all Publications

Swift, J., Luginbuehl, L.H., Hua, L., Schreier, T.B., Donald, R.M., Stanley, S., Wang, N., Lee, T.A., Nery, J.R., Ecker, J.R., Hibberd, J.M. Exaptation of ancestral cell-identity networks enables C photosynthesis. (2024) Nature. DOI: 10.1038/s41586-024-08204-3

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

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

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.