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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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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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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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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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