Cell Cell Cell Cell Genes Journal of Virology Nature PLOS Biomedical Computation Cell JCB Genes Discover Science Time Nature Cell
Selected Publications

all Publications


Cao, M., Platre, M.P., Tsai, H.H., Zhang, L., Nobori, T., Armengot, L., Chen, Y., He, W., Brent, L., Coll, N.S., Ecker, J.R., Geldner, N., Busch, W. Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. (2024) Nature. DOI: 10.1038/s41586-023-06891-y

+ expand abstract

Zhou, J., Luo, C., Liu, H., Heffel, M.G., Straub, R.E., Kleinman, J.E., Hyde, T.M., Ecker, J.R., Weinberger, D.R., Han, S. scMeFormer: a transformer-based deep learning model for imputing DNA methylation states in single cells enhances the detection of epigenetic alterations in schizophrenia. (2024) bioRxiv. DOI: 10.1101/2024.01.25.577200

+ expand abstract

Zhou, J., Zhang, Z., Wu, M., Liu, H., Pang, Y., Bartlett, A., Peng, Z., Ding, W., Rivkin, A., Lagos, W.N., Williams, E., Lee, C.T., Miyazaki, P.A., Aldridge, A., Zeng, Q., Salinda, J.L.A., Claffey, N., Liem, M., Fitzpatrick, C., Boggeman, L., Yao, Z., Smith, K.A., Tasic, B., Altshul, J., Kenworthy, M.A., Valadon, C., Nery, J.R., Castanon, R.G., Patne, N.S., Vu, M., Rashid, M., Jacobs, M., Ito, T., Osteen, J., Emerson, N., Lee, J., Cho, S., Rink, J., Huang, H.H., Pinto-Duartec, A., Dominguez, B., Smith, J.B., O’Connor, C., Zeng, H., Chen, S., Lee, K.F., Mukamel, E.A., Jin, X., Margarita Behrens, M., Ecker, J.R., Callaway, E.M. Brain-wide correspondence of neuronal epigenomics and distant projections. (2023) Nature. 624(7991):355-365. DOI: 10.1038/s41586-023-06823-w

+ expand abstract

Zemke, N.R., Armand, E.J., Wang, W., Lee, S., Zhou, J., Li, Y.E., Liu, H., Tian, W., Nery, J.R., Castanon, R.G., Bartlett, A., Osteen, J.K., Li, D., Zhuo, X., Xu, V., Chang, L., Dong, K., Indralingam, H.S., Rink, J.A., Xie, Y., Miller, M., Krienen, F.M., Zhang, Q., Taskin, N., Ting, J., Feng, G., McCarroll, S.A., Callaway, E.M., Wang, T., Lein, E.S., Behrens, M.M., Ecker, J.R., Ren, B. Conserved and divergent gene regulatory programs of the mammalian neocortex. (2023) Nature. 624(7991):390-402. DOI: 10.1038/s41586-023-06819-6

+ expand abstract

Zu, S., Li, Y.E., Wang, K., Armand, E.J., Mamde, S., Amaral, M.L., Wang, Y., Chu, A., Xie, Y., Miller, M., Xu, J., Wang, Z., Zhang, K., Jia, B., Hou, X., Lin, L., Yang, Q., Lee, S., Li, B., Kuan, S., Liu, H., Zhou, J., Pinto-Duarte, A., Lucero, J., Osteen, J., Nunn, M., Smith, K.A., Tasic, B., Yao, Z., Zeng, H., Wang, Z., Shang, J., Behrens, M.M., Ecker, J.R., Wang, A., Preissl, S., Ren, B. Single-cell analysis of chromatin accessibility in the adult mouse brain. (2023) Nature. 624(7991):378-389. DOI: 10.1038/s41586-023-06824-9

+ expand abstract

Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.A., Berube, P., Tian, W., Kenworthy, M., Altshul, J., Nery, J.R., Chen, H., Castanon, R.G., Zu, S., Li, Y.E., Lucero, J., Osteen, J.K., Pinto-Duarte, A., Lee, J., Rink, J., Cho, S., Emerson, N., Nunn, M., O’Connor, C., Wu, Z., Stoica, I., Yao, Z., Smith, K.A., Tasic, B., Luo, C., Dixon, J.R., Zeng, H., Ren, B., Behrens, M.M., Ecker, J.R. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. (2023) Nature. 624(7991):366-377. DOI: 10.1038/s41586-023-06805-y

+ expand abstract

Mukamel, E.A., Liu, H., Behrens, M.M., Ecker, J.R. Cell type-specific enrichment of somatic aneuploidy in the mammalian brain. (2023) bioRxiv. DOI: 10.1101/2023.12.18.572285

+ expand abstract

Raikhel, N., Ecker, J.R., Coruzzi, G. Remembering Philip N. Benfey: A visionary pioneer in plant biology and mentor extraordinaire. (2023) Proceedings of the National Academy of Sciences of the United States of America. 120(45):e2317677120. DOI: 10.1073/pnas.2317677120


Tian, W., Zhou, J., Bartlett, A., Zeng, Q., Liu, H., Castanon, R.G., Kenworthy, M., Altshul, J., Valadon, C., Aldridge, A., Nery, J.R., Chen, H., Xu, J., Johnson, N.D., Lucero, J., Osteen, J.K., Emerson, N., Rink, J., Lee, J., Li, Y.E., Siletti, K., Liem, M., Claffey, N., O’Connor, C., Yanny, A.M., Nyhus, J., Dee, N., Casper, T., Shapovalova, N., Hirschstein, D., Ding, S.L., Hodge, R., Levi, B.P., Keene, C.D., Linnarsson, S., Lein, E., Ren, B., Behrens, M.M., Ecker, J.R. Single-cell DNA methylation and 3D genome architecture in the human brain. Link to free full-text https://doi.org/10.1126/science.adf5357 (2023) Science. 382(6667):eadf5357. DOI: 10.1126/science.adf5357

+ expand abstract

Li, Y.E., Preissl, S., Miller, M., Johnson, N.D., Wang, Z., Jiao, H., Zhu, C., Wang, Z., Xie, Y., Poirion, O., Kern, C., Pinto-Duarte, A., Tian, W., Siletti, K., Emerson, N., Osteen, J., Lucero, J., Lin, L., Yang, Q., Zhu, Q., Zemke, N., Espinoza, S., Yanny, A.M., Nyhus, J., Dee, N., Casper, T., Shapovalova, N., Hirschstein, D., Hodge, R.D., Linnarsson, S., Bakken, T., Levi, B., Keene, C.D., Shang, J., Lein, E., Wang, A., Behrens, M.M., Ecker, J.R., Ren, B. A comparative atlas of single-cell chromatin accessibility in the human brain. (2023) Science. 382(6667):eadf7044. DOI: 10.1126/science.adf7044

+ expand abstract

Tian, W., Ding, W., Ecker, J.R. BAllC and BAllCools: Efficient Formatting and Operating for Single-Cell DNA Methylation Data. (2023) bioRxiv. DOI: 10.1101/2023.09.22.559047

+ expand abstract

Xie, F., Armand, E.J., Yao, Z., Liu, H., Bartlett, A., Behrens, M.M., Li, Y.E., Lucero, J.D., Luo, C., Nery, J.R., Pinto-Duarte, A., Poirion, O.B., Preissl, S., Rivkin, A.C., Tasic, B., Zeng, H., Ren, B., Ecker, J.R., Mukamel, E.A. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. (2023) Cell Genom. 3(7):100342. DOI: 10.1016/j.xgen.2023.100342

+ expand abstract

Nobori, T., Ecker, J.R. Yet uninfected? Resolving cell states of plants under pathogen attack. (2023) Cell Rep Methods. 3(7):100538. DOI: 10.1016/j.crmeth.2023.100538

+ expand abstract

Nobori, T., Oliva, M., Lister, R., Ecker, J.R. Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap. (2023) Nature Plants. DOI: 10.1038/s41477-023-01439-4

+ expand abstract

Hawrylycz, M., Martone, M.E., Ascoli, G.A., Bjaalie, J.G., Dong, H.W., Ghosh, S.S., Gillis, J., Hertzano, R., Haynor, D.R., Hof, P.R., Kim, Y., Lein, E., Liu, Y., Miller, J.A., Mitra, P.P., Mukamel, E., Ng, L., Osumi-Sutherland, D., Peng, H., Ray, P.L., Sanchez, R., Regev, A., Ropelewski, A., Scheuermann, R.H., Tan, S.Z.K., Thompson, C.L., Tickle, T., Tilgner, H., Varghese, M., Wester, B., White, O., Zeng, H., Aevermann, B., Allemang, D., Ament, S., Athey, T.L., Baker, C., Baker, K.S., Baker, P.M., Bandrowski, A., Banerjee, S., Bishwakarma, P., Carr, A., Chen, M., Choudhury, R., Cool, J., Creasy, H., D’Orazi, F., Degatano, K., Dichter, B., Ding, S.L., Dolbeare, T., Ecker, J.R., Fang, R., Fillion-Robin, J.C., Fliss, T.P., Gee, J., Gillespie, T., Gouwens, N., Zhang, G.Q., Halchenko, Y.O., Harris, N.L., Herb, B.R., Hintiryan, H., Hood, G., Horvath, S., Huo, B., Jarecka, D., Jiang, S., Khajouei, F., Kiernan, E.A., Kir, H., Kruse, L., Lee, C., Lelieveldt, B., Li, Y., Liu, H., Liu, L., Markuhar, A., Mathews, J., Mathews, K.L., Mezias, C., Miller, M.I., Mollenkopf, T., Mufti, S., Mungall, C.J., Orvis, J., Puchades, M.A., Qu, L., Receveur, J.P., Ren, B., Sjoquist, N., Staats, B., Tward, D., van Velthoven, C.T.J., Wang, Q., Xie, F., Xu, H., Yao, Z., Yun, Z., Zhang, Y.R., Zheng, W.J., Zingg, B. A guide to the BRAIN Initiative Cell Census Network data ecosystem. (2023) PLOS Biology. 21(6):e3002133. DOI: 10.1371/journal.pbio.3002133

+ expand abstract

Wang, W., Hariharan, M., Bartlett, A., Barragan, C., Castanon, R., Rothenberg, V., Song, H., Nery, J., Aldridge, A., Altshul, J., Kenworthy, M., Ding, W., Liu, H., Tian, W., Zhou, J., Chen, H., Wei, B., Gündüz, I.B., Norell, T., Broderick, T.J., McClain, M.T., Satterwhite, L.L., Burke, T.W., Petzold, E.A., Shen, X., Woods, C.W., Fowler, V.G., Ruffin, F., Panuwet, P., Barr, D.B., Beare, J.L., Smith, A.K., Spurbeck, R.R., Vangeti, S., Ramos, I., Nudelman, G., Sealfon, S.C., Castellino, F., Walley, A.M., Evans, T., Müller, F., Greenleaf, W.J., Ecker, J.R. Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures. (2023) bioRxiv. DOI: 10.1101/2023.06.29.546792

+ expand abstract

Zemke, N.R., Armand, E.J., Wang, W., Lee, S., Zhou, J., Li, Y.E., Liu, H., Tian, W., Nery, J.R., Castanon, R.G., Bartlett, A., Osteen, J.K., Li, D., Zhuo, X., Xu, V., Miller, M., Krienen, F.M., Zhang, Q., Taskin, N., Ting, J., Feng, G., McCarroll, S.A., Callaway, E.M., Wang, T., Behrens, M.M., Lein, E.S., Ecker, J.R., Ren, B. Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex. (2023) bioRxiv. DOI: 10.1101/2023.04.08.536119

+ expand abstract

Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.A., Berube, P., Tian, W., Kenworthy, M., Altshul, J., Nery, J.R., Chen, H., Castanon, R.G., Zu, S., Li, Y.E., Lucero, J., Osteen, J.K., Pinto-Duarte, A., Lee, J., Rink, J., Cho, S., Emerson, N., Nunn, M., O’Connor, C., Yao, Z., Smith, K.A., Tasic, B., Zeng, H., Luo, C., Dixon, J.R., Ren, B., Behrens, M.M., Ecker, J.R. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. (2023) bioRxiv. DOI: 10.1101/2023.04.16.536509

+ expand abstract

Yin, L., Zander, M., Huang, S.C., Xie, M., Song, L., Saldierna Guzmán, J.P., Hann, E., Shanbhag, B.K., Ng, S., Jain, S., Janssen, B.J., Clark, N.M., Walley, J.W., Beddoe, T., Bar-Joseph, Z., Lewsey, M.G., Ecker, J.R. Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways. (2023) bioRxiv. DOI: 10.1101/2023.03.07.531630

+ expand abstract

Procko, C., Lee, T., Borsuk, A., Bargmann, B.O.R., Dabi, T., Nery, J.R., Estelle, M., Baird, L., O’Connor, C., Brodersen, C., Ecker, J.R., Chory, J. Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection. (2022) Plant Cell. DOI: 10.1093/plcell/koac167

+ expand abstract

Li, J., Pinto-Duarte, A., Zander, M., Cuoco, M.S., Lai, C.Y., Osteen, J., Fang, L., Luo, C., Lucero, J.D., Gomez-Castanon, R., Nery, J.R., Silva-Garcia, I., Pang, Y., Sejnowski, T.J., Powell, S.B., Ecker, J.R., Mukamel, E.A., Behrens, M.M. Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. (2022) Elife. 11. DOI: 10.7554/eLife.66909

+ expand abstract

Luo, C., Liu, H., Xie, F., Armand, E.J., Siletti, K., Bakken, T.E., Fang, R., Doyle, W.I., Stuart, T., Hodge, R.D., Hu, L., Wang, B.A., Zhang, Z., Preissl, S., Lee, D.S., Zhou, J., Niu, S.Y., Castanon, R., Bartlett, A., Rivkin, A., Wang, X., Lucero, J., Nery, J.R., Davis, D.A., Mash, D.C., Satija, R., Dixon, J.R., Linnarsson, S., Lein, E., Behrens, M.M., Ren, B., Mukamel, E.A., Ecker, J.R. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. (2022) Cell Genom. 2(3). DOI: 10.1016/j.xgen.2022.100107

+ expand abstract

Swift, J., Greenham, K., Ecker, J.R., Coruzzi, G.M., McClung, C.R. The biology of time: dynamic responses of cell types to developmental, circadian, and environmental cues. (2021) Plant Journal. DOI: 10.1111/tpj.15589

+ expand abstract

Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J.K., Nery, J.R., Chen, H., Rivkin, A., Castanon, R.G., Clock, B., Li, Y.E., Hou, X., Poirion, O.B., Preissl, S., Pinto-Duarte, A., O’Connor, C., Boggeman, L., Fitzpatrick, C., Nunn, M., Mukamel, E.A., Zhang, Z., Callaway, E.M., Ren, B., Dixon, J.R., Behrens, M.M., Ecker, J.R. DNA methylation atlas of the mouse brain at single-cell resolution. (2021) Nature. 598(7879):120-128. DOI: 10.1038/s41586-020-03182-8

+ expand abstract

Zhang, Z., Zhou, J., Tan, P., Pang, Y., Rivkin, A.C., Kirchgessner, M.A., Williams, E., Lee, C.T., Liu, H., Franklin, A.D., Miyazaki, P.A., Bartlett, A., Aldridge, A.I., Vu, M., Boggeman, L., Fitzpatrick, C., Nery, J.R., Castanon, R.G., Rashid, M., Jacobs, M.W., Ito-Cole, T., O’Connor, C., Pinto-Duartec, A., Dominguez, B., Smith, J.B., Niu, S.Y., Lee, K.F., Jin, X., Mukamel, E.A., Behrens, M.M., Ecker, J.R., Callaway, E.M. Epigenomic diversity of cortical projection neurons in the mouse brain. (2021) Nature. 598(7879):167-173. DOI: 10.1038/s41586-021-03223-w

+ expand abstract

Li, Y.E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Qiu, Y., Poirion, O.B., Li, B., Chiou, J., Liu, H., Pinto-Duarte, A., Kubo, N., Yang, X., Fang, R., Wang, X., Han, J.Y., Lucero, J., Yan, Y., Miller, M., Kuan, S., Gorkin, D., Gaulton, K.J., Shen, Y., Nunn, M., Mukamel, E.A., Behrens, M.M., Ecker, J.R., Ren, B. An atlas of gene regulatory elements in adult mouse cerebrum. (2021) Nature. 598(7879):129-136. DOI: 10.1038/s41586-021-03604-1

+ expand abstract

Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R.S., Aldridge, A.I., Ament, S.A., Bartlett, A., Behrens, M.M., Van den Berge, K., Bertagnolli, D., de Bézieux, H.R., Biancalani, T., Booeshaghi, A.S., Bravo, H.C., Casper, T., Colantuoni, C., Crabtree, J., Creasy, H., Crichton, K., Crow, M., Dee, N., Dougherty, E.L., Doyle, W.I., Dudoit, S., Fang, R., Felix, V., Fong, O., Giglio, M., Goldy, J., Hawrylycz, M., Herb, B.R., Hertzano, R., Hou, X., Hu, Q., Kancherla, J., Kroll, M., Lathia, K., Li, Y.E., Lucero, J.D., Luo, C., Mahurkar, A., McMillen, D., Nadaf, N.M., Nery, J.R., Nguyen, T.N., Niu, S.Y., Ntranos, V., Orvis, J., Osteen, J.K., Pham, T., Pinto-Duarte, A., Poirion, O., Preissl, S., Purdom, E., Rimorin, C., Risso, D., Rivkin, A.C., Smith, K., Street, K., Sulc, J., Svensson, V., Tieu, M., Torkelson, A., Tung, H., Vaishnav, E.D., Vanderburg, C.R., van Velthoven, C., Wang, X., White, O.R., Huang, Z.J., Kharchenko, P.V., Pachter, L., Ngai, J., Regev, A., Tasic, B., Welch, J.D., Gillis, J., Macosko, E.Z., Ren, B., Ecker, J.R., Zeng, H., Mukamel, E.A. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. (2021) Nature. 598(7879):103-110. DOI: 10.1038/s41586-021-03500-8

+ expand abstract

Bakken, T.E., Jorstad, N.L., Hu, Q., Lake, B.B., Tian, W., Kalmbach, B.E., Crow, M., Hodge, R.D., Krienen, F.M., Sorensen, S.A., Eggermont, J., Yao, Z., Aevermann, B.D., Aldridge, A.I., Bartlett, A., Bertagnolli, D., Casper, T., Castanon, R.G., Crichton, K., Daigle, T.L., Dalley, R., Dee, N., Dembrow, N., Diep, D., Ding, S.L., Dong, W., Fang, R., Fischer, S., Goldman, M., Goldy, J., Graybuck, L.T., Herb, B.R., Hou, X., Kancherla, J., Kroll, M., Lathia, K., van Lew, B., Li, Y.E., Liu, C.S., Liu, H., Lucero, J.D., Mahurkar, A., McMillen, D., Miller, J.A., Moussa, M., Nery, J.R., Nicovich, P.R., Niu, S.Y., Orvis, J., Osteen, J.K., Owen, S., Palmer, C.R., Pham, T., Plongthongkum, N., Poirion, O., Reed, N.M., Rimorin, C., Rivkin, A., Romanow, W.J., Sedeño-Cortés, A.E., Siletti, K., Somasundaram, S., Sulc, J., Tieu, M., Torkelson, A., Tung, H., Wang, X., Xie, F., Yanny, A.M., Zhang, R., Ament, S.A., Behrens, M.M., Bravo, H.C., Chun, J., Dobin, A., Gillis, J., Hertzano, R., Hof, P.R., Höllt, T., Horwitz, G.D., Keene, C.D., Kharchenko, P.V., Ko, A.L., Lelieveldt, B.P., Luo, C., Mukamel, E.A., Pinto-Duarte, A., Preissl, S., Regev, A., Ren, B., Scheuermann, R.H., Smith, K., Spain, W.J., White, O.R., Koch, C., Hawrylycz, M., Tasic, B., Macosko, E.Z., McCarroll, S.A., Ting, J.T., Zeng, H., Zhang, K., Feng, G., Ecker, J.R., Linnarsson, S., Lein, E.S. Comparative cellular analysis of motor cortex in human, marmoset and mouse. (2021) Nature. 598(7879):111-119. DOI: 10.1038/s41586-021-03465-8

+ expand abstract

Farhy-Tselnicker, I., Boisvert, M.M., Liu, H., Dowling, C., Erikson, G.A., Blanco-Suarez, E., Farhy, C., Shokhirev, M.N., Ecker, J.R., Allen, N.J. Activity-dependent modulation of synapse-regulating genes in astrocytes. (2021) Elife. 10. DOI: 10.7554/eLife.70514

+ expand abstract

Gouveia-Mageste, B.C., Martins, L.G.C., Dal-Bianco, M., Machado, J.P.B., da Silva, J.C.F., Kim, A.Y., Yazaki, J., Dos Santos, A.A., Ecker, J.R., Fontes, E.P.B. A plant-specific syntaxin-6 protein contributes to the intracytoplasmic route for the begomovirus CabLCV. (2021) Plant Physiology. 187(1):158-173. DOI: 10.1093/plphys/kiab252

+ expand abstract

Willige, B.C., Zander, M., Yoo, C.Y., Phan, A., Garza, R.M., Trigg, S.A., He, Y., Nery, J.R., Chen, H., Chen, M., Ecker, J.R., Chory, J. PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. (2021) Nature Genetics. DOI: 10.1038/s41588-021-00882-3

+ expand abstract

Ruf-Zamojski, F., Zhang, Z., Zamojski, M., Smith, G.R., Mendelev, N., Liu, H., Nudelman, G., Moriwaki, M., Pincas, H., Castanon, R.G., Nair, V.D., Seenarine, N., Amper, M.A.S., Zhou, X., Ongaro, L., Toufaily, C., Schang, G., Nery, J.R., Bartlett, A., Aldridge, A., Jain, N., Childs, G.V., Troyanskaya, O.G., Ecker, J.R., Turgeon, J.L., Welt, C.K., Bernard, D.J., Sealfon, S.C. Single nucleus multi-omics regulatory landscape of the murine pituitary. (2021) Nature Communications. 12(1):2677. DOI: 10.1038/s41467-021-22859-w

+ expand abstract

Gao, C., Liu, J., Kriebel, A.R., Preissl, S., Luo, C., Castanon, R., Sandoval, J., Rivkin, A., Nery, J.R., Behrens, M.M., Ecker, J.R., Ren, B., Welch, J.D. Iterative single-cell multi-omic integration using online learning. (2021) Nature Biotechnology. DOI: 10.1038/s41587-021-00867-x

+ expand abstract

Fang, R., Preissl, S., Li, Y., Hou, X., Lucero, J., Wang, X., Motamedi, A., Shiau, A.K., Zhou, X., Xie, F., Mukamel, E.A., Zhang, K., Zhang, Y., Behrens, M.M., Ecker, J.R., Ren, B. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. (2021) Nature Communications. 12(1):1337. DOI: 10.1038/s41467-021-21583-9

+ expand abstract

de Mendoza, A., Poppe, D., Buckberry, S., Pflueger, J., Albertin, C.B., Daish, T., Bertrand, S., de la Calle-Mustienes, E., Gómez-Skarmeta, J.L., Nery, J.R., Ecker, J.R., Baer, B., Ragsdale, C.W., Grützner, F., Escriva, H., Venkatesh, B., Bogdanovic, O., Lister, R. The emergence of the brain non-CpG methylation system in vertebrates. (2021) Nat Ecol Evol. DOI: 10.1038/s41559-020-01371-2

+ expand abstract

Michael, T.P., Ernst, E., Hartwick, N., Chu, P., Bryant, D., Gilbert, S., Ortleb, S., Baggs, E.L., Sree, K.S., Appenroth, K.J., Fuchs, J., Jupe, F., Sandoval, J.P., Krasileva, K.V., Borisjuk, L., Mockler, T.C., Ecker, J., Martienssen, R.A., Lam, E. Genome and time-of-day transcriptome of link morphological minimization with gene loss and less growth control. (2020) Genome Research. DOI: 10.1101/gr.266429.120

+ expand abstract

ENCODE., Moore, J.E., Purcaro, M.J., Pratt, H.E., Epstein, C.B., Shoresh, N., Adrian, J., Kawli, T., Davis, C.A., Dobin, A., Kaul, R., Halow, J., Van Nostrand, E.L., Freese, P., Gorkin, D.U., Shen, Y., He, Y., Mackiewicz, M., Pauli-Behn, F., Williams, B.A., Mortazavi, A., Keller, C.A., Zhang, X.O., Elhajjajy, S.I., Huey, J., Dickel, D.E., Snetkova, V., Wei, X., Wang, X., Rivera-Mulia, J.C., Rozowsky, J., Zhang, J., Chhetri, S.B., Zhang, J., Victorsen, A., White, K.P., Visel, A., Yeo, G.W., Burge, C.B., Lécuyer, E., Gilbert, D.M., Dekker, J., Rinn, J., Mendenhall, E.M., Ecker, J.R., Kellis, M., Klein, R.J., Noble, W.S., Kundaje, A., Guigó, R., Farnham, P.J., Cherry, J.M., Myers, R.M., Ren, B., Graveley, B.R., Gerstein, M.B., Pennacchio, L.A., Snyder, M.P., Bernstein, B.E., Wold, B., Hardison, R.C., Gingeras, T.R., Stamatoyannopoulos, J.A., Weng, Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. (2020) Nature. 583(7818):699-710. DOI: 10.1038/s41586-020-2493-4

+ expand abstract

He, Y., Hariharan, M., Gorkin, D.U., Dickel, D.E., Luo, C., Castanon, R.G., Nery, J.R., Lee, A.Y., Zhao, Y., Huang, H., Williams, B.A., Trout, D., Amrhein, H., Fang, R., Chen, H., Li, B., Visel, A., Pennacchio, L.A., Ren, B., Ecker, J.R. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. (2020) Nature. 583(7818):752-759. DOI: 10.1038/s41586-020-2119-x

+ expand abstract

Gorkin, D.U., Barozzi, I., Zhao, Y., Zhang, Y., Huang, H., Lee, A.Y., Li, B., Chiou, J., Wildberg, A., Ding, B., Zhang, B., Wang, M., Strattan, J.S., Davidson, J.M., Qiu, Y., Afzal, V., Akiyama, J.A., Plajzer-Frick, I., Novak, C.S., Kato, M., Garvin, T.H., Pham, Q.T., Harrington, A.N., Mannion, B.J., Lee, E.A., Fukuda-Yuzawa, Y., He, Y., Preissl, S., Chee, S., Han, J.Y., Williams, B.A., Trout, D., Amrhein, H., Yang, H., Cherry, J.M., Wang, W., Gaulton, K., Ecker, J.R., Shen, Y., Dickel, D.E., Visel, A., Pennacchio, L.A., Ren, B. An atlas of dynamic chromatin landscapes in mouse fetal development. (2020) Nature. 583(7818):744-751. DOI: 10.1038/s41586-020-2093-3

+ expand abstract

Wierbowski, S.D., Vo, T.V., Falter-Braun, P., Jobe, T.O., Kruse, L.H., Wei, X., Liang, J., Meyer, M.J., Akturk, N., Rivera-Erick, C.A., Cordero, N.A., Paramo, M.I., Shayhidin, E.E., Bertolotti, M., Tippens, N.D., Akther, K., Sharma, R., Katayose, Y., Salehi-Ashtiani, K., Hao, T., Ronald, P.C., Ecker, J.R., Schweitzer, P.A., Kikuchi, S., Mizuno, H., Hill, D.E., Vidal, M., Moghe, G.D., McCouch, S.R., Yu, H. A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. (2020) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1918068117

+ expand abstract

Kim, E.J., Zhang, Z., Huang, L., Ito-Cole, T., Jacobs, M.W., Juavinett, A.L., Senturk, G., Hu, M., Ku, M., Ecker, J.R., Callaway, E.M. Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population. (2020) Neuron. DOI: 10.1016/j.neuron.2020.04.018

+ expand abstract

Lavery, L.A., Ure, K., Wan, Y.W., Luo, C., Trostle, A.J., Wang, W., Jin, H., Lopez, J., Lucero, J., Durham, M.A., Castanon, R., Nery, J.R., Liu, Z., Goodell, M., Ecker, J.R., Behrens, M.M., Zoghbi, H.Y. Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome. (2020) Elife. 9. DOI: 10.7554/eLife.52981

+ expand abstract

Zander, M., Lewsey, M.G., Clark, N.M., Yin, L., Bartlett, A., Saldierna Guzmán, J.P., Hann, E., Langford, A.E., Jow, B., Wise, A., Nery, J.R., Chen, H., Bar-Joseph, Z., Walley, J.W., Solano, R., Ecker, J.R. Integrated multi-omics framework of the plant response to jasmonic acid. (2020) Nature Plants. 6(3):290-302. DOI: 10.1038/s41477-020-0605-7

+ expand abstract

Burko, Y., Seluzicki, A., Zander, M., Pedmale, U., Ecker, J.R., Chory, J. Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism. (2020) Plant Cell. 32(2). DOI: 10.1105/tpc.19.00772

+ expand abstract

Sasaki, E., Kawakatsu, T., Ecker, J.R., Nordborg, M. Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana. (2019) PLOS Genetics. 15(12):e1008492. DOI: 10.1371/journal.pgen.1008492

+ expand abstract

Ortigosa, A., Fonseca, S., Franco-Zorrilla, J.M., Fernandez-Calvo, P., Zander, M., Lewsey, M.G., García-Casado, G., Fernández-Barbero, G., Ecker, J.R., Solano, R. The JA-pathway MYC transcription factors regulate photomorphogenic responses by targeting HY5 gene expression. (2019) Plant Journal. DOI: 10.1111/tpj.14618

+ expand abstract

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

+ expand abstract

Van Moerkercke, A., Duncan, O., Zander, M., Šimura, J., Broda, M., Vanden Bossche, R., Lewsey, M.G., Lama, S., Singh, K.B., Ljung, K., Ecker, J.R., Goossens, A., Millar, A.H., Van Aken, O. A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels. (2019) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1911758116

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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


Schultz, M.D., Schmitz, R.J., Ecker, J.R. ‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes. (2012) Trends in Genetics. 28(12):583-5. DOI: 10.1016/j.tig.2012.10.012


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

+ expand abstract

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

+ expand abstract

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 Chemical Biology. 7(8):1337-44. DOI: 10.1021/cb300229q

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

Lister, R., Pelizzola, M., Kida, Y.S., Hawkins, R.D., Nery, J.R., Hon, G., Antosiewicz-Bourget, J., O’Malley, R., Castanon, R., Klugman, S., Downes, M., Yu, R., Stewart, R., Ren, B., Thomson, J.A., Evans, R.M., Ecker, J.R. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. (2011) Nature. 471(7336):68-73. DOI: 10.1038/nature09798

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

Kwok, S.F., Solano, R., Tsuge, T., Chamovitz, D.A., Ecker, J.R., Matsui, M., Deng, X.W. Arabidopsis homologs of a c-Jun coactivator are present both in monomeric form and in the COP9 complex, and their abundance is differentially affected by the pleiotropic cop/det/fus mutations. (1998) Plant Cell. 10(11):1779-90.

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract

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.

+ expand abstract