Stem Cell. 20(1):112-119. DOI: 10.1016/j.stem.2016.10.001

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Luo, C., Lancaster, M.A., Castanon, R., Nery, J.R., Knoblich, J.A., Ecker, J.R. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain. (2016) Cell Reports. 17(12):3369-3384. DOI: 10.1016/j.celrep.2016.12.001

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Chin, C.S., Peluso, P., Sedlazeck, F.J., Nattestad, M., Concepcion, G.T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., Cramer, G.R., Delledonne, M., Luo, C., Ecker, J.R., Cantu, D., Rank, D.R., Schatz, M.C. Phased diploid genome assembly with single-molecule real-time sequencing. (2016) Nature Methods. 13(12):1050-1054. DOI: 10.1038/nmeth.4035

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Song, L., Huang, S.C., Wise, A., Castanon, R., Nery, J.R., Chen, H., Watanabe, M., Thomas, J., Bar-Joseph, Z., Ecker, J.R. A transcription factor hierarchy defines an environmental stress response network. (2016) Science. 354(6312). DOI: 10.1126/science.aag1550

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Zhang, F., Qi, B., Wang, L., Zhao, B., Rode, S., Riggan, N.D., Ecker, J.R., Qiao, H. EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling. (2016) Nature Communications. 7:13018. DOI: 10.1038/ncomms13018

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Theunissen, T.W., Friedli, M., He, Y., Planet, E., O'Neil, R.C., Markoulaki, S., Pontis, J., Wang, H., Iouranova, A., Imbeault, M., Duc, J., Cohen, M.A., Wert, K.J., Castanon, R., Zhang, Z., Huang, Y., Nery, J.R., Drotar, J., Lungjangwa, T., Trono, D., Ecker, J.R., Jaenisch, R. Molecular Criteria for Defining the Naive Human Pluripotent State. (2016) Cell Stem Cell. 19(4):502-515. DOI: 10.1016/j.stem.2016.06.011

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O'Malley, R.C., Huang, S.C., Song, L., Lewsey, M.G., Bartlett, A., Nery, J.R., Galli, M., Gallavotti, A., Ecker, J.R. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. (2016) Cell. 166(6):1598. DOI: 10.1016/j.cell.2016.08.063


Walley, J.W., Sartor, R.C., Shen, Z., Schmitz, R.J., Wu, K.J., Urich, M.A., Nery, J.R., Smith, L.G., Schnable, J.C., Ecker, J.R., Briggs, S.P. Integration of omic networks in a developmental atlas of maize. (2016) Science. 353(6301):814-8. DOI: 10.1126/science.aag1125

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Kawakatsu, T., Huang, S.C., Jupe, F., Sasaki, E., Schmitz, R.J., Urich, M.A., Castanon, R., Nery, J.R., Barragan, C., He, Y., Chen, H., Dubin, M., Lee, C.R., Wang, C., Bemm, F., Becker, C., O'Neil, R., O'Malley, R.C., Quarless, D.X., Schork, N.J., Weigel, D., Nordborg, M., Ecker, J.R. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. (2016) Cell. 166(2):492-505. DOI: 10.1016/j.cell.2016.06.044

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Yazaki, J., Galli, M., Kim, A.Y., Nito, K., Aleman, F., Chang, K.N., Carvunis, A.R., Quan, R., Nguyen, H., Song, L., Alvarez, J.M., Huang, S.S., Chen, H., Ramachandran, N., Altmann, S., Gutiérrez, R.A., Hill, D.E., Schroeder, J.I., Chory, J., LaBaer, J., Vidal, M., Braun, P., Ecker, J.R. Mapping transcription factor interactome networks using HaloTag protein arrays. (2016) Proceedings of the National Academy of Sciences of the United States of America. 113(29):E4238-47. DOI: 10.1073/pnas.1603229113

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Aleman, F., Yazaki, J., Lee, M., Takahashi, Y., Kim, A.Y., Li, Z., Kinoshita, T., Ecker, J.R., Schroeder, J.I. An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling. (2016) Scientific Reports. 6:28941. DOI: 10.1038/srep28941

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Song, L., Koga, Y., Ecker, J.R. Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq). (2016) Current Protocols in Plant Biology. 1(2):293-306. DOI: 10.1002/cppb.20014

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O'Malley, R.C., Huang, S.S., Song, L., Lewsey, M.G., Bartlett, A., Nery, J.R., Galli, M., Gallavotti, A., Ecker, J.R. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. (2016) Cell. 165(5):1280-92. DOI: 10.1016/j.cell.2016.04.038

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Prigge, M.J., Greenham, K., Zhang, Y., Santner, A., Castillejo, C., Mutka, A.M., O'Malley, R.C., Ecker, J.R., Kunkel, B.N., Estelle, M. The Arabidopsis Auxin Receptor F-Box Proteins AFB4 and AFB5 Are Required for Response to the Synthetic Auxin Picloram. (2016) G3. 6(5):1383-90. DOI: 10.1534/g3.115.025585

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Kawakatsu, T., Stuart, T., Valdes, M., Breakfield, N., Schmitz, R.J., Nery, J.R., Urich, M.A., Han, X., Lister, R., Benfey, P.N., Ecker, J.R. Unique cell-type-specific patterns of DNA methylation in the root meristem. (2016) Nature Plants. 2(5):16058. DOI: 10.1038/nplants.2016.58

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Bogdanović, O., Smits, A.H., de la Calle Mustienes, E., Tena, J.J., Ford, E., Williams, R., Senanayake, U., Schultz, M.D., Hontelez, S., van Kruijsbergen, I., Rayon, T., Gnerlich, F., Carell, T., Veenstra, G.J., Manzanares, M., Sauka-Spengler, T., Ecker, J.R., Vermeulen, M., Gómez-Skarmeta, J.L., Lister, R. Active DNA demethylation at enhancers during the vertebrate phylotypic period. (2016) Nature Genetics. 48(4):417-26. DOI: 10.1038/ng.3522

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Bergelson, J., Buckler, E.S., Ecker, J.R., Nordborg, M., Weigel, D. A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants. (2016) Plant Cell. 28(3):606-9. DOI: 10.1105/tpc.15.00502


Mo, A., Luo, C., Davis, F.P., Mukamel, E.A., Henry, G.L., Nery, J.R., Urich, M.A., Picard, S., Lister, R., Eddy, S.R., Beer, M.A., Ecker, J.R., Nathans, J. Epigenomic landscapes of retinal rods and cones. (2016) Elife. 5:e11613. DOI: 10.7554/eLife.11613

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Lewsey, M.G., Hardcastle, T.J., Melnyk, C.W., Molnar, A., Valli, A., Urich, M.A., Nery, J.R., Baulcombe, D.C., Ecker, J.R. Mobile small RNAs regulate genome-wide DNA methylation. (2016) Proceedings of the National Academy of Sciences of the United States of America. 113(6):E801-10. DOI: 10.1073/pnas.1515072113

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Sanchez-Mut, J.V., Heyn, H., Vidal, E., Moran, S., Sayols, S., Delgado-Morales, R., Schultz, M.D., Ansoleaga, B., Garcia-Esparcia, P., Pons-Espinal, M., de Lagran, M.M., Dopazo, J., Rabano, A., Avila, J., Dierssen, M., Lott, I., Ferrer, I., Ecker, J.R., Esteller, M. Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. (2016) Transl Psychiatry. 6:e718. DOI: 10.1038/tp.2015.214

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Pedmale, U.V., Huang, S.S., Zander, M., Cole, B.J., Hetzel, J., Ljung, K., Reis, P.A., Sridevi, P., Nito, K., Nery, J.R., Ecker, J.R., Chory, J. Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light. (2016) Cell. 164(1-2):233-45. DOI: 10.1016/j.cell.2015.12.018

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Kishore, K., de Pretis, S., Lister, R., Morelli, M.J., Bianchi, V., Amati, B., Ecker, J.R., Pelizzola, M. methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. (2015) BMC Bioinformatics. 16:313. DOI: 10.1186/s12859-015-0742-6

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Nagel, D.H., Doherty, C.J., Pruneda-Paz, J.L., Schmitz, R.J., Ecker, J.R., Kay, S.A. Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. (2015) Proceedings of the National Academy of Sciences of the United States of America. 112(34):E4802-10. DOI: 10.1073/pnas.1513609112

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Secco, D., Wang, C., Shou, H., Schultz, M.D., Chiarenza, S., Nussaume, L., Ecker, J.R., Whelan, J., Lister, R. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. (2015) Elife. 4. DOI: 10.7554/eLife.09343

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Schultz, M.D., He, Y., Whitaker, J.W., Hariharan, M., Mukamel, E.A., Leung, D., Rajagopal, N., Nery, J.R., Urich, M.A., Chen, H., Lin, S., Lin, Y., Jung, I., Schmitt, A.D., Selvaraj, S., Ren, B., Sejnowski, T.J., Wang, W., Ecker, J.R. Human body epigenome maps reveal noncanonical DNA methylation variation. (2015) Nature. 523(7559):212-6. DOI: 10.1038/nature14465

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Mo, A., Mukamel, E.A., Davis, F.P., Luo, C., Henry, G.L., Picard, S., Urich, M.A., Nery, J.R., Sejnowski, T.J., Lister, R., Eddy, S.R., Ecker, J.R., Nathans, J. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. (2015) Neuron. 86(6):1369-84. DOI: 10.1016/j.neuron.2015.05.018

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Luo, C., Ecker, J.R. Epigenetics. Exceptional epigenetics in the brain. (2015) Science. 348(6239):1094-5. DOI: 10.1126/science.aac5832


He, Y., Ecker, J.R. Non-CG Methylation in the Human Genome. (2015) Annual Review of Genomics and Human Genetics. 16:55-77. DOI: 10.1146/annurev-genom-090413-025437

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Wu, J., Okamura, D., Li, M., Suzuki, K., Luo, C., Ma, L., He, Y., Li, Z., Benner, C., Tamura, I., Krause, M.N., Nery, J.R., Du, T., Zhang, Z., Hishida, T., Takahashi, Y., Aizawa, E., Kim, N.Y., Lajara, J., Guillen, P., Campistol, J.M., Esteban, C.R., Ross, P.J., Saghatelian, A., Ren, B., Ecker, J.R., Izpisua Belmonte, J.C. An alternative pluripotent state confers interspecies chimaeric competency. (2015) Nature. 521(7552):316-21. DOI: 10.1038/nature14413

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Kida, Y.S., Kawamura, T., Wei, Z., Sogo, T., Jacinto, S., Shigeno, A., Kushige, H., Yoshihara, E., Liddle, C., Ecker, J.R., Yu, R.T., Atkins, A.R., Downes, M., Evans, R.M. ERRs Mediate a Metabolic Switch Required for Somatic Cell Reprogramming to Pluripotency. (2015) Cell Stem Cell. 16(5):547-55. DOI: 10.1016/j.stem.2015.03.001

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Urich, M.A., Nery, J.R., Lister, R., Schmitz, R.J., Ecker, J.R. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. (2015) Nature Protocols. 10(3):475-83. DOI: 10.1038/nprot.2014.114

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Leung, D., Jung, I., Rajagopal, N., Schmitt, A., Selvaraj, S., Lee, A.Y., Yen, C.A., Lin, S., Lin, Y., Qiu, Y., Xie, W., Yue, F., Hariharan, M., Ray, P., Kuan, S., Edsall, L., Yang, H., Chi, N.C., Zhang, M.Q., Ecker, J.R., Ren, B. Integrative analysis of haplotype-resolved epigenomes across human tissues. (2015) Nature. 518(7539):350-354. DOI: 10.1038/nature14217

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Dixon, J.R.*, Jung, I.*, Selvaraj, S.*, Shen, Y., Antosiewicz-Bourget, J.E., Lee, A.Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y., Liang, J., Zhao, H., Lobanenkov, V.V., Ecker, J.R., Thomson, J.A., Ren, B. Chromatin architecture reorganization during stem cell differentiation. (2015) Nature. 518(7539):331-6. DOI: 10.1038/nature14222

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Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., Ziller, M.J., Amin, V., Whitaker, J.W., Schultz, M.D., Ward, L.D., Sarkar, A., Quon, G., Sandstrom, R.S., Eaton, M.L., Wu, Y.C., Pfenning, A.R., Wang, X., Claussnitzer, M., Liu, Y., Coarfa, C., Harris, R.A., Shoresh, N., Epstein, C.B., Gjoneska, E., Leung, D., Xie, W., Hawkins, R.D., Lister, R., Hong, C., Gascard, P., Mungall, A.J., Moore, R., Chuah, E., Tam, A., Canfield, T.K., Hansen, R.S., Kaul, R., Sabo, P.J., Bansal, M.S., Carles, A., Dixon, J.R., Farh, K.H., Feizi, S., Karlic, R., Kim, A.R., Kulkarni, A., Li, D., Lowdon, R., Elliott, G., Mercer, T.R., Neph, S.J., Onuchic, V., Polak, P., Rajagopal, N., Ray, P., Sallari, R.C., Siebenthall, K.T., Sinnott-Armstrong, N.A., Stevens, M., Thurman, R.E., Wu, J., Zhang, B., Zhou, X., Beaudet, A.E., Boyer, L.A., De Jager, P.L., Farnham, P.J., Fisher, S.J., Haussler, D., Jones, S.J., Li, W., Marra, M.A., McManus, M.T., Sunyaev, S., Thomson, J.A., Tlsty, T.D., Tsai, L.H., Wang, W., Waterland, R.A., Zhang, M.Q., Chadwick, L.H., Bernstein, B.E., Costello, J.F., Ecker, J.R., Hirst, M., Meissner, A., Milosavljevic, A., Ren, B., Stamatoyannopoulos, J.A., Wang, T., Kellis, M. Integrative analysis of 111 reference human epigenomes. (2015) Nature. 518(7539):317-30. DOI: 10.1038/nature14248

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O'Malley, R.C., Barragan, C.C., Ecker, J.R. A user's guide to the Arabidopsis T-DNA insertion mutant collections. (2015) Methods in Molecular Biology. 1284:323-42. DOI: 10.1007/978-1-4939-2444-8_16

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Lin, S., Lin, Y., Nery, J.R., Urich, M.A., Breschi, A., Davis, C.A., Dobin, A., Zaleski, C., Beer, M.A., Chapman, W.C., Gingeras, T.R., Ecker, J.R., Snyder, M.P. Comparison of the transcriptional landscapes between human and mouse tissues. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(48):17224-9. DOI: 10.1073/pnas.1413624111

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Yu, W., McIntosh, C., Lister, R., Zhu, I., Han, Y., Ren, J., Landsman, D., Lee, E., Briones, V., Terashima, M., Leighty, R., Ecker, J.R., Muegge, K. Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways. (2014) Genome Research. 24(10):1613-23. DOI: 10.1101/gr.172015.114

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Weirauch, M.T., Yang, A., Albu, M., Cote, A., Montenegro-Montero, A., Drewe, P., Najafabadi, H.S., Lambert, S.A., Mann, I., Cook, K., Zheng, H., Goity, A., van Bakel, H., Lozano, J.C., Galli, M., Lewsey, M., Huang, E., Mukherjee, T., Chen, X., Reece-Hoyes, J.S., Govindarajan, S., Shaulsky, G., Walhout, A.J.M., Bouget, F.Y., Ratsch, G., Larrondo, L.F., Ecker, J.R., Hughes, T.R. Determination and inference of eukaryotic transcription factor sequence specificity. (2014) Cell. 158(6):1431-1443. DOI: 10.1016/j.cell.2014.08.009

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Weßling, R., Epple, P., Altmann, S., He, Y., Yang, L., Henz, S.R., McDonald, N., Wiley, K., Bader, K.C., Gläßer, C., Mukhtar, M.S., Haigis, S., Ghamsari, L., Stephens, A.E., Ecker, J.R., Vidal, M., Jones, J.D., Mayer, K.F., Ver Loren van Themaat, E., Weigel, D., Schulze-Lefert, P., Dangl, J.L., Panstruga, R., Braun, P. Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. (2014) Cell Host & Microbe. 16(3):364-75. DOI: 10.1016/j.chom.2014.08.004

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Buganim, Y., Markoulaki, S., van Wietmarschen, N., Hoke, H., Wu, T., Ganz, K., Akhtar-Zaidi, B., He, Y., Abraham, B.J., Porubsky, D., Kulenkampff, E., Faddah, D.A., Shi, L., Gao, Q., Sarkar, S., Cohen, M., Goldmann, J., Nery, J.R., Schultz, M.D., Ecker, J.R., Xiao, A., Young, R.A., Lansdorp, P.M., Jaenisch, R. The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. (2014) Cell Stem Cell. 15(3):295-309. DOI: 10.1016/j.stem.2014.07.003

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Catalá, R., López-Cobollo, R., Mar Castellano, M., Angosto, T., Alonso, J.M., Ecker, J.R., Salinas, J. The Arabidopsis 14-3-3 protein RARE COLD INDUCIBLE 1A links low-temperature response and ethylene biosynthesis to regulate freezing tolerance and cold acclimation. (2014) Plant Cell. 26(8):3326-42. DOI: 10.1105/tpc.114.127605

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Pruneda-Paz, J.L., Breton, G., Nagel, D.H., Kang, S.E., Bonaldi, K., Doherty, C.J., Ravelo, S., Galli, M., Ecker, J.R., Kay, S.A. A genome-scale resource for the functional characterization of Arabidopsis transcription factors. (2014) Cell Reports. 8(2):622-32. DOI: 10.1016/j.celrep.2014.06.033

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Ma, H., Morey, R., O'Neil, R.C., He, Y., Daughtry, B., Schultz, M.D., Hariharan, M., Nery, J.R., Castanon, R., Sabatini, K., Thiagarajan, R.D., Tachibana, M., Kang, E., Tippner-Hedges, R., Ahmed, R., Gutierrez, N.M., Van Dyken, C., Polat, A., Sugawara, A., Sparman, M., Gokhale, S., Amato, P., Wolf, D.P., Ecker, J.R., Laurent, L.C., Mitalipov, S. Abnormalities in human pluripotent cells due to reprogramming mechanisms. (2014) Nature. 511(7508):177-83. DOI: 10.1038/nature13551

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Dinh, T.T., Gao, L., Liu, X., Li, D., Li, S., Zhao, Y., O'Leary, M., Le, B., Schmitz, R.J., Manavella, P.A., Manavella, P., Li, S., Weigel, D., Pontes, O., Ecker, J.R., Chen, X. DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. (2014) PLOS Genetics. 10(7):e1004446. DOI: 10.1371/journal.pgen.1004446

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Yu, W., Briones, V., Lister, R., McIntosh, C., Han, Y., Lee, E.Y., Ren, J., Terashima, M., Leighty, R.M., Ecker, J.R., Muegge, K. CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(16):5890-5. DOI: 10.1073/pnas.1320945111

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Looney, T.J., Zhang, L., Chen, C.H., Lee, J.H., Chari, S., Mao, F.F., Pelizzola, M., Zhang, L., Lister, R., Baker, S.W., Fernandes, C.J., Gaetz, J., Foshay, K.M., Clift, K.L., Zhang, Z., Li, W.Q., Vallender, E.J., Wagner, U., Qin, J.Y., Michelini, K.J., Bugarija, B., Park, D., Aryee, E., Stricker, T., Zhou, J., White, K.P., Ren, B., Schroth, G.P., Ecker, J.R., Xiang, A.P., Lahn, B.T. Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. (2014) Genome Research. 24(2):267-80. DOI: 10.1101/gr.143891.112

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Wang, T., Liu, J., Shen, L., Tonti-Filippini, J., Zhu, Y., Jia, H., Lister, R., Whitaker, J.W., Ecker, J.R., Millar, A.H., Ren, B., Wang, W. STAR: an integrated solution to management and visualization of sequencing data. (2013) Bioinformatics. 29(24):3204-10. DOI: 10.1093/bioinformatics/btt558

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Schmitz, R.J., He, Y., Valdés-López, O., Khan, S.M., Joshi, T., Urich, M.A., Nery, J.R., Diers, B., Xu, D., Stacey, G., Ecker, J.R. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. (2013) Genome Research. 23(10):1663-74. DOI: 10.1101/gr.152538.112

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Hua, Z., Pool, J.E., Schmitz, R.J., Schultz, M.D., Shiu, S.H., Ecker, J.R., Vierstra, R.D. Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(42):16927-32. DOI: 10.1073/pnas.1316009110

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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.*, Ecker, J.R.* Global epigenomic reconfiguration during mammalian brain development. (2013) Science. 341(6146):1237905. DOI: 10.1126/science.1237905

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Qiao, H., Shen, Z., Huang, S.S., Schmitz, R.J., Urich, M.A., Briggs, S.P., Ecker, J.R. Response to perspective: "separation anxiety: an analysis of ethylene-induced cleavage of EIN2". (2013) Plant Signaling & Behavior. 8(8). DOI: 10.4161/psb.25037

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Schweizer, F., Fernández-Calvo, P., Zander, M., Diez-Diaz, M., Fonseca, S., Glauser, G., Lewsey, M.G., Ecker, J.R., Solano, R., Reymond, P. Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. (2013) Plant Cell. 25(8):3117-32. DOI: 10.1105/tpc.113.115139

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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., Ecker, J.R. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. (2013) Elife. 2:e00675. DOI: 10.7554/eLife.00675

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Xie, W., Schultz, M.D., Lister, R., Hou, Z., Rajagopal, N., Ray, P., Whitaker, J.W., Tian, S., Hawkins, R.D., Leung, D., Yang, H., Wang, T., Lee, A.Y., Swanson, S.A., Zhang, J., Zhu, Y., Kim, A., Nery, J.R., Urich, M.A., Kuan, S., Yen, C.A., Klugman, S., Yu, P., Suknuntha, K., Propson, N.E., Chen, H., Edsall, L.E., Wagner, U., Li, Y., Ye, Z., Kulkarni, A., Xuan, Z., Chung, W.Y., Chi, N.C., Antosiewicz-Bourget, J.E., Slukvin, I., Stewart, R., Zhang, M.Q., Wang, W., Thomson, J.A., Ecker, J.R., Ren, B. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. (2013) Cell. 153(5):1134-48. DOI: 10.1016/j.cell.2013.04.022

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Hill, K., Mathews, D.E., Kim, H.J., Street, I.H., Wildes, S.L., Chiang, Y.H., Mason, M.G., Alonso, J.M., Ecker, J.R., Kieber, J.J., Schaller, G.E. Functional characterization of type-B response regulators in the Arabidopsis cytokinin response. (2013) Plant Physiology. 162(1):212-24. DOI: 10.1104/pp.112.208736

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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., Ecker, J.R. Patterns of population epigenomic diversity. (2013) Nature. 495(7440):193-8. DOI: 10.1038/nature11968

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Ecker, J.R. Epigenetic trigger for tomato ripening. (2013) Nature Biotechnology. 31(2):119-20. DOI: 10.1038/nbt.2497


Woodson, J.D., Perez-Ruiz, J.M., Schmitz, R.J., Ecker, J.R., Chory, J. Sigma factor-mediated plastid retrograde signals control nuclear gene expression. (2013) Plant Journal. 73(1):1-13. DOI: 10.1111/tpj.12011

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O'Malley, R.C., Ecker, J.R. Epiallelic variation in Arabidopsis thaliana. (2012) Cold Spring Harbor Symposia on Quantitative Biology. 77:135-45. DOI: 10.1101/sqb.2012.77.014571

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Vollmers, C., Schmitz, R.J., Nathanson, J., Yeo, G., Ecker, J.R., Panda, S. Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. (2012) Cell Metabolism. 16(6):833-45. DOI: 10.1016/j.cmet.2012.11.004

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Beck, S., Bernstein, B.E., Campbell, R.M., Costello, J.F., Dhanak, D., Ecker, J.R., Greally, J.M., Issa, J.P., Laird, P.W., Polyak, K., Tycko, B., Jones, P.A., AACR Cancer Epigenome Task Force A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. (2012) Cancer Research. 72(24):6319-24. DOI: 10.1158/0008-5472.CAN-12-3658


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Qiao, H., Shen, Z., Huang, S.S., Schmitz, R.J., Urich, M.A., Briggs, S.P., Ecker, J.R. Processing and subcellular trafficking of ER-tethered EIN2 control response to ethylene gas. (2012) Science. 338(6105):390-3. DOI: 10.1126/science.1225974

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Ecker, J.R., Bickmore, W.A., Barroso, I., Pritchard, J.K., Gilad, Y., Segal, E. Genomics: ENCODE explained. (2012) Nature. 489(7414):52-5. DOI: 10.1038/489052a


Dowen, R.H., Pelizzola, M., Schmitz, R.J., Lister, R., Dowen, J.M., Nery, J.R., Dixon, J.E., Ecker, J.R. Widespread dynamic DNA methylation in response to biotic stress. (2012) Proceedings of the National Academy of Sciences of the United States of America. 109(32):E2183-91. DOI: 10.1073/pnas.1209329109

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Johnson, D.B., Wang, C., Xu, J., Schultz, M.D., Schmitz, R.J., Ecker, J.R., Wang, L. Release factor one is nonessential in Escherichia coli. (2012) ACS Chem. Biol. 7(8):1337-44. DOI: 10.1021/cb300229q

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Wierzbicki, A.T., Cocklin, R., Mayampurath, A., Lister, R., Rowley, M.J., Gregory, B.D., Ecker, J.R., Tang, H., Pikaard, C.S. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. (2012) Genes & Development. 26(16):1825-36. DOI: 10.1101/gad.197772.112

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Peng, Q., Ecker, J.R. Detection of allele-specific methylation through a generalized heterogeneous epigenome model. (2012) Bioinformatics. 28(12):i163-71. DOI: 10.1093/bioinformatics/bts231

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Li, L., Ljung, K., Breton, G., Schmitz, R.J., Pruneda-Paz, J., Cowing-Zitron, C., Cole, B.J., Ivans, L.J., Pedmale, U.V., Jung, H.S., Ecker, J.R., Kay, S.A., Chory, J. Linking photoreceptor excitation to changes in plant architecture. (2012) Genes & Development. 26(8):785-90. DOI: 10.1101/gad.187849.112

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Kurihara, Y., Schmitz, R.J., Nery, J.R., Schultz, M.D., Okubo-Kurihara, E., Morosawa, T., Tanaka, M., Toyoda, T., Seki, M., Ecker, J.R. Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis. (2012) G3. 2(4):487-98. DOI: 10.1534/g3.111.001362

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Schmitz, R.J., Ecker, J.R. Epigenetic and epigenomic variation in Arabidopsis thaliana. (2012) Trends in Plant Science. 17(3):149-54. DOI: 10.1016/j.tplants.2012.01.001

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Hon, G.C., Hawkins, R.D., Caballero, O.L., Lo, C., Lister, R., Pelizzola, M., Valsesia, A., Ye, Z., Kuan, S., Edsall, L.E., Camargo, A.A., Stevenson, B.J., Ecker, J.R., Bafna, V., Strausberg, R.L., Simpson, A.J., Ren, B. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. (2012) Genome Research. 22(2):246-58. DOI: 10.1101/gr.125872.111

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Hotto, A.M., Schmitz, R.J., Fei, Z., Ecker, J.R., Stern, D.B. Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome. (2011) G3. 1(7):559-70. DOI: 10.1534/g3.111.000752

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Elling, U., Taubenschmid, J., Wirnsberger, G., O'Malley, R., Demers, S.P., Vanhaelen, Q., Shukalyuk, A.I., Schmauss, G., Schramek, D., Schnuetgen, F., von Melchner, H., Ecker, J.R., Stanford, W.L., Zuber, J., Stark, A., Penninger, J.M. Forward and reverse genetics through derivation of haploid mouse embryonic stem cells. (2011) Cell Stem Cell. 9(6):563-74. DOI: 10.1016/j.stem.2011.10.012

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Schmitz, R.J., Schultz, M.D., Lewsey, M.G., O'Malley, R.C., Urich, M.A., Libiger, O., Schork, N.J., Ecker, J.R. Transgenerational epigenetic instability is a source of novel methylation variants. (2011) Science. 334(6054):369-73. DOI: 10.1126/science.1212959

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Johnson, D.B., Xu, J., Shen, Z., Takimoto, J.K., Schultz, M.D., Schmitz, R.J., Xiang, Z., Ecker, J.R., Briggs, S.P., Wang, L. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. (2011) Nature Chemical Biology. 7(11):779-86. DOI: 10.1038/nchembio.657

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Pelizzola, M., Ecker, J.R. The DNA methylome. (2011) FEBS Lett. 585(13):1994-2000. DOI: 10.1016/j.febslet.2010.10.061

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Mukhtar, M.S., Carvunis, A.R., Dreze, M., Epple, P., Steinbrenner, J., Moore, J., Tasan, 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. Independently evolved virulence effectors converge onto hubs in a plant immune system network. (2011) Science. 333(6042):596-601. DOI: 10.1126/science.1203659

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Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. (2011) Science. 333(6042):601-7. DOI: 10.1126/science.1203877

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Pastor, W.A., Pape, U.J., Huang, Y., Henderson, H.R., Lister, R., Ko, M., McLoughlin, E.M., Brudno, Y., Mahapatra, S., Kapranov, P., Tahiliani, M., Daley, G.Q., Liu, X.S., Ecker, J.R., Milos, P.M., Agarwal, S., Rao, A. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. (2011) Nature. 473(7347):394-7. DOI: 10.1038/nature10102

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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., Ecker, J.R. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. (2011) Nature. 471(7336):68-73. DOI: 10.1038/nature09798

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Bernstein, B.E., Stamatoyannopoulos, J.A., Costello, J.F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M.A., Beaudet, A.L., Ecker, J.R., Farnham, P.J., Hirst, M., Lander, E.S., Mikkelsen, T.S., Thomson, J.A. The NIH Roadmap Epigenomics Mapping Consortium. (2010) Nature Biotechnology. 28(10):1045-8. DOI: 10.1038/nbt1010-1045

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Harris, R.A., Wang, T., Coarfa, C., Nagarajan, R.P., Hong, C., Downey, S.L., Johnson, B.E., Fouse, S.D., Delaney, A., Zhao, Y., Olshen, A., Ballinger, T., Zhou, X., Forsberg, K.J., Gu, J., Echipare, L., O'Geen, H., Lister, R., Pelizzola, M., Xi, Y., Epstein, C.B., Bernstein, B.E., Hawkins, R.D., Ren, B., Chung, W.Y., Gu, H., Bock, C., Gnirke, A., Zhang, M.Q., Haussler, D., Ecker, J.R., Li, W., Farnham, P.J., Waterland, R.A., Meissner, A., Marra, M.A., Hirst, M., Milosavljevic, A., Costello, J.F. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. (2010) Nature Biotechnology. 28(10):1097-105. DOI: 10.1038/nbt.1682

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Boutrot, F., Segonzac, C., Chang, K.N., Qiao, H., Ecker, J.R., Zipfel, C., Rathjen, J.P. Direct transcriptional control of the Arabidopsis immune receptor FLS2 by the ethylene-dependent transcription factors EIN3 and EIL1. (2010) Proceedings of the National Academy of Sciences of the United States of America. 107(32):14502-7. DOI: 10.1073/pnas.1003347107

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An, F., Zhao, Q., Ji, Y., Li, W., Jiang, Z., Yu, X., Zhang, C., Han, Y., He, W., Liu, Y., Zhang, S., Ecker, J.R., Guo, H. 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. (2010) Plant Cell. 22(7):2384-401. DOI: 10.1105/tpc.110.076588

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Atwell, S., Huang, Y.S., Vilhjálmsson, B.J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A.M., Hu, T.T., Jiang, R., Muliyati, N.W., Zhang, X., Amer, M.A., Baxter, I., Brachi, B., Chory, J., Dean, C., Debieu, M., de Meaux, J., Ecker, J.R., Faure, N., Kniskern, J.M., Jones, J.D., Michael, T., Nemri, A., Roux, F., Salt, D.E., Tang, C., Todesco, M., Traw, M.B., Weigel, D., Marjoram, P., Borevitz, J.O., Bergelson, J., Nordborg, M. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. (2010) Nature. 465(7298):627-31. DOI: 10.1038/nature08800

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Ecker, J.R. Zeroing in on DNA methylomes with no BS. (2010) Nature Methods. 7(6):435-7. DOI: 10.1038/nmeth0610-435


Hawkins, R.D., Hon, G.C., Lee, L.K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L.E., Kuan, S., Luu, Y., Klugman, S., Antosiewicz-Bourget, J., Ye, Z., Espinoza, C., Agarwahl, S., Shen, L., Ruotti, V., Wang, W., Stewart, R., Thomson, J.A., Ecker, J.R., Ren, B. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. (2010) Cell Stem Cell. 6(5):479-91. DOI: 10.1016/j.stem.2010.03.018

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O'Malley, R.C., Ecker, J.R. Linking genotype to phenotype using the Arabidopsis unimutant collection. (2010) Plant Journal. 61(6):928-40. DOI: 10.1111/j.1365-313X.2010.04119.x

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Endres, M.W., Gregory, B.D., Gao, Z., Foreman, A.W., Mlotshwa, S., Ge, X., Pruss, G.J., Ecker, J.R., Bowman, L.H., Vance, V. Two plant viral suppressors of silencing require the ethylene-inducible host transcription factor RAV2 to block RNA silencing. (2010) PLOS pathogens. 6(1):e1000729. DOI: 10.1371/journal.ppat.1000729

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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., Ecker, J.R. Human DNA methylomes at base resolution show widespread epigenomic differences. (2009) Nature. 462(7271):315-22. DOI: 10.1038/nature08514

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Tsuchisaka, A., Yu, G., Jin, H., Alonso, J.M., Ecker, J.R., Zhang, X., Gao, S., Theologis, A. A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana. (2009) Genetics. 183(3):979-1003. DOI: 10.1534/genetics.109.107102

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97. Toronto International Data Release Workshop Au, Birney, E., Hudson, T.J., Green, E.D., Gunter, C., Eddy, S., Rogers, J., Harris, J.R., Ehrlich, S.D., Apweiler, R., Austin, C.P., Berglund, L., Bobrow, M., Bountra, C., Brookes, A.J., Cambon-Thomsen, A., Carter, N.P., Chisholm, R.L., Contreras, J.L., Cooke, R.M., Crosby, W.L., Dewar, K., Durbin, R., Dyke, S.O., Ecker, J.R., El Emam, K., Feuk, L., Gabriel, S.B., Gallacher, J., Gelbart, W.M., Granell, A., Guarner, F., Hubbard, T., Jackson, S.A., Jennings, J.L., Joly, Y., Jones, S.M., Kaye, J., Kennedy, K.L., Knoppers, B.M., Kyrpides, N.C., Lowrance, W.W., Luo, J., MacKay, J.J., Martín-Rivera, L., McCombie, W.R., McPherson, J.D., Miller, L., Miller, W., Moerman, D., Mooser, V., Morton, C.C., Ostell, J.M., Ouellette, B.F., Parkhill, J., Raina, P.S., Rawlings, C., Scherer, S.E., Scherer, S.W., Schofield, P.N., Sensen, C.W., Stodden, V.C., Sussman, M.R., Tanaka, T., Thornton, J., Tsunoda, T., Valle, D., Vuorio, E.I., Walker, N.M., Wallace, S., Weinstock, G., Whitman, W.B., Worley, K.C., Wu, C., Wu, J., Yu, J. Prepublication data sharing. (2009) Nature. 461(7261):168-70. DOI: 10.1038/461168a

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Lister, R., Ecker, J.R. Finding the fifth base: genome-wide sequencing of cytosine methylation. (2009) Genome Research. 19(6):959-66. DOI: 10.1101/gr.083451.108

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Liljegren, S.J., Leslie, M.E., Darnielle, L., Lewis, M.W., Taylor, S.M., Luo, R., Geldner, N., Chory, J., Randazzo, P.A., Yanofsky, M.F., Ecker, J.R. Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein. (2009) Development. 136(11):1909-18. DOI: 10.1242/dev.033605

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Dowen, R.H., Engel, J.L., Shao, F., Ecker, J.R., Dixon, J.E. A family of bacterial cysteine protease type III effectors utilizes acylation-dependent and -independent strategies to localize to plasma membranes. (2009) Journal of Biological Chemistry. 284(23):15867-79. DOI: 10.1074/jbc.M900519200

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Lister, R., Gregory, B.D., Ecker, J.R. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. (2009) Current Opinion in Plant Biology. 12(2):107-18. DOI: 10.1016/j.pbi.2008.11.004

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Qiao, H., Chang, K.N., Yazaki, J., Ecker, J.R. Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis. (2009) Genes & Development. 23(4):512-21. DOI: 10.1101/gad.1765709

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Hazen, S.P., Naef, F., Quisel, T., Gendron, J.M., Chen, H., Ecker, J.R., Borevitz, J.O., Kay, S.A. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. (2009) Genome Biology. 10(2):R17. DOI: 10.1186/gb-2009-10-2-r17

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Cusick, M.E., Yu, H., Smolyar, A., Venkatesan, K., Carvunis, A.R., Simonis, N., Rual, J.F., Borick, H., Braun, P., Dreze, M., Vandenhaute, J., Galli, M., Yazaki, J., Hill, D.E., Ecker, J.R., Roth, F.P., Vidal, M. Literature-curated protein interaction datasets. (2009) Nature Methods. 6(1):39-46. DOI: 10.1038/nmeth.1284

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Gregory, B.D., O'Malley, R.C., Lister, R., Urich, M.A., Tonti-Filippini, J., Chen, H., Millar, A.H., Ecker, J.R. A link between RNA metabolism and silencing affecting Arabidopsis development. (2008) Developmental Cell. 14(6):854-66. DOI: 10.1016/j.devcel.2008.04.005

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Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H., Ecker, J.R. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. (2008) Cell. 133(3):523-36. DOI: 10.1016/j.cell.2008.03.029

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Gregory, B.D., Yazaki, J., Ecker, J.R. Utilizing tiling microarrays for whole-genome analysis in plants. (2008) Plant Journal. 53(4):636-44. DOI: 10.1111/j.1365-313X.2007.03320.x

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Hu, J., Mitchum, M.G., Barnaby, N., Ayele, B.T., Ogawa, M., Nam, E., Lai, W.C., Hanada, A., Alonso, J.M., Ecker, J.R., Swain, S.M., Yamaguchi, S., Kamiya, Y., Sun, T.P. Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. (2008) Plant Cell. 20(2):320-36. DOI: 10.1105/tpc.107.057752

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Leivar, P., Monte, E., Al-Sady, B., Carle, C., Storer, A., Alonso, J.M., Ecker, J.R., Quail, P.H. The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. (2008) Plant Cell. 20(2):337-52. DOI: 10.1105/tpc.107.052142

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Chekanova, J.A., Gregory, B.D., Reverdatto, S.V., Chen, H., Kumar, R., Hooker, T., Yazaki, J., Li, P., Skiba, N., Peng, Q., Alonso, J., Brukhin, V., Grossniklaus, U., Ecker, J.R., Belostotsky, D.A. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. (2007) Cell. 131(7):1340-53. DOI: 10.1016/j.cell.2007.10.056

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Yazaki, J., Gregory, B.D., Ecker, J.R. Mapping the genome landscape using tiling array technology. (2007) Current Opinion in Plant Biology. 10(5):534-42. DOI: 10.1016/j.pbi.2007.07.006

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Kim, S., Plagnol, V., Hu, T.T., Toomajian, C., Clark, R.M., Ossowski, S., Ecker, J.R., Weigel, D., Nordborg, M. Recombination and linkage disequilibrium in Arabidopsis thaliana. (2007) Nature Genetics. 39(9):1151-5. DOI: 10.1038/ng2115

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Li, H., He, Z., Lu, G., Lee, S.C., Alonso, J., Ecker, J.R., Luan, S. A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. (2007) Plant Cell. 19(8):2403-16. DOI: 10.1105/tpc.107.053579

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Borevitz, J.O., Hazen, S.P., Michael, T.P., Morris, G.P., Baxter, I.R., Hu, T.T., Chen, H., Werner, J.D., Nordborg, M., Salt, D.E., Kay, S.A., Chory, J., Weigel, D., Jones, J.D., Ecker, J.R. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. (2007) Proceedings of the National Academy of Sciences of the United States of America. 104(29):12057-62. DOI: 10.1073/pnas.0705323104

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Gentry, M.S., Dowen, R.H., Worby, C.A., Mattoo, S., Ecker, J.R., Dixon, J.E. The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease. (2007) Journal of Cell Biology. 178(3):477-88. DOI: 10.1083/jcb.200704094

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Clark, R.M., 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., Weigel, D. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. (2007) Science. 317(5836):338-42. DOI: 10.1126/science.1138632

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Puig, S., Mira, H., Dorcey, E., Sancenón, V., Andrés-Colás, N., Garcia-Molina, A., Burkhead, J.L., Gogolin, K.A., Abdel-Ghany, S.E., Thiele, D.J., Ecker, J.R., Pilon, M., Peñarrubia, L. Higher plants possess two different types of ATX1-like copper chaperones. (2007) Biochemical and Biophysical Research Communications. 354(2):385-90. DOI: 10.1016/j.bbrc.2006.12.215

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Swiezewski, S., Crevillen, P., Liu, F., Ecker, J.R., Jerzmanowski, A., Dean, C. Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC. (2007) Proceedings of the National Academy of Sciences of the United States of America. 104(9):3633-8. DOI: 10.1073/pnas.0611459104

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O'Malley, R.C., Alonso, J.M., Kim, C.J., Leisse, T.J., Ecker, J.R. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. (2007) Nature Protocols. 2(11):2910-7. DOI: 10.1038/nprot.2007.425

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Chilley, P.M., Casson, S.A., Tarkowski, P., Hawkins, N., Wang, K.L., Hussey, P.J., Beale, M., Ecker, J.R., Sandberg, G.K., Lindsey, K. The POLARIS peptide of Arabidopsis regulates auxin transport and root growth via effects on ethylene signaling. (2006) Plant Cell. 18(11):3058-72. DOI: 10.1105/tpc.106.040790

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Hutchison, C.E., Li, J., Argueso, C., Gonzalez, M., Lee, E., Lewis, M.W., Maxwell, B.B., Perdue, T.D., Schaller, G.E., Alonso, J.M., Ecker, J.R., Kieber, J.J. The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling. (2006) Plant Cell. 18(11):3073-87. DOI: 10.1105/tpc.106.045674

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Kim, S.A., Punshon, T., Lanzirotti, A., Li, L., Alonso, J.M., Ecker, J.R., Kaplan, J., Guerinot, M.L. Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1. (2006) Science. 314(5803):1295-8. DOI: 10.1126/science.1132563

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Mori, I.C., Murata, Y., Yang, Y., Munemasa, S., Wang, Y.F., Andreoli, S., Tiriac, H., Alonso, J.M., Harper, J.F., Ecker, J.R., Kwak, J.M., Schroeder, J.I. CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion- and Ca(2+)-permeable channels and stomatal closure. (2006) PLOS Biology. 4(10):e327. DOI: 10.1371/journal.pbio.0040327

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Yoshida, H., Wang, K.L., Chang, C.M., Mori, K., Uchida, E., Ecker, J.R. The ACC synthase TOE sequence is required for interaction with ETO1 family proteins and destabilization of target proteins. (2006) Plant Molecular Biology. 62(3):427-37. DOI: 10.1007/s11103-006-9029-7

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Olmedo, G., Guo, H., Gregory, B.D., Nourizadeh, S.D., Aguilar-Henonin, L., Li, H., An, F., Guzman, P., Ecker, J.R. ETHYLENE-INSENSITIVE5 encodes a 5'-->3' exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103(36):13286-93. DOI: 10.1073/pnas.0605528103

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Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S.W., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E., Ecker, J.R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. (2006) Cell. 126(6):1189-201. DOI: 10.1016/j.cell.2006.08.003

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Barr, S.D., Ciuffi, A., Leipzig, J., Shinn, P., Ecker, J.R., Bushman, F.D. HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry. (2006) Mol. Ther. 14(2):218-25. DOI: 10.1016/j.ymthe.2006.03.012

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Chen, J.G., Ullah, H., Temple, B., Liang, J., Guo, J., Alonso, J.M., Ecker, J.R., Jones, A.M. RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis. (2006) J. Exp. Bot. 57(11):2697-708. DOI: 10.1093/jxb/erl035

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Rudella, A., Friso, G., Alonso, J.M., Ecker, J.R., van Wijk, K.J. Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis. (2006) Plant Cell. 18(7):1704-21. DOI: 10.1105/tpc.106.042861

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Alonso, J.M., Ecker, J.R. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. (2006) Nature Reviews. Genetics. 7(7):524-36. DOI: 10.1038/nrg1893

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Lewinski, M.K., Yamashita, M., Emerman, M., Ciuffi, A., Marshall, H., Crawford, G., Collins, F., Shinn, P., Leipzig, J., Hannenhalli, S., Berry, C.C., Ecker, J.R., Bushman, F.D. Retroviral DNA integration: viral and cellular determinants of target-site selection. (2006) PLOS pathogens. 2(6):e60. DOI: 10.1371/journal.ppat.0020060

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Lariguet, P., Schepens, I., Hodgson, D., Pedmale, U.V., Trevisan, M., Kami, C., de Carbonnel, M., Alonso, J.M., Ecker, J.R., Liscum, E., Fankhauser, C. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism. (2006) Proceedings of the National Academy of Sciences of the United States of America. 103(26):10134-9. DOI: 10.1073/pnas.0603799103

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Ciuffi, A., Mitchell, R.S., Hoffmann, C., Leipzig, J., Shinn, P., Ecker, J.R., Bushman, F.D. Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts. (2006) Mol. Ther. 13(2):366-73. DOI: 10.1016/j.ymthe.2005.10.009

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Andrés-Colás, N., Sancenón, V., Rodríguez-Navarro, S., Mayo, S., Thiele, D.J., Ecker, J.R., Puig, S., Peñarrubia, L. The Arabidopsis heavy metal P-type ATPase HMA5 interacts with metallochaperones and functions in copper detoxification of roots. (2006) Plant Journal. 45(2):225-36. DOI: 10.1111/j.1365-313X.2005.02601.x

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Ciuffi, A., Llano, M., Poeschla, E., Hoffmann, C., Leipzig, J., Shinn, P., Ecker, J.R., Bushman, F. A role for LEDGF/p75 in targeting HIV DNA integration. (2005) Nature Medicine. 11(12):1287-9. DOI: 10.1038/nm1329

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Overvoorde, P.J., Okushima, Y., Alonso, J.M., Chan, A., Chang, C., Ecker, J.R., Hughes, B., Liu, A., Onodera, C., Quach, H., Smith, A., Yu, G., Theologis, A. Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana. (2005) Plant Cell. 17(12):3282-300. DOI: 10.1105/tpc.105.036723

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Mason, M.G., Mathews, D.E., Argyros, D.A., Maxwell, B.B., Kieber, J.J., Alonso, J.M., Ecker, J.R., Schaller, G.E. Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. (2005) Plant Cell. 17(11):3007-18. DOI: 10.1105/tpc.105.035451

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Nagpal, P., Ellis, C.M., Weber, H., Ploense, S.E., Barkawi, L.S., Guilfoyle, T.J., Hagen, G., Alonso, J.M., Cohen, J.D., Farmer, E.E., Ecker, J.R., Reed, J.W. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. (2005) Development. 132(18):4107-18. DOI: 10.1242/dev.01955

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Barr, S.D., Leipzig, J., Shinn, P., Ecker, J.R., Bushman, F.D. Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome. (2005) Journal of Virology. 79(18):12035-44. DOI: 10.1128/JVI.79.18.12035-12044.2005

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Yoshida, H., Nagata, M., Saito, K., Wang, K.L., Ecker, J.R. Arabidopsis ETO1 specifically interacts with and negatively regulates type 2 1-aminocyclopropane-1-carboxylate synthases. (2005) BMC Plant Biology. 5:14. DOI: 10.1186/1471-2229-5-14

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Werner, J.D., Borevitz, J.O., Uhlenhaut, N.H., Ecker, J.R., Chory, J., Weigel, D. FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions. (2005) Genetics. 170(3):1197-207. DOI: 10.1534/genetics.104.036533

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Hazen, S.P., Schultz, T.F., Pruneda-Paz, J.L., Borevitz, J.O., Ecker, J.R., Kay, S.A. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. (2005) Proceedings of the National Academy of Sciences of the United States of America. 102(29):10387-92. DOI: 10.1073/pnas.0503029102

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Wilmoth, J.C., Wang, S., Tiwari, S.B., Joshi, A.D., Hagen, G., Guilfoyle, T.J., Alonso, J.M., Ecker, J.R., Reed, J.W. NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. (2005) Plant Journal. 43(1):118-30. DOI: 10.1111/j.1365-313X.2005.02432.x

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Lewinski, M.K., Bisgrove, D., Shinn, P., Chen, H., Hoffmann, C., Hannenhalli, S., Verdin, E., Berry, C.C., Ecker, J.R., Bushman, F.D. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. (2005) Journal of Virology. 79(11):6610-9. DOI: 10.1128/JVI.79.11.6610-6619.2005

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Hazen, S.P., Borevitz, J.O., Harmon, F.G., Pruneda-Paz, J.L., Schultz, T.F., Yanovsky, M.J., Liljegren, S.J., Ecker, J.R., Kay, S.A. Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. (2005) Plant Physiology. 138(2):990-7. DOI: 10.1104/pp.105.061408

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Zhang, X., Odom, D.T., Koo, S.H., Conkright, M.D., Canettieri, G., Best, J., Chen, H., Jenner, R., Herbolsheimer, E., Jacobsen, E., Kadam, S., Ecker, J.R., Emerson, B., Hogenesch, J.B., Unterman, T., Young, R.A., Montminy, M. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. (2005) Proceedings of the National Academy of Sciences of the United States of America. 102(12):4459-64. DOI: 10.1073/pnas.0501076102

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Werner, J.D., Borevitz, J.O., Warthmann, N., Trainer, G.T., Ecker, J.R., Chory, J., Weigel, D. Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation. (2005) Proceedings of the National Academy of Sciences of the United States of America. 102(7):2460-5. DOI: 10.1073/pnas.0409474102

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Ryu, J.S., Kim, J.I., Kunkel, T., Kim, B.C., Cho, D.S., Hong, S.H., Kim, S.H., Fernández, A.P., Kim, Y., Alonso, J.M., Ecker, J.R., Nagy, F., Lim, P.O., Song, P.S., Schäfer, E., Nam, H.G. Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer. (2005) Cell. 120(3):395-406. DOI: 10.1016/j.cell.2004.12.019

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Okushima, Y., Overvoorde, P.J., Arima, K., Alonso, J.M., Chan, A., Chang, C., Ecker, J.R., Hughes, B., Lui, A., Nguyen, D., Onodera, C., Quach, H., Smith, A., Yu, G., Theologis, A. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. (2005) Plant Cell. 17(2):444-63. DOI: 10.1105/tpc.104.028316

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Mockler, T.C., Chan, S., Sundaresan, A., Chen, H., Jacobsen, S.E., Ecker, J.R. Applications of DNA tiling arrays for whole-genome analysis. (2005) Genomics. 85(1):1-15. DOI: 10.1016/j.ygeno.2004.10.005

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Liu, G., Holub, E.B., Alonso, J.M., Ecker, J.R., Fobert, P.R. An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance. (2005) Plant Journal. 41(2):304-18. DOI: 10.1111/j.1365-313X.2004.02296.x

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Prigge, M.J., Otsuga, D., Alonso, J.M., Ecker, J.R., Drews, G.N., Clark, S.E. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. (2005) Plant Cell. 17(1):61-76. DOI: 10.1105/tpc.104.026161

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Monte, E., Tepperman, J.M., Al-Sady, B., Kaczorowski, K.A., Alonso, J.M., Ecker, J.R., Li, X., Zhang, Y., Quail, P.H. The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(46):16091-8. DOI: 10.1073/pnas.0407107101

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Shibuya, K., Barry, K.G., Ciardi, J.A., Loucas, H.M., Underwood, B.A., Nourizadeh, S., Ecker, J.R., Klee, H.J., Clark, D.G. The central role of PhEIN2 in ethylene responses throughout plant development in petunia. (2004) Plant Physiology. 136(2):2900-12. DOI: 10.1104/pp.104.046979

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Binder, B.M., Mortimore, L.A., Stepanova, A.N., Ecker, J.R., Bleecker, A.B. Short-term growth responses to ethylene in Arabidopsis seedlings are EIN3/EIL1 independent. (2004) Plant Physiology. 136(2):2921-7. DOI: 10.1104/pp.104.050393

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Mockler, T.C., Yu, X., Shalitin, D., Parikh, D., Michael, T.P., Liou, J., Huang, J., Smith, Z., Alonso, J.M., Ecker, J.R., Chory, J., Lin, C. Regulation of flowering time in Arabidopsis by K homology domain proteins. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(34):12759-64. DOI: 10.1073/pnas.0404552101

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Li, H., Johnson, P., Stepanova, A., Alonso, J.M., Ecker, J.R. Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. (2004) Developmental Cell. 7(2):193-204. DOI: 10.1016/j.devcel.2004.07.002

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Mitchell, R.S., Beitzel, B.F., Schroder, A.R., Shinn, P., Chen, H., Berry, C.C., Ecker, J.R., Bushman, F.D. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. (2004) PLOS Biology. 2(8):E234. DOI: 10.1371/journal.pbio.0020234

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Page, M.L., Hamel, P.P., Gabilly, S.T., Zegzouti, H., Perea, J.V., Alonso, J.M., Ecker, J.R., Theg, S.M., Christensen, S.K., Merchant, S. A homolog of prokaryotic thiol disulfide transporter CcdA is required for the assembly of the cytochrome b6f complex in Arabidopsis chloroplasts. (2004) Journal of Biological Chemistry. 279(31):32474-82. DOI: 10.1074/jbc.M404285200

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Wolyn, D.J., Borevitz, J.O., Loudet, O., Schwartz, C., Maloof, J., Ecker, J.R., Berry, C.C., Chory, J. Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. (2004) Genetics. 167(2):907-17. DOI: 10.1534/genetics.103.024810

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Pfund, C., Tans-Kersten, J., Dunning, F.M., Alonso, J.M., Ecker, J.R., Allen, C., Bent, A.F. Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana. (2004) Molecular Plant-Microbe Interactions. 17(6):696-706. DOI: 10.1094/MPMI.2004.17.6.696

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Chen, J.G., Pandey, S., Huang, J., Alonso, J.M., Ecker, J.R., Assmann, S.M., Jones, A.M. GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination. (2004) Plant Physiology. 135(2):907-15. DOI: 10.1104/pp.104.038992

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Tyler, L., Thomas, S.G., Hu, J., Dill, A., Alonso, J.M., Ecker, J.R., Sun, T.P. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. (2004) Plant Physiology. 135(2):1008-19. DOI: 10.1104/pp.104.039578

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Wang, K.L., Yoshida, H., Lurin, C., Ecker, J.R. Regulation of ethylene gas biosynthesis by the Arabidopsis ETO1 protein. (2004) Nature. 428(6986):945-50. DOI: 10.1038/nature02516

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Novillo, F., Alonso, J.M., Ecker, J.R., Salinas, J. CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. (2004) Proceedings of the National Academy of Sciences of the United States of America. 101(11):3985-90. DOI: 10.1073/pnas.0303029101

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To, J.P., Haberer, G., Ferreira, F.J., Deruère, J., Mason, M.G., Schaller, G.E., Alonso, J.M., Ecker, J.R., Kieber, J.J. Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling. (2004) Plant Cell. 16(3):658-71. DOI: 10.1105/tpc.018978

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Guo, H., Ecker, J.R. The ethylene signaling pathway: new insights. (2004) Current Opinion in Plant Biology. 7(1):40-9.

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Borevitz, J.O., Ecker, J.R. Plant genomics: the third wave. (2004) Annual Review of Genomics and Human Genetics. 5:443-77. DOI: 10.1146/annurev.genom.5.061903.180017

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Guo, H., Ecker, J.R. Plant responses to ethylene gas are mediated by SCF(EBF1/EBF2)-dependent proteolysis of EIN3 transcription factor. (2003) Cell. 115(6):667-77.

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Lariguet, P., Boccalandro, H.E., Alonso, J.M., Ecker, J.R., Chory, J., Casal, J.J., Fankhauser, C. A growth regulatory loop that provides homeostasis to phytochrome a signaling. (2003) Plant Cell. 15(12):2966-78. DOI: 10.1105/tpc.014563

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Catala, R., Santos, E., Alonso, J.M., Ecker, J.R., Martinez-Zapater, J.M., Salinas, J. Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis. (2003) Plant Cell. 15(12):2940-51. DOI: 10.1105/tpc.015248

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Michael, T.P., Salomé, P.A., Yu, H.J., Spencer, T.R., Sharp, E.L., McPeek, M.A., Alonso, J.M., Ecker, J.R., McClung, C.R. Enhanced fitness conferred by naturally occurring variation in the circadian clock. (2003) Science. 302(5647):1049-53. DOI: 10.1126/science.1082971

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Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Wu, H.C., Kim, C., Nguyen, M., Pham, P., Cheuk, R., Karlin-Newmann, G., Liu, S.X., Lam, B., Sakano, H., Wu, T., Yu, G., Miranda, M., Quach, H.L., Tripp, M., Chang, C.H., Lee, J.M., Toriumi, M., Chan, M.M., Tang, C.C., Onodera, C.S., Deng, J.M., Akiyama, K., Ansari, Y., Arakawa, T., Banh, J., Banno, F., Bowser, L., Brooks, S., Carninci, P., Chao, Q., Choy, N., Enju, A., Goldsmith, A.D., Gurjal, M., Hansen, N.F., Hayashizaki, Y., Johnson-Hopson, C., Hsuan, V.W., Iida, K., Karnes, M., Khan, S., Koesema, E., Ishida, J., Jiang, P.X., Jones, T., Kawai, J., Kamiya, A., Meyers, C., Nakajima, M., Narusaka, M., Seki, M., Sakurai, T., Satou, M., Tamse, R., Vaysberg, M., Wallender, E.K., Wong, C., Yamamura, Y., Yuan, S., Shinozaki, K., Davis, R.W., Theologis, A., Ecker, J.R. Empirical analysis of transcriptional activity in the Arabidopsis genome. (2003) Science. 302(5646):842-6. DOI: 10.1126/science.1088305

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Monte, E., Alonso, J.M., Ecker, J.R., Zhang, Y., Li, X., Young, J., Austin-Phillips, S., Quail, P.H. Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. (2003) Plant Cell. 15(9):1962-80.

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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., Ecker, J.R. Genome-wide insertional mutagenesis of Arabidopsis thaliana. (2003) Science. 301(5633):653-7. DOI: 10.1126/science.1086391

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Jones, A.M., Ecker, J.R., Chen, J.G. A reevaluation of the role of the heterotrimeric G protein in coupling light responses in Arabidopsis. (2003) Plant Physiology. 131(4):1623-7. DOI: 10.1104/pp.102.017624

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Alonso, J.M., Stepanova, A.N., Solano, R., Wisman, E., Ferrari, S., Ausubel, F.M., Ecker, J.R. Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. (2003) Proceedings of the National Academy of Sciences of the United States of America. 100(5):2992-7. DOI: 10.1073/pnas.0438070100

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Larkin, R.M., Alonso, J.M., Ecker, J.R., Chory, J. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. (2003) Science. 299(5608):902-6. DOI: 10.1126/science.1079978

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Mackey, D., Belkhadir, Y., Alonso, J.M., Ecker, J.R., Dangl, J.L. Arabidopsis RIN4 is a target of the type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance. (2003) Cell. 112(3):379-89.

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Ullah, H., Chen, J.G., Temple, B., Boyes, D.C., Alonso, J.M., Davis, K.R., Ecker, J.R., Jones, A.M. The beta-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes. (2003) Plant Cell. 15(2):393-409.

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Strand, A., Asami, T., Alonso, J., Ecker, J.R., Chory, J. Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. (2003) Nature. 421(6918):79-83. DOI: 10.1038/nature01204

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Zhao, Y., Hull, A.K., Gupta, N.R., Goss, K.A., Alonso, J., Ecker, J.R., Normanly, J., Chory, J., Celenza, J.L. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. (2002) Genes & Development. 16(23):3100-12. DOI: 10.1101/gad.1035402

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Beachy, R., Bennetzen, J.L., Chassy, B.M., Chrispeels, M., Chory, J., Ecker, J.R., Noel, J.P., Kay, S.A., Dean, C., Lamb, C., Jones, J., Santerre, C.R., Schroeder, J.I., Umen, J., Yanofsky, M., Wessler, S., Zhao, Y., Parrott, W. Divergent perspectives on GM food. (2002) Nature Biotechnology. 20(12):1195-6; author reply 1197. DOI: 10.1038/nbt1202-1195


Yoshida, R., Hobo, T., Ichimura, K., Mizoguchi, T., Takahashi, F., Aronso, J., Ecker, J.R., Shinozaki, K. ABA-activated SnRK2 protein kinase is required for dehydration stress signaling in Arabidopsis. (2002) Plant & Cell Physiology. 43(12):1473-83.

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Friedrichsen, D.M., Nemhauser, J., Muramitsu, T., Maloof, J.N., Alonso, J., Ecker, J.R., Furuya, M., Chory, J. Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. (2002) Genetics. 162(3):1445-56.

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Schroeder, D.F., Gahrtz, M., Maxwell, B.B., Cook, R.K., Kan, J.M., Alonso, J.M., Ecker, J.R., Chory, J. De-etiolated 1 and damaged DNA binding protein 1 interact to regulate Arabidopsis photomorphogenesis. (2002) Current Biology. 12(17):1462-72.

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Schröder, A.R., Shinn, P., Chen, H., Berry, C., Ecker, J.R., Bushman, F. HIV-1 integration in the human genome favors active genes and local hotspots. (2002) Cell. 110(4):521-9.

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Wang, K.L., Li, H., Ecker, J.R. Ethylene biosynthesis and signaling networks. (2002) Plant Cell. 14 Suppl:S131-51.


Zheng, H., Bednarek, S.Y., Sanderfoot, A.A., Alonso, J., Ecker, J.R., Raikhel, N.V. NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE. (2002) Plant Physiology. 129(2):530-9. DOI: 10.1104/pp.003970

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Jarillo, J.A., Gabrys, H., Capel, J., Alonso, J.M., Ecker, J.R., Cashmore, A.R. Phototropin-related NPL1 controls chloroplast relocation induced by blue light. (2001) Nature. 410(6831):952-4. DOI: 10.1038/35073622

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Jarillo, J.A., Capel, J., Tang, R.H., Yang, H.Q., Alonso, J.M., Ecker, J.R., Cashmore, A.R. An Arabidopsis circadian clock component interacts with both CRY1 and phyB. (2001) Nature. 410(6827):487-90. DOI: 10.1038/35068589

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Alonso, J.M., Ecker, J.R. The ethylene pathway: a paradigm for plant hormone signaling and interaction. (2001) Sci. STKE. 2001(70):re1. DOI: 10.1126/stke.2001.70.re1

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Theologis, A., Ecker, J.R., Palm, C.J., Federspiel, N.A., Kaul, S., White, O., Alonso, J., Altafi, H., Araujo, R., Bowman, C.L., Brooks, S.Y., Buehler, E., Chan, A., Chao, Q., Chen, H., Cheuk, R.F., Chin, C.W., Chung, M.K., Conn, L., Conway, A.B., Conway, A.R., Creasy, T.H., Dewar, K., Dunn, P., Etgu, P., Feldblyum, T.V., Feng, J., Fong, B., Fujii, C.Y., Gill, J.E., Goldsmith, A.D., Haas, B., Hansen, N.F., Hughes, B., Huizar, L., Hunter, J.L., Jenkins, J., Johnson-Hopson, C., Khan, S., Khaykin, E., Kim, C.J., Koo, H.L., Kremenetskaia, I., Kurtz, D.B., Kwan, A., Lam, B., Langin-Hooper, S., Lee, A., Lee, J.M., Lenz, C.A., Li, J.H., Li, Y., Lin, X., Liu, S.X., Liu, Z.A., Luros, J.S., Maiti, R., Marziali, A., Militscher, J., Miranda, M., Nguyen, M., Nierman, W.C., Osborne, B.I., Pai, G., Peterson, J., Pham, P.K., Rizzo, M., Rooney, T., Rowley, D., Sakano, H., Salzberg, S.L., Schwartz, J.R., Shinn, P., Southwick, A.M., Sun, H., Tallon, L.J., Tambunga, G., Toriumi, M.J., Town, C.D., Utterback, T., Van Aken, S., Vaysberg, M., Vysotskaia, V.S., Walker, M., Wu, D., Yu, G., Fraser, C.M., Venter, J.C., Davis, R.W. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. (2000) Nature. 408(6814):816-20. DOI: 10.1038/35048500

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Stepanova, A.N., Ecker, J.R. Ethylene signaling: from mutants to molecules. (2000) Current Opinion in Plant Biology. 3(5):353-60.

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Chory, J., Ecker, J.R., Briggs, S., Caboche, M., Coruzzi, G.M., Cook, D., Dangl, J., Grant, S., Guerinot, M.L., Henikoff, S., Martienssen, R., Okada, K., Raikhel, N.V., Somerville, C.R., Weigel, D. National Science Foundation-Sponsored Workshop Report: "The 2010 Project" functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. (2000) Plant Physiology. 123(2):423-6.


Curie, C., Alonso, J.M., Le Jean, M., Ecker, J.R., Briat, J.F. Involvement of NRAMP1 from Arabidopsis thaliana in iron transport. (2000) Biochemical Journal. 347 Pt 3:749-55.

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Raz, V., Ecker, J.R. Regulation of differential growth in the apical hook of Arabidopsis. (1999) Development. 126(16):3661-8.

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Mozo, T., Dewar, K., Dunn, P., Ecker, J.R., Fischer, S., Kloska, S., Lehrach, H., Marra, M., Martienssen, R., Meier-Ewert, S., Altmann, T. A complete BAC-based physical map of the Arabidopsis thaliana genome. (1999) Nature Genetics. 22(3):271-5. DOI: 10.1038/10334

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Alonso, J.M., Hirayama, T., Roman, G., Nourizadeh, S., Ecker, J.R. EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. (1999) Science. 284(5423):2148-52.

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Hirayama, T., Kieber, J.J., Hirayama, N., Kogan, M., Guzman, P., Nourizadeh, S., Alonso, J.M., Dailey, W.P., Dancis, A., Ecker, J.R. RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson disease-related copper transporter, is required for ethylene signaling in Arabidopsis. (1999) Cell. 97(3):383-93.

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Solano, R., Stepanova, A., Chao, Q., Ecker, J.R. Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. (1998) Genes & Development. 12(23):3703-14.

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Solano, R., Ecker, J.R. Ethylene gas: perception, signaling and response. (1998) Current Opinion in Plant Biology. 1(5):393-8.

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Hua, J., Sakai, H., Nourizadeh, S., Chen, Q.G., Bleecker, A.B., Ecker, J.R., Meyerowitz, E.M. EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis. (1998) Plant Cell. 10(8):1321-32.

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Johnson, P.R., Ecker, J.R. The ethylene gas signal transduction pathway: a molecular perspective. (1998) Annual Review of Genetics. 32:227-54. DOI: 10.1146/annurev.genet.32.1.227

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Ecker, J.R. Genome sequencing. Genes blossom from a weed. (1998) Nature. 391(6666):438-9. DOI: 10.1038/35030


Ecker, J.R. BRI-ghtening the pathway to steroid hormone signaling events in plants. (1997) Cell. 90(5):825-7.


Chao, Q., Rothenberg, M., Solano, R., Roman, G., Terzaghi, W., Ecker, J.R. Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins. (1997) Cell. 89(7):1133-44.

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Mulligan, R.M., Chory, J., Ecker, J.R. Signaling in plants. (1997) Proceedings of the National Academy of Sciences of the United States of America. 94(7):2793-5.

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Lehman, A., Black, R., Ecker, J.R. HOOKLESS1, an ethylene response gene, is required for differential cell elongation in the Arabidopsis hypocotyl. (1996) Cell. 85(2):183-94.

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Goodman, H.M., Ecker, J.R., Dean, C. The genome of Arabidopsis thaliana. (1995) Proceedings of the National Academy of Sciences of the United States of America. 92(24):10831-5.

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Roman, G., Ecker, J.R. Genetic analysis of a seedling stress response to ethylene in Arabidopsis. (1995) Philos. Trans. R. Soc. Lond., B, Biol. Sci. 350(1331):75-81. DOI: 10.1098/rstb.1995.0140

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Ecker, J.R. The ethylene signal transduction pathway in plants. (1995) Science. 268(5211):667-75.

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Roman, G., Lubarsky, B., Kieber, J.J., Rothenberg, M., Ecker, J.R. Genetic analysis of ethylene signal transduction in Arabidopsis thaliana: five novel mutant loci integrated into a stress response pathway. (1995) Genetics. 139(3):1393-409.

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Bell, C.J., Ecker, J.R. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. (1994) Genomics. 19(1):137-44. DOI: 10.1006/geno.1994.1023

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Kieber, J.J., Ecker, J.R. Ethylene gas: it's not just for ripening any more! (1993) Trends in Genetics. 9(10):356-62.

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Kieber, J.J., Rothenberg, M., Roman, G., Feldmann, K.A., Ecker, J.R. CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. (1993) Cell. 72(3):427-41.

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Bent, A.F., Innes, R.W., Ecker, J.R., Staskawicz, B.J. Disease development in ethylene-insensitive Arabidopsis thaliana infected with virulent and avirulent Pseudomonas and Xanthomonas pathogens. (1992) Molecular Plant-Microbe Interactions. 5(5):372-8.

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Schindler, U., Menkens, A.E., Beckmann, H., Ecker, J.R., Cashmore, A.R. Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF bZIP proteins. (1992) EMBO Journal. 11(4):1261-73.

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Ewens, W.J., Bell, C.J., Donnelly, P.J., Dunn, P., Matallana, E., Ecker, J.R. Genome mapping with anchored clones: theoretical aspects. (1991) Genomics. 11(4):799-805.

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Schindler, U., Ecker, J.R., Cashmore, A.R. An Arabidopsis thaliana G-box-binding protein similar to the wheat leucine zipper protein identified as HBP-1. (1991) Symp. Soc. Exp. Biol. 45:211-8.

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Guzmán, P., Ecker, J.R. Exploiting the triple response of Arabidopsis to identify ethylene-related mutants. (1990) Plant Cell. 2(6):513-23. DOI: 10.1105/tpc.2.6.513

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Monia, B.P., Haskell, K.M., Ecker, J.R., Ecker, D.J., Crooke, S.T. Chromosomal mapping of the ubiquitin gene family in Saccharomyces cerevisiae by pulsed field gel electrophoresis. (1989) Nucleic Acids Research. 17(9):3611-2.


Guzmán, P., Ecker, J.R. Development of large DNA methods for plants: molecular cloning of large segments of Arabidopsis and carrot DNA into yeast. (1988) Nucleic Acids Research. 16(23):11091-105.

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Ecker, J.R., Davis, R.W. Plant defense genes are regulated by ethylene. (1987) Proceedings of the National Academy of Sciences of the United States of America. 84(15):5202-6.

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Ecker, J.R., Davis, R.W. Inhibition of gene expression in plant cells by expression of antisense RNA. (1986) Proceedings of the National Academy of Sciences of the United States of America. 83(15):5372-6.

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Ecker, J.R., Kudler, L., Hyman, R.W. Variation in the structure of varicella-zoster virus DNA. (1984) Intervirology. 21(1):25-37.

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Pichini, B., Ecker, J.R., Grose, C., Hyman, R.W. DNA mapping of paired varicella-zoster virus isolates from patients with shingles. (1983) Lancet. 2(8361):1223-5.

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Hyman, R.W., Ecker, J.R., Tenser, R.B. Varicella-zoster virus RNA in human trigeminal ganglia. (1983) Lancet. 2(8354):814-6.

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Ecker, J.R., Hyman, R.W. Varicella zoster virus DNA exists as two isomers. (1982) Proceedings of the National Academy of Sciences of the United States of America. 79(1):156-60.

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Ecker, J.R., Hyman, R.W. Varicella-zoster virus vaccine DNA differs from the parental virus DNA. (1981) Journal of Virology. 40(1):314-8.

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Ecker, J.R., Hyman, R.W. Analysis of interruptions in the phosphodiester backbone of herpes simplex virus DNA. (1981) Virology. 110(1):213-6.


Ecker, J.R., Hyman, R.W. Variables that may influence the alkaline sedimentation pattern of herpes simplex virus DNA. (1981) Arch. Virol. 68(3-4):221-8.

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Education

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

  • 2019 Chan Zuckerberg Initiative to expand Human Cell Atlas
  • 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