all Publications

Heffel, M.G., Zhou, J., Zhang, Y., Lee, D.S., Hou, K., Pastor-Alonso, O., Abuhanna, K.D., Galasso, J., Kern, C., Tai, C.Y., Garcia-Padilla, C., Nafisi, M., Zhou, Y., Schmitt, A.D., Li, T., Haeussler, M., Wick, B., Zhang, M.J., Xie, F., Ziffra, R.S., Mukamel, E.A., Eskin, E., Nowakowski, T.J., Dixon, J.R., Pasaniuc, B., Ecker, J.R., Zhu, Q., Bintu, B., Paredes, M.F., Luo, C. Temporally distinct 3D multi-omic dynamics in the developing human brain. (2024) Nature. DOI: 10.1038/s41586-024-08030-7

Johansen, N.J., Kempynck, N., Zemke, N.R., Somasundaram, S., De Winter, S., Hooper, M., Dwivedi, D., Lohia, R., Wehbe, F., Li, B., Abaffyová, D., Armand, E.J., De Man, J., Eksi, E.C., Hecker, N., Hulselmans, G., Konstantakos, V., Mauduit, D., Mich, J.K., Partel, G., Daigle, T.L., Levi, B.P., Zhang, K., Tanaka, Y., Gillis, J., Ting, J.T., Ben-Simon, Y., Miller, J., Ecker, J.R., Ren, B., Aerts, S., Lein, E.S., Tasic, B., Bakken, T.E. Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex. (2024) bioRxiv. DOI: 10.1101/2024.08.21.609075

Denyer, T., Wu, P.J., Colt, K., Abramson, B., Pang, Z., Solansky, P., Mamerto, A., Nobori, T., Ecker, J., Lam, E., Michael, T.P., Timmermans, M.C. Streamlined spatial and environmental expression signatures characterize the minimalist duckweed . (2024) Genome Research. DOI: 10.1101/gr.279091.124

Gonzalez, S., Swift, J., Yaaran, A., Xu, J., Miller, C., Illouz-Eliaz, N., Nery, J.R., Busch, W., Zait, Y., Ecker, J.R. Arabidopsis transcriptome responses to low water potential using high-throughput plate assays. (2024) Elife. 12. DOI: 10.7554/eLife.84747

Tian, W., Ding, W., Shen, J., Li, D., Wang, T., Ecker, J.R. BAllC and BAllCools: Efficient formatting and operating for Single-Cell DNA methylation data. (2024) Bioinformatics . DOI: 10.1093/bioinformatics/btae404

Zhang, S., Shu, H., Zhou, J., Rubin-Sigler, J., Yang, X., Liu, Y., Cooper-Knock, J., Monte, E., Zhu, C., Tu, S., Li, H., Tong, M., Ecker, J.R., Ichida, J.K., Shen, Y., Zeng, J., Tsao, P.S., Snyder, M.P. Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases. (2024) bioRxiv. DOI: 10.1101/2024.05.14.594252

Chien, J.F., Liu, H., Wang, B.A., Luo, C., Bartlett, A., Castanon, R., Johnson, N.D., Nery, J.R., Osteen, J., Li, J., Altshul, J., Kenworthy, M., Valadon, C., Liem, M., Claffey, N., O’Connor, C., Seeker, L.A., Ecker, J.R., Behrens, M.M., Mukamel, E.A. Cell-type-specific effects of age and sex on human cortical neurons. (2024) Neuron. DOI: 10.1016/j.neuron.2024.05.013

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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.

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

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

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

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

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.

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.

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

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

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.

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.

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.

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.

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

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

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

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

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

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

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.

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

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

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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

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

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.

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

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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

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.

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

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.

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.

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.