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

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) Wissenschaft. 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) Wissenschaft. 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) Natur. 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) Wissenschaft. 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) Wissenschaft. 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) Wissenschaft. 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) Wissenschaft. 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) Natur. 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) Natur. 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) Natur. 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) Natur. 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) Wissenschaft. 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) Natur. 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) Wissenschaft. 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.