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Joseph R. Ecker, Ph.D. - Publications

Affiliations: 
HHMI-The Salk Institute for Biological Studies 
Area:
epigenetics, molecular genetics
Website:
http://www.salk.edu/faculty/ecker.html

303 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Procko C, Lee T, Borsuk A, Bargmann BOR, Dabi T, Nery JR, Estelle M, Baird L, O'Connor C, Brodersen C, Ecker JR, Chory J. Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection. The Plant Cell. PMID 35666176 DOI: 10.1093/plcell/koac167  0.8
2022 Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, ... Ecker JR, et al. knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. Elife. 11. PMID 35604009 DOI: 10.7554/eLife.66909  0.807
2022 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, ... ... Ecker JR, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3  0.671
2022 Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, ... ... Ecker JR, et al. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genomics. 2. PMID 35419551 DOI: 10.1016/j.xgen.2022.100107  0.79
2022 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Ecker JR, et al. Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. PMID 35319013 DOI: 10.1038/s41586-022-04562-y  0.759
2022 Potok ME, Zhong Z, Picard CL, Liu Q, Do T, Jacobsen CE, Sakr O, Naranbaatar B, Thilakaratne R, Khnkoyan Z, Purl M, Cheng H, Vervaet H, Feng S, Rayatpisheh S, ... ... Ecker JR, et al. The role of ATXR6 expression in modulating genome stability and transposable element repression in . Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35027454 DOI: 10.1073/pnas.2115570119  0.706
2021 Swift J, Greenham K, Ecker JR, Coruzzi GM, McClung CR. The biology of time: dynamic responses of cell types to developmental, circadian, and environmental cues. The Plant Journal : For Cell and Molecular Biology. PMID 34797944 DOI: 10.1111/tpj.15589  0.784
2021 Gouveia-Mageste BC, Martins LGC, Dal-Bianco M, Machado JPB, da Silva JCF, Kim AY, Yazaki J, Dos Santos AA, Ecker JR, Fontes EPB. A plant-specific syntaxin-6 protein contributes to the intracytoplasmic route for the begomovirus CabLCV. Plant Physiology. 187: 158-173. PMID 34618135 DOI: 10.1093/plphys/kiab252  0.695
2021 Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, ... ... Ecker JR, et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 598: 129-136. PMID 34616068 DOI: 10.1038/s41586-021-03604-1  0.814
2021 Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, ... ... Ecker JR, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 598: 103-110. PMID 34616066 DOI: 10.1038/s41586-021-03500-8  0.794
2021 Zhang Z, Zhou J, Tan P, Pang Y, Rivkin AC, Kirchgessner MA, Williams E, Lee CT, Liu H, Franklin AD, Miyazaki PA, Bartlett A, Aldridge AI, Vu M, Boggeman L, ... ... Ecker JR, et al. Epigenomic diversity of cortical projection neurons in the mouse brain. Nature. 598: 167-173. PMID 34616065 DOI: 10.1038/s41586-021-03223-w  0.766
2021 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, ... ... Ecker JR, et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 598: 111-119. PMID 34616062 DOI: 10.1038/s41586-021-03465-8  0.804
2021 Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, ... ... Ecker JR, et al. DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 598: 120-128. PMID 34616061 DOI: 10.1038/s41586-020-03182-8  0.812
2021 Farhy-Tselnicker I, Boisvert MM, Liu H, Dowling C, Erikson GA, Blanco-Suarez E, Farhy C, Shokhirev MN, Ecker JR, Allen NJ. Activity-dependent modulation of synapse-regulating genes in astrocytes. Elife. 10. PMID 34494546 DOI: 10.7554/eLife.70514  0.592
2021 Willige BC, Zander M, Yoo CY, Phan A, Garza RM, Trigg SA, He Y, Nery JR, Chen H, Chen M, Ecker JR, Chory J. PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. Nature Genetics. PMID 34140685 DOI: 10.1038/s41588-021-00882-3  0.813
2021 Ruf-Zamojski F, Zhang Z, Zamojski M, Smith GR, Mendelev N, Liu H, Nudelman G, Moriwaki M, Pincas H, Castanon RG, Nair VD, Seenarine N, Amper MAS, Zhou X, Ongaro L, ... ... Ecker JR, et al. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nature Communications. 12: 2677. PMID 33976139 DOI: 10.1038/s41467-021-22859-w  0.642
2021 Gao C, Liu J, Kriebel AR, Preissl S, Luo C, Castanon R, Sandoval J, Rivkin A, Nery JR, Behrens MM, Ecker JR, Ren B, Welch JD. Iterative single-cell multi-omic integration using online learning. Nature Biotechnology. PMID 33875866 DOI: 10.1038/s41587-021-00867-x  0.678
2021 de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, et al. The emergence of the brain non-CpG methylation system in vertebrates. Nature Ecology & Evolution. PMID 33462491 DOI: 10.1038/s41559-020-01371-2  0.683
2021 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Ecker JR, et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. PMID 33398137 DOI: 10.1038/s41586-020-03089-4  0.582
2020 Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe F, Sandoval JP, Krasileva KV, Borisjuk L, ... ... Ecker J, et al. Genome and time-of-day transcriptome of link morphological minimization with gene loss and less growth control. Genome Research. PMID 33361111 DOI: 10.1101/gr.266429.120  0.805
2020 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Ecker JR, et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. PMID 33037424 DOI: 10.1038/s41586-020-2841-4  0.58
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Ecker JR, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.729
2020 He Y, Hariharan M, Gorkin DU, Dickel DE, Luo C, Castanon RG, Nery JR, Lee AY, Zhao Y, Huang H, Williams BA, Trout D, Amrhein H, Fang R, Chen H, ... ... Ecker JR, et al. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature. 583: 752-759. PMID 32728242 DOI: 10.1038/S41586-020-2119-X  0.814
2020 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, ... ... Ecker JR, et al. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 583: 744-751. PMID 32728240 DOI: 10.1038/S41586-020-2093-3  0.683
2020 Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, ... Ecker JR, et al. Publisher Correction: Integrated multi-omics framework of the plant response to jasmonic acid. Nature Plants. PMID 32694625 DOI: 10.1038/S41477-020-0743-Y  0.775
2020 Paniza T, Deshpande M, Wang N, O'Neil R, Zuccaro MV, Smith ME, Madireddy A, James D, Ecker J, Rosenwaks Z, Egli D, Gerhardt J. Pluripotent stem cells with low differentiation potential contain incompletely reprogrammed DNA replication. The Journal of Cell Biology. 219. PMID 32673399 DOI: 10.1083/Jcb.201909163  0.368
2020 Wierbowski SD, Vo TV, Falter-Braun P, Jobe TO, Kruse LH, Wei X, Liang J, Meyer MJ, Akturk N, Rivera-Erick CA, Cordero NA, Paramo MI, Shayhidin EE, Bertolotti M, Tippens ND, ... ... Ecker JR, et al. A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proceedings of the National Academy of Sciences of the United States of America. PMID 32398372 DOI: 10.1073/Pnas.1918068117  0.327
2020 Kim EJ, Zhang Z, Huang L, Ito-Cole T, Jacobs MW, Juavinett AL, Senturk G, Hu M, Ku M, Ecker JR, Callaway EM. Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population. Neuron. PMID 32396852 DOI: 10.1016/J.Neuron.2020.04.018  0.743
2020 Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, ... Ecker JR, et al. Integrated multi-omics framework of the plant response to jasmonic acid. Nature Plants. 6: 290-302. PMID 32170290 DOI: 10.1038/S41477-020-0605-7  0.821
2020 Lavery LA, Ure K, Wan YW, Luo C, Trostle AJ, Wang W, Jin H, Lopez J, Lucero J, Durham MA, Castanon R, Nery JR, Liu Z, Goodell M, Ecker JR, et al. Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome. Elife. 9. PMID 32159514 DOI: 10.7554/Elife.52981  0.721
2020 Burko Y, Seluzicki A, Zander M, Pedmale U, Ecker JR, Chory J. Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism. The Plant Cell. PMID 32086365 DOI: 10.1105/Tpc.19.00772  0.778
2020 Lavery LA, Ure K, Wan Y, Luo C, Trostle AJ, Wang W, Jin H, Lopez J, Lucero J, Durham MA, Castanon R, Nery JR, Liu Z, Goodell M, Ecker JR, et al. Author response: Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome Elife. DOI: 10.7554/Elife.52981.Sa2  0.686
2020 Ruf-Zamojski FM, Zamojski MA, Nudelman G, Ge Y, Mendelev N, Smith GR, Zhou X, Toufaily C, Schang G, Gambino LO, Liu H, Gomez Castanon RG, Moriwaki M, Nair V, Pincas H, ... ... Ecker JR, et al. SAT-298 Integrative Single-Cell Transcriptomic and Epigenomic Landscape of Mouse Anterior Pituitary Cell Types Journal of the Endocrine Society. 4. DOI: 10.1210/Jendso/Bvaa046.593  0.67
2020 Behrens M, Lai C, Pinto-Duarte A, Li J, Luo C, Powell S, Ecker J, Mukamel E. Using the Power of Single-Nucleus Epigenomics to Map the Molecular Complexity of the Adult Brain Biological Psychiatry. 87: S61-S62. DOI: 10.1016/J.Biopsych.2020.02.179  0.763
2019 Sasaki E, Kawakatsu T, Ecker JR, Nordborg M. Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana. Plos Genetics. 15: e1008492. PMID 31887137 DOI: 10.1371/Journal.Pgen.1008492  0.67
2019 Ortigosa A, Fonseca S, Franco-Zorrilla JM, Fernandez-Calvo P, Zander M, Lewsey MG, García-Casado G, Fernández-Barbero G, Ecker JR, Solano R. The JA-pathway MYC transcription factors regulate photomorphogenic responses by targeting HY5 gene expression. The Plant Journal : For Cell and Molecular Biology. PMID 31755159 DOI: 10.1111/Tpj.14618  0.809
2019 Van Moerkercke A, Duncan O, Zander M, Šimura J, Broda M, Vanden Bossche R, Lewsey MG, Lama S, Singh KB, Ljung K, Ecker JR, Goossens A, Millar AH, Van Aken O. A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels. Proceedings of the National Academy of Sciences of the United States of America. PMID 31662474 DOI: 10.1073/Pnas.1911758116  0.813
2019 Brigidi GS, Hayes MGB, Delos Santos NP, Hartzell AL, Texari L, Lin PA, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL. Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers. Cell. 179: 373-391.e27. PMID 31585079 DOI: 10.1016/J.Cell.2019.09.004  0.345
2019 Lee DS, Luo C, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nature Methods. PMID 31501549 DOI: 10.1038/S41592-019-0547-Z  0.82
2019 Salehin M, Li B, Tang M, Katz E, Song L, Ecker JR, Kliebenstein DJ, Estelle M. Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels. Nature Communications. 10: 4021. PMID 31492889 DOI: 10.1038/S41467-019-12002-1  0.573
2019 Kawakatsu T, Ecker JR. Diversity and dynamics of DNA methylation: epigenomic resources and tools for crop breeding. Breeding Science. 69: 191-204. PMID 31481828 DOI: 10.1270/Jsbbs.19005  0.681
2019 Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nery JR, Chen H, Zhang Z, Jupe F, Stepanova A, ... ... Ecker JR, et al. Epigenetic silencing of a multifunctional plant stress regulator. Elife. 8. PMID 31418686 DOI: 10.7554/Elife.47835  0.802
2019 Zhou J, Ma J, Chen Y, Cheng C, Bao B, Peng J, Sejnowski TJ, Dixon JR, Ecker JR. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31235599 DOI: 10.1073/Pnas.1901423116  0.77
2019 Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, Slotkin RK, Chen H, Castanon R, Nery JR, Ecker JR. The complex architecture and epigenomic impact of plant T-DNA insertions. Plos Genetics. 15: e1007819. PMID 30657772 DOI: 10.1371/Journal.Pgen.1007819  0.811
2019 Luo C, Lee QY, Wapinski O, Castanon R, Nery JR, Mall M, Kareta MS, Cullen SM, Goodell MA, Chang HY, Wernig M, Ecker JR. Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. Elife. 8. PMID 30644360 DOI: 10.7554/Elife.40197  0.728
2019 Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nery JR, Chen H, Zhang Z, Jupe F, Stepanova A, ... ... Ecker JR, et al. Author response: Epigenetic silencing of a multifunctional plant stress regulator Elife. DOI: 10.7554/Elife.47835.027  0.784
2018 Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, ... Ecker JR, et al. OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. Elife. 7. PMID 30325306 DOI: 10.7554/Elife.34870  0.799
2018 Luo C, Hajkova P, Ecker JR. Dynamic DNA methylation: In the right place at the right time. Science (New York, N.Y.). 361: 1336-1340. PMID 30262495 DOI: 10.1126/Science.Aat6806  0.747
2018 Luo C, Rivkin A, Zhou J, Sandoval JP, Kurihara L, Lucero J, Castanon R, Nery JR, Pinto-Duarte A, Bui B, Fitzpatrick C, O'Connor C, Ruga S, Van Eden ME, Davis DA, ... ... Ecker JR, et al. Robust single-cell DNA methylome profiling with snmC-seq2. Nature Communications. 9: 3824. PMID 30237449 DOI: 10.1038/S41467-018-06355-2  0.795
2018 Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. Elife. 7. PMID 30188322 DOI: 10.7554/Elife.36187  0.715
2018 Yazaki J, Galli M, Kim AY, Ecker JR. Profiling Interactome Networks with the HaloTag-NAPPA In Situ Protein Array. Current Protocols in Plant Biology. e20071. PMID 30106517 DOI: 10.1002/cppb.20071  0.78
2018 Michael TP, Jupe F, Bemm F, Motley ST, Sandoval JP, Lanz C, Loudet O, Weigel D, Ecker JR. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nature Communications. 9: 541. PMID 29416032 DOI: 10.1038/S41467-018-03016-2  0.757
2018 Luo C, Lee QY, Wapinski O, Castanon R, Nery JR, Mall M, Kareta MS, Cullen SM, Goodell MA, Chang HY, Wernig M, Ecker JR. Author response: Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons Elife. DOI: 10.7554/Elife.40197.020  0.712
2018 Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. Author response: Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells Elife. DOI: 10.7554/Elife.36187.042  0.68
2017 Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, et al. Challenges and recommendations for epigenomics in precision health. Nature Biotechnology. 35: 1128-1132. PMID 29220033 DOI: 10.1038/Nbt.4030  0.361
2017 Huang SC, Ecker JR. Piecing together cis-regulatory networks: insights from epigenomics studies in plants. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 29194997 DOI: 10.1002/Wsbm.1411  0.705
2017 Kawakatsu T, Nery JR, Castanon R, Ecker JR. Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biology. 18: 171. PMID 28911331 DOI: 10.1186/S13059-017-1251-X  0.681
2017 Luo C, Keown CL, Kurihara L, Zhou J, He Y, Li J, Castanon R, Lucero J, Nery JR, Sandoval JP, Bui B, Sejnowski TJ, Harkins TT, Mukamel EA, Behrens MM, ... Ecker JR, et al. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science (New York, N.Y.). 357: 600-604. PMID 28798132 DOI: 10.1126/Science.Aan3351  0.792
2017 Bartlett A, O'Malley RC, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker JR. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nature Protocols. 12: 1659-1672. PMID 28726847 DOI: 10.1038/Nprot.2017.055  0.809
2017 Trigg SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nature Methods. PMID 28650476 DOI: 10.1038/Nmeth.4343  0.791
2017 Hsia MM, O'Malley R, Cartwright A, Nieu R, Gordon SP, Kelly S, Williams TG, Wood DF, Zhao Y, Bragg J, Jordan M, Pauly M, Ecker JR, Gu Y, Vogel JP. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. The Plant Journal : For Cell and Molecular Biology. PMID 28432803 DOI: 10.1111/Tpj.13582  0.707
2017 Keown CL, Berletch JB, Castanon R, Nery JR, Disteche CM, Ecker JR, Mukamel EA. Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain. Proceedings of the National Academy of Sciences of the United States of America. PMID 28320934 DOI: 10.1073/Pnas.1611905114  0.392
2017 He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR. Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28193886 DOI: 10.1073/Pnas.1618353114  0.681
2017 Shani E, Salehin M, Zhang Y, Sanchez SE, Doherty C, Wang R, Mangado CC, Song L, Tal I, Pisanty O, Ecker JR, Kay SA, Pruneda-Paz J, Estelle M. Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. Current Biology : Cb. PMID 28111153 DOI: 10.1016/J.Cub.2016.12.016  0.597
2017 Hossain MS, Kawakatsu T, Kim KD, Ning Z, Nguyen CT, Khan SM, Batek JM, Joshi T, Schmutz J, Grimwood J, Schmitz RJ, Xu D, Jackson SA, Ecker JR, Stacey G. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. The New Phytologist. PMID 28106918 DOI: 10.1111/Nph.14421  0.76
2017 Trigg S, Garza R, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang Z, Galli M, Ecker JR. CrY2H-seq interactome screening Protocol Exchange. DOI: 10.1038/Protex.2017.058  0.746
2016 Song L, Koga Y, Ecker JR. Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq). Current Protocols in Plant Biology. 1: 293-306. PMID 28782043 DOI: 10.1002/cppb.20014  0.56
2016 Luo C, Lancaster MA, Castanon R, Nery JR, Knoblich JA, Ecker JR. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain. Cell Reports. 17: 3369-3384. PMID 28009303 DOI: 10.1016/J.Celrep.2016.12.001  0.693
2016 Gimenez-Ibanez S, Boter M, Ortigosa A, García-Casado G, Chini A, Lewsey MG, Ecker JR, Ntoukakis V, Solano R. JAZ2 controls stomata dynamics during bacterial invasion. The New Phytologist. PMID 28005270 DOI: 10.1111/Nph.14354  0.784
2016 Narsai R, Secco D, Schultz MD, Ecker JR, 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. The Plant Journal : For Cell and Molecular Biology. PMID 27859855 DOI: 10.1111/Tpj.13418  0.645
2016 Ma H, O'Neil RC, Marti Gutierrez N, Hariharan M, Zhang ZZ, He Y, Cinnioglu C, Kayali R, Kang E, Lee Y, Hayama T, Koski A, Nery J, Castanon R, Tippner-Hedges R, ... ... Ecker JR, et al. Functional Human Oocytes Generated by Transfer of Polar Body Genomes. Cell Stem Cell. PMID 27840020 DOI: 10.1016/J.Stem.2016.10.001  0.79
2016 Song L, Huang SC, Wise A, Castanon R, Nery JR, Chen H, Watanabe M, Thomas J, Bar-Joseph Z, Ecker JR. A transcription factor hierarchy defines an environmental stress response network. Science (New York, N.Y.). 354. PMID 27811239 DOI: 10.1126/Science.Aag1550  0.727
2016 Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods. PMID 27749838 DOI: 10.1038/Nmeth.4035  0.782
2016 Zhang F, Qi B, Wang L, Zhao B, Rode S, Riggan ND, Ecker JR, Qiao H. EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling. Nature Communications. 7: 13018. PMID 27694846 DOI: 10.1038/Ncomms13018  0.811
2016 O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 166: 1598. PMID 27610578 DOI: 10.1016/J.Cell.2016.08.063  0.779
2016 Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP. Integration of omic networks in a developmental atlas of maize. Science (New York, N.Y.). 353: 814-8. PMID 27540173 DOI: 10.1126/Science.Aag1125  0.58
2016 Theunissen TW, Friedli M, He Y, Planet E, O'Neil RC, Markoulaki S, Pontis J, Wang H, Iouranova A, Imbeault M, Duc J, Cohen MA, Wert KJ, Castanon R, Zhang Z, ... ... Ecker JR, et al. Molecular Criteria for Defining the Naive Human Pluripotent State. Cell Stem Cell. PMID 27424783 DOI: 10.1016/J.Stem.2016.06.011  0.785
2016 Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, ... ... Ecker JR, et al. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 166: 492-505. PMID 27419873 DOI: 10.1016/J.Cell.2016.06.044  0.822
2016 Aleman F, Yazaki J, Lee M, Takahashi Y, Kim AY, Li Z, Kinoshita T, Ecker JR, Schroeder JI. An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling. Scientific Reports. 6: 28941. PMID 27357749 DOI: 10.1038/Srep28941  0.727
2016 Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SC, Chen H, Ramachandran N, Altmann S, ... ... Ecker JR, et al. Mapping transcription factor interactome networks using HaloTag protein arrays. Proceedings of the National Academy of Sciences of the United States of America. PMID 27357687 DOI: 10.1073/Pnas.1603229113  0.802
2016 Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. Unique cell-type-specific patterns of DNA methylation in the root meristem. Nature Plants. 2: 16058. PMID 27243651 DOI: 10.1038/Nplants.2016.58  0.83
2016 O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 165: 1280-1292. PMID 27203113 DOI: 10.1016/J.Cell.2016.04.038  0.806
2016 Prigge M, Greenham K, Zhang Y, Santner A, Castillejo C, Mutka AM, O'Malley RC, Ecker JR, Kunkel BN, Estelle M. The Arabidopsis Auxin Receptor F-box proteins AFB4 and AFB5 are Required for Response to the Synthetic Auxin Picloram. G3 (Bethesda, Md.). PMID 26976444 DOI: 10.1534/G3.115.025585  0.689
2016 Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J. Epigenomic landscapes of retinal rods and cones. Elife. 5. PMID 26949250 DOI: 10.7554/Elife.11613  0.802
2016 Bogdanović O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra GJ, Manzanares M, ... ... Ecker JR, et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nature Genetics. PMID 26928226 DOI: 10.1038/Ng.3522  0.672
2016 Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR. Mobile small RNAs regulate genome-wide DNA methylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26787884 DOI: 10.1073/Pnas.1515072113  0.829
2016 Sanchez-Mut JV, Heyn H, Vidal E, Moran S, Sayols S, Delgado-Morales R, Schultz MD, Ansoleaga B, Garcia-Esparcia P, Pons-Espinal M, de Lagran MM, Dopazo J, Rabano A, Avila J, Dierssen M, ... ... Ecker JR, et al. Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. Translational Psychiatry. 6: e718. PMID 26784972 DOI: 10.1038/Tp.2015.214  0.327
2015 Pedmale UV, Huang SC, Zander M, Cole BJ, Hetzel J, Ljung K, Reis PA, Sridevi P, Nito K, Nery JR, Ecker JR, Chory J. Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light. Cell. PMID 26724867 DOI: 10.1016/J.Cell.2015.12.018  0.798
2015 Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, ... ... Ecker JR, et al. Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. PMID 26605523 DOI: 10.1038/Nature16179  0.65
2015 Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M. methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. Bmc Bioinformatics. 16: 313. PMID 26415965 DOI: 10.1186/S12859-015-0742-6  0.694
2015 Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella PA, Li S, Weigel D, Pontes O, Ecker JR, Chen X. Correction: DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis. Plos Genetics. 11: e1005452. PMID 26379054 DOI: 10.1371/journal.pgen.1005452  0.583
2015 Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker JR, Kay SA. Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 112: E4802-10. PMID 26261339 DOI: 10.1073/Pnas.1513609112  0.639
2015 Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife. 4. PMID 26196146 DOI: 10.7554/Elife.09343  0.679
2015 Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron. 86: 1369-84. PMID 26087164 DOI: 10.1016/J.Neuron.2015.05.018  0.795
2015 He Y, Ecker JR. Non-CG Methylation in the Human Genome. Annual Review of Genomics and Human Genetics. 16: 55-77. PMID 26077819 DOI: 10.1146/Annurev-Genom-090413-025437  0.692
2015 Luo C, Ecker JR. Exceptional epigenetics in the brain Science. 348: 1094-1095. PMID 26045424 DOI: 10.1126/Science.Aac5832  0.731
2015 Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, ... ... Ecker JR, et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 523: 212-6. PMID 26030523 DOI: 10.1038/Nature14465  0.673
2015 Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, ... ... Ecker JR, et al. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 521: 316-21. PMID 25945737 DOI: 10.1038/Nature14413  0.776
2015 O'Malley RC, Barragan CC, Ecker JR. A user's guide to the Arabidopsis T-DNA insertion mutant collections. Methods in Molecular Biology (Clifton, N.J.). 1284: 323-42. PMID 25757780 DOI: 10.1007/978-1-4939-2444-8_16  0.698
2015 Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, ... ... Ecker JR, et al. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 518: 350-4. PMID 25693566 DOI: 10.1038/Nature14217  0.342
2015 Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 518: 331-6. PMID 25693564 DOI: 10.1038/Nature14222  0.411
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Ecker JR, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.656
2015 Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols. 10: 475-83. PMID 25692984 DOI: 10.1038/Nprot.2014.114  0.76
2015 Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J. Author response: Epigenomic landscapes of retinal rods and cones Elife. DOI: 10.7554/Elife.11613.056  0.742
2015 Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. Author response: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements Elife. DOI: 10.7554/Elife.09343.035  0.65
2015 Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing Nature Protocols. 10: 475-483. DOI: 10.1038/nprot.2014.114  0.563
2014 Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. Comparison of the transcriptional landscapes between human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America. 111: 17224-9. PMID 25413365 DOI: 10.1073/Pnas.1413624111  0.476
2014 Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, ... ... Ecker JR, et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 158: 1431-43. PMID 25215497 DOI: 10.1016/J.Cell.2014.08.009  0.81
2014 Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, ... ... Ecker JR, et al. The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. Cell Stem Cell. 15: 295-309. PMID 25192464 DOI: 10.1016/J.Stem.2014.07.003  0.695
2014 Yu W, McIntosh C, Lister R, Zhu I, Han Y, Ren J, Landsman D, Lee E, Briones V, Terashima M, Leighty R, Ecker JR, Muegge K. Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways. Genome Research. 24: 1613-23. PMID 25170028 DOI: 10.1101/Gr.172015.114  0.686
2014 Catalá R, López-Cobollo R, Mar Castellano M, Angosto T, Alonso JM, Ecker JR, 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. The Plant Cell. 26: 3326-42. PMID 25122152 DOI: 10.1105/Tpc.114.127605  0.527
2014 Pruneda-Paz JL, Breton G, Nagel DH, Kang SE, Bonaldi K, Doherty CJ, Ravelo S, Galli M, Ecker JR, Kay SA. A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Reports. 8: 622-32. PMID 25043187 DOI: 10.1016/J.Celrep.2014.06.033  0.765
2014 Ma H, Morey R, O'Neil RC, He Y, Daughtry B, Schultz MD, Hariharan M, Nery JR, Castanon R, Sabatini K, Thiagarajan RD, Tachibana M, Kang E, Tippner-Hedges R, Ahmed R, ... ... Ecker JR, et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature. 511: 177-83. PMID 25008523 DOI: 10.1038/Nature13551  0.646
2014 Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella P, Weigel D, Pontes O, Ecker JR, Chen X. DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis Plos Genetics. 10. PMID 24992598 DOI: 10.1371/Journal.Pgen.1004446  0.649
2014 Yu W, Briones V, Lister R, McIntosh C, Han Y, Lee EY, Ren J, Terashima M, Leighty RM, Ecker JR, Muegge K. CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity. Proceedings of the National Academy of Sciences of the United States of America. 111: 5890-5. PMID 24711395 DOI: 10.1073/Pnas.1320945111  0.677
2014 Looney TJ, Zhang L, Chen CH, Lee JH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker SW, Fernandes CJ, Gaetz J, Foshay KM, Clift KL, Zhang Z, ... ... Ecker JR, et al. Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Genome Research. 24: 267-80. PMID 24310002 DOI: 10.1101/Gr.143891.112  0.669
2014 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, ... ... Ecker JR, et al. Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells Nature. 514: 126. DOI: 10.1038/Nature13843  0.737
2014 Valdés-López O, Khan SM, Schmitz RJ, Cui S, Qiu J, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. Genotypic variation of gene expression during the soybean innate immunity response Plant Genetic Resources: Characterisation and Utilisation. 12: S27-S30. DOI: 10.1017/S1479262114000197  0.609
2013 Hua Z, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR, Vierstra RD. Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis Proceedings of the National Academy of Sciences of the United States of America. 110: 16927-16932. PMID 24082131 DOI: 10.1073/Pnas.1316009110  0.671
2013 Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics (Oxford, England). 29: 3204-3210. PMID 24078702 DOI: 10.1093/Bioinformatics/Btt558  0.567
2013 Schweizer F, Fernández-Calvo P, Zander M, Diez-Diaz M, Fonseca S, Glauser G, Lewsey MG, Ecker JR, Solano R, Reymond P. Arabidopsis basic helix-loop-helix transcription factors MYC2,MYC3, andMYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior Plant Cell. 25: 3117-3132. PMID 23943862 DOI: 10.1105/Tpc.113.115139  0.813
2013 Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, ... ... Ecker JR, et al. Global epigenomic reconfiguration during mammalian brain development. Science (New York, N.Y.). 341: 1237905. PMID 23828890 DOI: 10.1126/Science.1237905  0.657
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, ... ... Ecker JR, et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2: e00675. PMID 23795294 DOI: 10.7554/Elife.00675  0.814
2013 Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Research. 23: 1663-74. PMID 23739894 DOI: 10.1101/Gr.152538.112  0.753
2013 Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. Response to perspective: "separation anxiety: an analysis of ethylene-induced cleavage of EIN2". Plant Signaling & Behavior. 8. PMID 23733051 DOI: 10.4161/Psb.25037  0.674
2013 Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, ... ... Ecker JR, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/J.Cell.2013.04.022  0.668
2013 Hill K, Mathews DE, Kim HJ, Street IH, Wildes SL, Chiang YH, Mason MG, Alonso JM, Ecker JR, Kieber JJ, Schaller GE. Functional characterization of type-B response regulators in the Arabidopsis cytokinin response. Plant Physiology. 162: 212-24. PMID 23482873 DOI: 10.1104/Pp.112.208736  0.691
2013 Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR. Patterns of population epigenomic diversity. Nature. 495: 193-8. PMID 23467092 DOI: 10.1038/Nature11968  0.627
2013 Ecker JR. Epigenetic trigger for tomato ripening Nature Biotechnology. 31: 119-120. PMID 23392509 DOI: 10.1038/Nbt.2497  0.334
2013 Woodson JD, Perez-Ruiz JM, Schmitz RJ, Ecker JR, Chory J. Sigma factor-mediated plastid retrograde signals control nuclear gene expression. The Plant Journal : For Cell and Molecular Biology. 73: 1-13. PMID 22950756 DOI: 10.1111/Tpj.12011  0.707
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SC, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, ... ... Ecker JR, et al. Author response: Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis Elife. DOI: 10.7554/Elife.00675.022  0.785
2013 Chung W, Schmitz RJ, Biorac T, Ye D, Dudas M, Meredith GD, Adams CC, Ecker JR, Zhang MQ. Constructing Hepitypes: Phasing Local Genotype and DNA Methylation Journal of Neuroscience and Neuroengineering. 2: 335-346. DOI: 10.1166/Jnsne.2013.1067  0.636
2012 O'Malley RC, Ecker JR. Epiallelic variation in Arabidopsis thaliana. Cold Spring Harbor Symposia On Quantitative Biology. 77: 135-45. PMID 23223383 DOI: 10.1101/Sqb.2012.77.014571  0.72
2012 Vollmers C, Schmitz RJ, Nathanson J, Yeo G, Ecker JR, Panda S. Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome Cell Metabolism. 16: 833-845. PMID 23217262 DOI: 10.1016/J.Cmet.2012.11.004  0.619
2012 Schultz MD, Schmitz RJ, Ecker JR. 'Leveling' the playing field for analyses of single-base resolution DNA methylomes Trends in Genetics. 28: 583-585. PMID 23131467 DOI: 10.1016/J.Tig.2012.10.012  0.621
2012 Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. Processing and subcellular trafficking of ER-tethered EIN2 control response to ethylene gas. Science (New York, N.Y.). 338: 390-3. PMID 22936567 DOI: 10.1126/Science.1225974  0.701
2012 Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Jordan Rowley M, Gregory BD, Ecker JR, Tang H, Pikaard CS. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome Genes and Development. 26: 1825-1836. PMID 22855789 DOI: 10.1101/Gad.197772.112  0.748
2012 Berger F, Cao X, Chandler V, Dennis L, Martienssen R, Meyers B, Pikaard C, Peacock J, Richards E, Wagner D, Weigel D, Colot V, Deal R, Dean C, Ecker J, et al. Reading the second code: Mapping epigenomes to understand plant growth, development, and adaptation to the environment Plant Cell. 24: 2257-2261. PMID 22751210 DOI: 10.1105/tpc.112.100636  0.569
2012 Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the National Academy of Sciences of the United States of America. 109: E2183-91. PMID 22733782 DOI: 10.1073/Pnas.1209329109  0.826
2012 Peng Q, Ecker JR. Detection of allele-specific methylation through a generalized heterogeneous epigenome model Bioinformatics. 28: i163-i171. PMID 22689757 DOI: 10.1093/Bioinformatics/Bts231  0.524
2012 Johnson DBF, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker JR, Wang L. Release factor one is nonessential in escherichia coli Acs Chemical Biology. 7: 1337-1344. PMID 22662873 DOI: 10.1021/Cb300229Q  0.555
2012 Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Okubo-Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker JR. Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis. G3 (Bethesda, Md.). 2: 487-98. PMID 22540040 DOI: 10.1534/G3.111.001362  0.759
2012 Li L, Ljung K, Breton G, Schmitz RJ, Pruneda-Paz J, Cowing-Zitron C, Cole BJ, Ivans LJ, Pedmale UV, Jung HS, Ecker JR, Kay SA, Chory J. Linking photoreceptor excitation to changes in plant architecture. Genes & Development. 26: 785-90. PMID 22508725 DOI: 10.1101/Gad.187849.112  0.705
2012 Schmitz RJ, Ecker JR. Epigenetic and epigenomic variation in Arabidopsis thaliana Trends in Plant Science. 17: 149-154. PMID 22342533 DOI: 10.1016/J.Tplants.2012.01.001  0.62
2012 Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research. 22: 246-58. PMID 22156296 DOI: 10.1101/Gr.125872.111  0.649
2011 Hotto AM, Schmitz RJ, Fei Z, Ecker JR, Stern DB. Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome. G3 (Bethesda, Md.). 1: 559-70. PMID 22384367 DOI: 10.1534/G3.111.000752  0.601
2011 Elling U, Taubenschmid J, Wirnsberger G, O'Malley R, Demers SP, Vanhaelen Q, Shukalyuk AI, Schmauss G, Schramek D, Schnuetgen F, Von Melchner H, Ecker JR, Stanford WL, Zuber J, Stark A, et al. Forward and reverse genetics through derivation of haploid mouse embryonic stem cells Cell Stem Cell. 9: 563-574. PMID 22136931 DOI: 10.1016/J.Stem.2011.10.012  0.676
2011 Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD, Schmitz RJ, Xiang Z, Ecker JR, Briggs SP, Wang L. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nature Chemical Biology. 7: 779-86. PMID 21926996 DOI: 10.1038/Nchembio.657  0.555
2011 Schmitz RJ, Schultz MD, Lewsey MG, O'Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. Transgenerational epigenetic instability is a source of novel methylation variants. Science (New York, N.Y.). 334: 369-73. PMID 21921155 DOI: 10.1126/Science.1212959  0.81
2011 Mukhtar MS, Carvunis AR, Dreze M, Epple P, Steinbrenner J, Moore J, Tasan M, Galli M, Hao T, Nishimura MT, Pevzner SJ, Donovan SE, Ghamsari L, Santhanam B, Romero V, ... ... Ecker JR, et al. Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science (New York, N.Y.). 333: 596-601. PMID 21798943 DOI: 10.1126/Science.1203659  0.718
2011 Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 473: 394-7. PMID 21552279 DOI: 10.1038/Nature10102  0.687
2011 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, ... ... Ecker JR, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. PMID 21289626 DOI: 10.1038/Nature09798  0.778
2011 Pelizzola M, Ecker JR. The DNA methylome Febs Letters. 585: 1994-2000. PMID 21056564 DOI: 10.1016/J.Febslet.2010.10.061  0.414
2010 Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, ... ... Ecker JR, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/Nbt.1682  0.624
2010 Boutrot F, Segonzac C, Chang KN, Qiao H, Ecker JR, Zipfel C, Rathjen JP. Direct transcriptional control of the Arabidopsis immune receptor FLS2 by the ethylene-dependent transcription factors EIN3 and EIL1 Proceedings of the National Academy of Sciences of the United States of America. 107: 14502-14507. PMID 20663954 DOI: 10.1073/Pnas.1003347107  0.763
2010 An F, Zhao Q, Ji Y, Li W, Jiang Z, Yu X, Zhang C, Han Y, He W, Liu Y, Zhang S, Ecker JR, 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 Plant Cell. 22: 2384-2401. PMID 20647342 DOI: 10.1105/Tpc.110.076588  0.69
2010 Ecker JR. Zeroing in on DNA methylomes with no BS Nature Methods. 7: 435-436. PMID 20508637 DOI: 10.1038/Nmeth0610-435  0.328
2010 Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, ... ... Ecker JR, et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6: 479-91. PMID 20452322 DOI: 10.1016/J.Stem.2010.03.018  0.668
2010 O'Malley RC, Ecker JR. Linking genotype to phenotype using the Arabidopsis unimutant collection. The Plant Journal : For Cell and Molecular Biology. 61: 928-40. PMID 20409268 DOI: 10.1111/J.1365-313X.2010.04119.X  0.719
2010 Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, ... ... Ecker JR, et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 465: 627-31. PMID 20336072 DOI: 10.1038/Nature08800  0.693
2010 Endres MW, Gregory BD, Gao Z, Foreman AW, Mlotshwa S, Ge X, Pruss GJ, Ecker JR, Bowman LH, Vance V. Two plant viral suppressors of silencing require the ethylene-inducible host transcription factor RAV2 to block RNA silencing Plos Pathogens. 6. PMID 20084269 DOI: 10.1371/Journal.Ppat.1000729  0.649
2009 Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, ... ... Ecker JR, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462: 315-22. PMID 19829295 DOI: 10.1038/Nature08514  0.822
2009 Tsuchisaka A, Yu G, Jin H, Alonso JM, Ecker JR, Zhang X, Gao S, Theologis A. A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana. Genetics. 183: 979-1003. PMID 19752216 DOI: 10.1534/Genetics.109.107102  0.56
2009 Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, ... ... Ecker JR, et al. Prepublication data sharing. Nature. 461: 168-70. PMID 19741685 DOI: 10.1038/461168A  0.572
2009 Liljegren SJ, Leslie ME, Darnielle L, Lewis MW, Taylor SM, Luo R, Geldner N, Chory J, Randazzo PA, Yanofsky MF, Ecker JR. Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein. Development (Cambridge, England). 136: 1909-18. PMID 19429787 DOI: 10.1242/Dev.033605  0.808
2009 Dowen RH, Engel JL, Shao F, Ecker JR, Dixon JE. A family of bacterial cysteine protease type III effectors utilizes acylation-dependent and -independent strategies to localize to plasma membranes. The Journal of Biological Chemistry. 284: 15867-79. PMID 19346252 DOI: 10.1074/Jbc.M900519200  0.78
2009 Lister R, Ecker JR. Finding the fifth base: Genome-wide sequencing of cytosine methylation Genome Research. 19: 959-966. PMID 19273618 DOI: 10.1101/Gr.083451.108  0.657
2009 Li H, Wai SW, Zhu L, Hong WG, Ecker J, Li N. Phosphoproteomic analysis of ethylene-regulated protein phosphorylation in etiolated seedlings of Arabidopsis mutant ein2 using two-dimensional separations coupled with a hybrid quadrupole time-of-flight mass spectrometer Proteomics. 9: 1646-1661. PMID 19253305 DOI: 10.1002/Pmic.200800420  0.351
2009 Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biology. 10: R17. PMID 19210792 DOI: 10.1186/Gb-2009-10-2-R17  0.657
2009 Qiao H, Chang KN, Yazaki J, Ecker JR. Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis Genes and Development. 23: 512-521. PMID 19196655 DOI: 10.1101/Gad.1765709  0.803
2009 Lister R, Gregory BD, Ecker JR. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond Current Opinion in Plant Biology. 12: 107-118. PMID 19157957 DOI: 10.1016/J.Pbi.2008.11.004  0.763
2009 Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis AR, Simonis N, Rual JF, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, et al. Literature-curated protein interaction datasets. Nature Methods. 6: 39-46. PMID 19116613 DOI: 10.1038/Nmeth.1284  0.772
2009 Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis A, Simonis N, Rual J, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, et al. Addendum: Literature-curated protein interaction datasets Nature Methods. 6: 934-935. DOI: 10.1038/Nmeth1209-934  0.765
2008 Bender J, Benfey P, Bergmann D, Borevitz J, Coruzzi G, Dangl J, Dean C, Ecker J, Estelle M, Glazebrook J, Grant S, Guerinot ML, Gutierrez R, Long J, Nordborg M, et al. 2020 vision for biology: the role of plants in addressing grand challenges in biology. Molecular Plant. 1: 561-3. PMID 19825561 DOI: 10.1093/Mp/Ssn040  0.723
2008 Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR. A link between RNA metabolism and silencing affecting Arabidopsis development. Developmental Cell. 14: 854-66. PMID 18486559 DOI: 10.1016/J.Devcel.2008.04.005  0.786
2008 Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 133: 523-36. PMID 18423832 DOI: 10.1016/J.Cell.2008.03.029  0.824
2008 Hu J, Mitchum MG, Barnaby N, Ayele BT, Ogawa M, Nam E, Lai WC, Hanada A, Alonso JM, Ecker JR, Swain SM, Yamaguchi S, Kamiya Y, Sun TP. Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. The Plant Cell. 20: 320-36. PMID 18310462 DOI: 10.1105/Tpc.107.057752  0.503
2008 Gregory BD, Yazaki J, Ecker JR. Utilizing tiling microarrays for whole-genome analysis in plants Plant Journal. 53: 636-644. PMID 18269573 DOI: 10.1111/J.1365-313X.2007.03320.X  0.788
2008 Leivar P, Monte E, Al-Sady B, Carle C, Storer A, Alonso JM, Ecker JR, Quail PH. The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. The Plant Cell. 20: 337-52. PMID 18252845 DOI: 10.1105/Tpc.107.052142  0.479
2008 Ecker JR, Lister R, O'Malley RC, Tonti-Filippini J, Berry CC, Millar AH. Genome meets epigenome: Sequencing and analysis of the DNA methylome Developmental Biology. 319: 462. DOI: 10.1016/J.Ydbio.2008.05.004  0.771
2007 Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, Alonso J, Brukhin V, Grossniklaus U, Ecker JR, Belostotsky DA. Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome Cell. 131: 1340-1353. PMID 18160042 DOI: 10.1016/J.Cell.2007.10.056  0.796
2007 O'Malley RC, Alonso JM, Kim CJ, Leisse TJ, Ecker JR. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. Nature Protocols. 2: 2910-7. PMID 18007627 DOI: 10.1038/Nprot.2007.425  0.736
2007 Li H, He Z, Lu G, Lee SC, Alonso J, Ecker JR, Luan S. A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. The Plant Cell. 19: 2403-16. PMID 17704213 DOI: 10.1105/Tpc.107.053579  0.555
2007 Yazaki J, Gregory BD, Ecker JR. Mapping the genome landscape using tiling array technology Current Opinion in Plant Biology. 10: 534-542. PMID 17703988 DOI: 10.1016/J.Pbi.2007.07.006  0.806
2007 Gentry MS, Dowen RH, Worby CA, Mattoo S, Ecker JR, Dixon JE. The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease. The Journal of Cell Biology. 178: 477-88. PMID 17646401 DOI: 10.1083/Jcb.200704094  0.789
2007 Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Schölkopf B, Nordborg M, ... ... Ecker JR, et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (New York, N.Y.). 317: 338-42. PMID 17641193 DOI: 10.1126/Science.1138632  0.317
2007 Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter IR, Hu TT, Chen H, Werner JD, Nordborg M, Salt DE, Kay SA, Chory J, Weigel D, Jones JD, Ecker JR. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America. 104: 12057-62. PMID 17626786 DOI: 10.1073/Pnas.0705323104  0.716
2007 Swiezewski S, Crevillen P, Liu F, Ecker JR, Jerzmanowski A, Dean C. Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC. Proceedings of the National Academy of Sciences of the United States of America. 104: 3633-8. PMID 17360694 DOI: 10.1073/Pnas.0611459104  0.36
2006 Chilley PM, Casson SA, Tarkowski P, Hawkins N, Wang KLC, Hussey PJ, Beale M, Ecker JR, Sandberg GK, Lindsey K. The POLARIS peptide of Arabidopsis regulates auxin transport root growth via effects on ethylene signaling Plant Cell. 18: 3058-3072. PMID 17138700 DOI: 10.1105/Tpc.106.040790  0.515
2006 Hutchison CE, Li J, Argueso C, Gonzalez M, Lee E, Lewis MW, Maxwell BB, Perdue TD, Schaller GE, Alonso JM, Ecker JR, Kieber JJ. The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling. The Plant Cell. 18: 3073-87. PMID 17122069 DOI: 10.1105/Tpc.106.045674  0.798
2006 Kim SA, Punshon T, Lanzirotti A, Li L, Alonso JM, Ecker JR, Kaplan J, Guerinot ML. Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1. Science (New York, N.Y.). 314: 1295-8. PMID 17082420 DOI: 10.1126/Science.1132563  0.417
2006 Mori IC, Murata Y, Yang Y, Munemasa S, Wang YF, Andreoli S, Tiriac H, Alonso JM, Harper JF, Ecker JR, Kwak JM, Schroeder JI. CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion- and Ca(2+)-permeable channels and stomatal closure. Plos Biology. 4: e327. PMID 17032064 DOI: 10.1371/Journal.Pbio.0040327  0.475
2006 Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 126: 1189-201. PMID 16949657 DOI: 10.1016/J.Cell.2006.08.003  0.815
2006 Olmedo G, Guo H, Gregory BD, Nourizadeh SD, Aguilar-Henonin L, Li H, An F, Guzman P, Ecker JR. ETHYLENE-INSENSITIVE5 encodes a 5′→3′ exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2 Proceedings of the National Academy of Sciences of the United States of America. 103: 13286-13293. PMID 16920797 DOI: 10.1073/Pnas.0605528103  0.725
2006 Yoshida H, Wang KLC, Chang CM, Mori K, Uchida E, Ecker JR. The ACC synthase TOE sequence is required for interaction with ETO1 family proteins and destabilization of target proteins Plant Molecular Biology. 62: 427-437. PMID 16897471 DOI: 10.1007/S11103-006-9029-7  0.666
2006 Chen JG, Ullah H, Temple B, Liang J, Guo J, Alonso JM, Ecker JR, Jones AM. RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis. Journal of Experimental Botany. 57: 2697-708. PMID 16829549 DOI: 10.1093/Jxb/Erl035  0.538
2006 Lariguet P, Schepens I, Hodgson D, Pedmale UV, Trevisan M, Kami C, de Carbonnel M, Alonso JM, Ecker JR, Liscum E, Fankhauser C. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism. Proceedings of the National Academy of Sciences of the United States of America. 103: 10134-9. PMID 16777956 DOI: 10.1073/Pnas.0603799103  0.497
2006 Rudella A, Friso G, Alonso JM, Ecker JR, van Wijk KJ. Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis. The Plant Cell. 18: 1704-21. PMID 16766689 DOI: 10.1105/Tpc.106.042861  0.484
2006 Alonso JM, Ecker JR. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nature Reviews. Genetics. 7: 524-36. PMID 16755288 DOI: 10.1038/Nrg1893  0.539
2006 Ciuffi A, Mitchell RS, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman FD. Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts. Molecular Therapy : the Journal of the American Society of Gene Therapy. 13: 366-73. PMID 16325473 DOI: 10.1016/J.Ymthe.2005.10.009  0.328
2005 Ciuffi A, Llano M, Poeschla E, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman F. A role for LEDGF/p75 in targeting HIV DNA integration Nature Medicine. 11: 1287-1289. PMID 16311605 DOI: 10.1038/Nm1329  0.304
2005 Overvoorde PJ, Okushima Y, Alonso JM, Chan A, Chang C, Ecker JR, 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. The Plant Cell. 17: 3282-300. PMID 16284307 DOI: 10.1105/Tpc.105.036723  0.551
2005 Mason MG, Mathews DE, Argyros DA, Maxwell BB, Kieber JJ, Alonso JM, Ecker JR, Schaller GE. Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. The Plant Cell. 17: 3007-18. PMID 16227453 DOI: 10.1105/Tpc.105.035451  0.702
2005 Barr SD, Leipzig J, Shinn P, Ecker JR, Bushman FD. Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome Journal of Virology. 79: 12035-12044. PMID 16140779 DOI: 10.1128/Jvi.79.18.12035-12044.2005  0.319
2005 Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker JR, Reed JW. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development (Cambridge, England). 132: 4107-18. PMID 16107481 DOI: 10.1242/Dev.01955  0.537
2005 Yoshida H, Nagata M, Saito K, Kevin WLC, Ecker JR. Arabidopsis ETO1 specifically interacts with and negatively regulates type 2 1-aminocyclopropane-1-carboxylate synthases Bmc Plant Biology. 5. PMID 16091151 DOI: 10.1186/1471-2229-5-14  0.608
2005 Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proceedings of the National Academy of Sciences of the United States of America. 102: 10387-92. PMID 16006522 DOI: 10.1073/Pnas.0503029102  0.644
2005 Wilmoth JC, Wang S, Tiwari SB, Joshi AD, Hagen G, Guilfoyle TJ, Alonso JM, Ecker JR, Reed JW. NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. The Plant Journal : For Cell and Molecular Biology. 43: 118-30. PMID 15960621 DOI: 10.1111/J.1365-313X.2005.02432.X  0.54
2005 Werner JD, Borevitz JO, Uhlenhaut NH, Ecker JR, Chory J, Weigel D. FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions. Genetics. 170: 1197-207. PMID 15911588 DOI: 10.1534/Genetics.104.036533  0.7
2005 Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker JR, Kay SA. Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. Plant Physiology. 138: 990-7. PMID 15908595 DOI: 10.1104/Pp.105.061408  0.804
2005 Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. Journal of Virology. 79: 6610-9. PMID 15890899 DOI: 10.1128/Jvi.79.11.6610-6619.2005  0.342
2005 Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker JR, Emerson B, Hogenesch JB, Unterman T, et al. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proceedings of the National Academy of Sciences of the United States of America. 102: 4459-64. PMID 15753290 DOI: 10.1073/Pnas.0501076102  0.534
2005 Ryu JS, Kim JI, Kunkel T, Kim BC, Cho DS, Hong SH, Kim SH, Fernández AP, Kim Y, Alonso JM, Ecker JR, Nagy F, Lim PO, Song PS, Schäfer E, et al. Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer. Cell. 120: 395-406. PMID 15707897 DOI: 10.1016/J.Cell.2004.12.019  0.472
2005 Werner JD, Borevitz JO, Warthmann N, Trainer GT, Ecker JR, Chory J, Weigel D. Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation. Proceedings of the National Academy of Sciences of the United States of America. 102: 2460-5. PMID 15695584 DOI: 10.1073/Pnas.0409474102  0.728
2005 Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, 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. The Plant Cell. 17: 444-63. PMID 15659631 DOI: 10.1105/Tpc.104.028316  0.555
2005 Liu G, Holub EB, Alonso JM, Ecker JR, Fobert PR. An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance. The Plant Journal : For Cell and Molecular Biology. 41: 304-18. PMID 15634206 DOI: 10.1111/J.1365-313X.2004.02296.X  0.554
2005 Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR. Applications of DNA tiling arrays for whole-genome analysis. Genomics. 85: 1-15. PMID 15607417 DOI: 10.1016/J.Ygeno.2004.10.005  0.652
2005 Prigge MJ, Otsuga D, Alonso JM, Ecker JR, Drews GN, Clark SE. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. The Plant Cell. 17: 61-76. PMID 15598805 DOI: 10.1105/Tpc.104.026161  0.506
2005 Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR. Corrigendum to ‘‘Applications of DNA tiling arrays for whole-genome analysis’’ [Genomics 85 (2005) 1–15] Genomics. 85: 655. DOI: 10.1016/J.Ygeno.2005.01.004  0.325
2004 Monte E, Tepperman JM, Al-Sady B, Kaczorowski KA, Alonso JM, Ecker JR, Li X, Zhang Y, Quail PH. The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Proceedings of the National Academy of Sciences of the United States of America. 101: 16091-8. PMID 15505214 DOI: 10.1073/Pnas.0407107101  0.528
2004 Borevitz JO, Ecker JR. Plant genomics: the third wave. Annual Review of Genomics and Human Genetics. 5: 443-77. PMID 15485356 DOI: 10.1146/Annurev.Genom.5.061903.180017  0.641
2004 Shibuya K, Barry KG, Ciardi JA, Loucas HM, Underwood BA, Nourizadeh S, Ecker JR, Klee HJ, Clark DG. The central role of PhEIN2 in ethylene responses throughout plant development in petunia1 Plant Physiology. 136: 2900-2912. PMID 15466231 DOI: 10.1104/Pp.104.046979  0.392
2004 Binder BM, Mortimore LA, Stepanova AN, Ecker JR, Bleecker AB. Short-term growth responses to ethylene in Arabidopsis seedlings are EIN3/EIL1 independent. Plant Physiology. 136: 2921-7. PMID 15466219 DOI: 10.1104/Pp.104.050393  0.563
2004 Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry CC, Ecker JR, Bushman FD. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. Plos Biology. 2: E234. PMID 15314653 DOI: 10.1371/Journal.Pbio.0020234  0.335
2004 Mockler TC, Yu X, Shalitin D, Parikh D, Michael TP, Liou J, Huang J, Smith Z, Alonso JM, Ecker JR, Chory J, Lin C. Regulation of flowering time in Arabidopsis by K homology domain proteins. Proceedings of the National Academy of Sciences of the United States of America. 101: 12759-64. PMID 15310842 DOI: 10.1073/Pnas.0404552101  0.751
2004 Li H, Johnson P, Stepanova A, Alonso JM, Ecker JR. Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. Developmental Cell. 7: 193-204. PMID 15296716 DOI: 10.1016/J.Devcel.2004.07.002  0.734
2004 Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker JR, Berry CC, Chory J. Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics. 167: 907-17. PMID 15238539 DOI: 10.1534/Genetics.103.024810  0.689
2004 Pfund C, Tans-Kersten J, Dunning FM, Alonso JM, Ecker JR, Allen C, Bent AF. Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana. Molecular Plant-Microbe Interactions : Mpmi. 17: 696-706. PMID 15195952 DOI: 10.1094/Mpmi.2004.17.6.696  0.488
2004 Chen JG, Pandey S, Huang J, Alonso JM, Ecker JR, Assmann SM, Jones AM. GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination. Plant Physiology. 135: 907-15. PMID 15181210 DOI: 10.1104/Pp.104.038992  0.497
2004 Tyler L, Thomas SG, Hu J, Dill A, Alonso JM, Ecker JR, Sun TP. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiology. 135: 1008-19. PMID 15173565 DOI: 10.1104/Pp.104.039578  0.52
2004 Page ML, Hamel PP, Gabilly ST, Zegzouti H, Perea JV, Alonso JM, Ecker JR, Theg SM, Christensen SK, Merchant S. A homolog of prokaryotic thiol disulfide transporter CcdA is required for the assembly of the cytochrome b6f complex in Arabidopsis chloroplasts. The Journal of Biological Chemistry. 279: 32474-82. PMID 15159384 DOI: 10.1074/Jbc.M404285200  0.483
2004 Wang KLC, Yoshida H, Lurin C, Ecker JR. Regulation of ethylene gas biosynthesis by the Arabidopsis ETO1 protein Nature. 428: 945-950. PMID 15118728 DOI: 10.1038/Nature02516  0.676
2004 Novillo F, Alonso JM, Ecker JR, 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. Proceedings of the National Academy of Sciences of the United States of America. 101: 3985-90. PMID 15004278 DOI: 10.1073/Pnas.0303029101  0.536
2004 To JP, Haberer G, Ferreira FJ, Deruère J, Mason MG, Schaller GE, Alonso JM, Ecker JR, Kieber JJ. Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling. The Plant Cell. 16: 658-71. PMID 14973166 DOI: 10.1105/Tpc.018978  0.811
2004 Guo H, Ecker JR. The ethylene signaling pathway: New insights Current Opinion in Plant Biology. 7: 40-49. PMID 14732440 DOI: 10.1016/J.Pbi.2003.11.011  0.564
2004 Ecker JR. Reentry of the ethylene MPK6 module Plant Cell. 16: 3169-3173. DOI: 10.1105/Tpc.104.161210  0.313
2004 Ecker JR, Cook D. Genome studies and molecular genetics: Unwrapping new layers of complexity in plant genomes Current Opinion in Plant Biology. 7: 99-101. DOI: 10.1016/J.Pbi.2004.01.017  0.323
2003 Guo H, Ecker JR. Plant responses to ethylene gas are mediated by SCFEBF1/EBF2- dependent proteolysis of EIN3 transcription factor Cell. 115: 667-677. PMID 14675532 DOI: 10.1016/S0092-8674(03)00969-3  0.597
2003 Catala R, Santos E, Alonso JM, Ecker JR, Martinez-Zapater JM, Salinas J. Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis. The Plant Cell. 15: 2940-51. PMID 14630965 DOI: 10.1105/Tpc.015248  0.488
2003 Lariguet P, Boccalandro HE, Alonso JM, Ecker JR, Chory J, Casal JJ, Fankhauser C. A growth regulatory loop that provides homeostasis to phytochrome a signaling. The Plant Cell. 15: 2966-78. PMID 14615593 DOI: 10.1105/Tpc.014563  0.643
2003 Michael TP, Salomé PA, Yu HJ, Spencer TR, Sharp EL, McPeek MA, Alonso JM, Ecker JR, McClung CR. Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science (New York, N.Y.). 302: 1049-53. PMID 14605371 DOI: 10.1126/Science.1082971  0.465
2003 Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, ... ... Ecker JR, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (New York, N.Y.). 302: 842-6. PMID 14593172 DOI: 10.1126/Science.1088305  0.817
2003 Monte E, Alonso JM, Ecker JR, Zhang Y, Li X, Young J, Austin-Phillips S, Quail PH. Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. The Plant Cell. 15: 1962-80. PMID 12953104 DOI: 10.1105/Tpc.012971  0.517
2003 Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, Gadrinab C, Heller C, Jeske A, Koesema E, Meyers CC, ... ... Ecker JR, et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science (New York, N.Y.). 301: 653-7. PMID 12893945 DOI: 10.1126/Science.1086391  0.721
2003 Alonso JM, Stepanova AN, Solano R, Wisman E, Ferrari S, Ausubel FM, Ecker JR. Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 100: 2992-7. PMID 12606727 DOI: 10.1073/Pnas.0438070100  0.808
2003 Mackey D, Belkhadir Y, Alonso JM, Ecker JR, Dangl JL. Arabidopsis RIN4 is a target of the type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance. Cell. 112: 379-89. PMID 12581527 DOI: 10.1016/S0092-8674(03)00040-0  0.492
2003 Larkin RM, Alonso JM, Ecker JR, Chory J. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science (New York, N.Y.). 299: 902-6. PMID 12574634 DOI: 10.1126/Science.1079978  0.613
2003 Ullah H, Chen JG, Temple B, Boyes DC, Alonso JM, Davis KR, Ecker JR, Jones AM. The beta-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes. The Plant Cell. 15: 393-409. PMID 12566580 DOI: 10.1105/Tpc.006148  0.534
2003 Strand A, Asami T, Alonso J, Ecker JR, Chory J. Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinix Nature. 421: 79-83. PMID 12511958 DOI: 10.1038/Nature01204  0.644
2002 Yoshida R, Hobo T, Ichimura K, Mizoguchi T, Takahashi F, Aronso J, Ecker JR, Shinozaki K. ABA-activated SnRK2 protein kinase is required for dehydration stress signaling in Arabidopsis Plant and Cell Physiology. 43: 1473-1483. PMID 12514244 DOI: 10.1093/Pcp/Pcf188  0.356
2002 Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker JR, Normanly J, Chory J, Celenza JL. Trp-dependent auxin biosynthesis in Arabidopsis: Involvement of cytochrome P450s CYP79B2 and CYP79B3 Genes and Development. 16: 3100-3112. PMID 12464638 DOI: 10.1101/Gad.1035402  0.638
2002 Beachy R, Bennetzen JL, Chassy BM, Chrispeels M, Chory J, Ecker JR, Noel JP, Kay SA, Dean C, Lamb C, Jones J, Santerre CR, Schroeder JI, Umen J, Yanofsky M, et al. Divergent perspectives on GM food. Nature Biotechnology. 20: 1195-6; author reply. PMID 12454665 DOI: 10.1038/Nbt1202-1195  0.631
2002 Friedrichsen DM, Nemhauser J, Muramitsu T, Maloof JN, Alonso J, Ecker JR, Furuya M, Chory J. Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth Genetics. 162: 1445-1456. PMID 12454087  0.641
2002 Schroeder DF, Gahrtz M, Maxwell BB, Cook RK, Kan JM, Alonso JM, Ecker JR, Chory J. De-etiolated 1 and damaged DNA binding protein 1 interact to regulate Arabidopsis photomorphogenesis Current Biology. 12: 1462-1472. PMID 12225661 DOI: 10.1016/S0960-9822(02)01106-5  0.654
2002 Schröder ARW, Shinn P, Chen H, Berry C, Ecker JR, Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots Cell. 110: 521-529. PMID 12202041 DOI: 10.1016/S0092-8674(02)00864-4  0.306
2002 Hu J, Aguirre M, Peto C, Alonso J, Ecker J, Chory J. A role for peroxisomes in photomorphogenesis and development of Arabidopsis. Science (New York, N.Y.). 297: 405-9. PMID 12130786 DOI: 10.1126/Science.1073633  0.649
2002 Ichimura K, Shinozaki K, Tena G, Sheen J, Henry Y, Champion A, Kreis M, Zhang S, Hirt H, Wilson C, Heberle-Bors E, Ellis BE, Morris PC, Innes RW, Ecker JR, et al. Mitogen-activated protein kinase cascades in plants: a new nomenclature Trends in Plant Science. 7: 301-308. PMID 12119167 DOI: 10.1016/S1360-1385(02)02302-6  0.329
2002 Zheng H, Bednarek SY, Sanderfoot AA, Alonso J, Ecker JR, Raikhel NV. NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE. Plant Physiology. 129: 530-9. PMID 12068098 DOI: 10.1104/Pp.003970  0.51
2002 Wang KLC, Li H, Ecker JR. Ethylene biosynthesis and signaling networks Plant Cell. 14: S131-S151. PMID 12045274 DOI: 10.1105/Tpc.001768  0.584
2002 Beachy R, Bennetzen JL, Chassy BM, Chrispeels M, Chory J, Ecker JR, Noel JP, Kay SA, Dean C, Lamb C, Jones J, Santerre CR, Schroeder JI, Umen J, Yanofsky M, et al. Reply to 'Divergent perspectives on GM food' Nature Biotechnology. 20: 1197-1197. DOI: 10.1038/Nbt1202-1197A  0.631
2001 Alonso JM, Ecker JR. The ethylene pathway: a paradigm for plant hormone signaling and interaction Science"S Stke [Electronic Resource] : Signal Transduction Knowledge Environment. 2001: RE1. PMID 11752640 DOI: 10.1126/Stke.2001.70.Re1  0.531
2001 Jarillo JA, Gabrys H, Capel J, Alonso JM, Ecker JR, Cashmore AR. Phototropin-related NPL1 controls chloroplast relocation induced by blue light Nature. 410: 952-954. PMID 11309623 DOI: 10.1038/35073622  0.302
2001 Jarillo JA, Capel J, Tang RH, Yang HQ, Alonso JM, Ecker JR, Cashmore AR. An Arabidopsis circadian clock component interacts with both CRY1 and phyB Nature. 410: 487-490. PMID 11260718 DOI: 10.1038/35068589  0.329
2000 Theologis A, Ecker JR, Palm CJ, Federspiel NA, Kaul S, White O, Alonso J, Altafi H, Araujo R, Bowman CL, Brooks SY, Buehler E, Chan A, Chao Q, Chen H, et al. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature. 408: 816-20. PMID 11130712 DOI: 10.1038/35048500  0.589
2000 Stepanova AN, Ecker JR. Ethylene signaling: From mutants to molecules Current Opinion in Plant Biology. 3: 353-360. PMID 11019801 DOI: 10.1016/S1369-5266(00)00096-0  0.647
2000 Chory J, Ecker JR, Briggs S, Caboche M, Coruzzi GM, Cook D, Dangl J, Grant S, Guerinot ML, Henikoff S, Martienssen R, Okada K, Raikhel NV, Somerville CR, 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 Plant Physiology. 123: 423-425. PMID 10859172 DOI: 10.1104/Pp.123.2.423  0.667
2000 Curie C, Alonso JM, Le Jean M, Ecker JR, Briat JF. Involvement of NRAMP1 from Arabidopsis thaliana in iron transport Biochemical Journal. 347: 749-755. PMID 10769179 DOI: 10.1042/0264-6021:3470749  0.32
1999 Mozo T, Dewar K, Dunn P, Ecker JR, 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 Nature Genetics. 22: 271-275. PMID 10391215 DOI: 10.1038/10334  0.333
1999 Alonso JM, Hirayama T, Roman G, Nourizadeh S, Ecker JR. EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. Science (New York, N.Y.). 284: 2148-52. PMID 10381874 DOI: 10.1126/Science.284.5423.2148  0.556
1999 Hirayama T, Kieber JJ, Hirayama N, Kogan M, Guzman P, Nourizadeh S, Alonso JM, Dailey WP, Dancis A, Ecker JR. RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson disease-related copper transporter, is required for ethylene signaling in Arabidopsis. Cell. 97: 383-93. PMID 10319818 DOI: 10.1016/S0092-8674(00)80747-3  0.682
1998 Solano R, Ecker JR. Ethylene gas: Perception, signaling and response Current Opinion in Plant Biology. 1: 393-398. PMID 10066624 DOI: 10.1016/S1369-5266(98)80262-8  0.761
1998 Johnson PR, Ecker JR. The ethylene gas signal transduction pathway: A molecular perspective Annual Review of Genetics. 32: 227-254. PMID 9928480 DOI: 10.1146/Annurev.Genet.32.1.227  0.379
1998 Solano R, Stepanova A, Chao Q, Ecker JR. Nuclear events in ethylene signaling: A transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1 Genes and Development. 12: 3703-3714. PMID 9851977 DOI: 10.1101/Gad.12.23.3703  0.825
1998 Kwok SF, Solano R, Tsuge T, Chamovitz DA, Ecker JR, Matsui M, Deng XW. 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 Plant Cell. 10: 1779-1790. PMID 9811788 DOI: 10.1105/Tpc.10.11.1779  0.749
1998 Hua J, Sakai H, Nourizadeh S, Chen QG, Bleecker AB, Ecker JR, Meyerowitz EM. EIN4 and ERS2 are members of the putative ethylene receptor gene family in arabidopsis Plant Cell. 10: 1321-1332. PMID 9707532 DOI: 10.1105/Tpc.10.8.1321  0.356
1998 Ecker JR. Genes blossom from a weed: The arabidopais genome initiative Faseb Journal. 12: A1306. DOI: 10.1038/35030  0.365
1998 Walden R, Ecker JR. Cell signalling and gene regulation: piecing the puzzle together Current Opinion in Plant Biology. 1: 375-377. DOI: 10.1016/S1369-5266(98)80258-6  0.339
1998 McGrath RB, Ecker JR. Ethylene signaling in Arabidopsis: Events from the membrane to the nucleus Plant Physiology and Biochemistry. 36: 103-113. DOI: 10.1016/S0981-9428(98)80095-8  0.386
1997 Ecker JR. BRI-ghtening the pathway to steroid hormone signaling events in plants Cell. 90: 825-827. PMID 9298893 DOI: 10.1016/S0092-8674(00)80346-3  0.305
1997 Chao Q, Rothenberg M, Solano R, Roman G, Terzaghi W, Ecker JR. Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins. Cell. 89: 1133-44. PMID 9215635 DOI: 10.1016/S0092-8674(00)80300-1  0.797
1997 Mulligan RM, Chory J, Ecker JR. Signaling in plants Proceedings of the National Academy of Sciences of the United States of America. 94: 2793-2795. PMID 9096297 DOI: 10.1073/Pnas.94.7.2793  0.577
1996 Lehman A, Black R, Ecker JR. HOOKLESS1, an ethylene response gene, is required for differential cell elongation in the Arabidopsis hypocotyl. Cell. 85: 183-94. PMID 8612271 DOI: 10.1016/S0092-8674(00)81095-8  0.387
1995 Roman G, Ecker JR. Genetic analysis of a seedling stress response to ethylene in Arabidopsis. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 350: 75-81. PMID 8577853 DOI: 10.1098/Rstb.1995.0140  0.554
1995 Roman G, Lubarsky B, Kieber JJ, Rothenberg M, Ecker JR. Genetic analysis of ethylene signal transduction in Arabidopsis thaliana: five novel mutant loci integrated into a stress response pathway. Genetics. 139: 1393-409. PMID 7768447  0.691
1995 Goodman HM, Ecker JR, Dean C. The genome of Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America. 92: 10831-5. PMID 7479893 DOI: 10.1073/Pnas.92.24.10831  0.384
1994 Ecker JR, Theologis A. 19 Ethylene: A Unique Plant Signaling Molecule Cold Spring Harbor Monograph Archive. 27: 485-521. DOI: 10.1101/087969428.27.485  0.324
1993 Kieber JJ, Rothenberg M, Roman G, Feldmann KA, Ecker JR. CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell. 72: 427-41. PMID 8431946 DOI: 10.1016/0092-8674(93)90119-B  0.72
1993 Kieber JJ, Ecker JR. Ethylene gas: it's not just for ripening any more! Trends in Genetics : Tig. 9: 356-62. PMID 8273151 DOI: 10.1016/0168-9525(93)90041-F  0.617
1993 Rothenberg M, Ecker JR. Mutant analysis as an experimental approach towards understanding plant hormone action Seminars in Developmental Biology. 4: 3-13. DOI: 10.1006/Sedb.1993.1002  0.34
1992 Guzmán P, Ecker JR. Exploiting the triple response of Arabidopsis to identify ethylene-related mutants. The Plant Cell. 2: 513-23. PMID 2152173 DOI: 10.1105/Tpc.2.6.513  0.32
1992 Bent AF, Innes RW, Ecker JR, Staskawicz BJ. Disease development in ethylene-insensitive Arabidopsis thaliana infected with virulent and avirulent Pseudomonas and Xanthomonas pathogens Molecular Plant-Microbe Interactions : Mpmi. 5: 372-378. PMID 1472714 DOI: 10.1094/Mpmi-5-372  0.305
1992 Schindler U, Menkens AE, Beckmann H, Ecker JR, Cashmore AR. Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF bZIP proteins. The Embo Journal. 11: 1261-1273. DOI: 10.1002/J.1460-2075.1992.Tb05170.X  0.373
1990 Ecker JR. PFGE and YAC analysis of the Arabidopsis genome Methods. 1: 186-194. DOI: 10.1016/S1046-2023(05)80134-3  0.346
1989 Guzmán P, Ecker JR. Development of large DNA methods for plants: molecular cloning of large segments of Arabidopsis and carrot DNA into yeast. Nucleic Acids Research. 16: 11091-105. PMID 3060856 DOI: 10.1093/Nar/16.23.11091  0.363
1987 Ecker JR, Davis RW. Plant defense genes are regulated by ethylene. Proceedings of the National Academy of Sciences of the United States of America. 84: 5202-6. PMID 16593860 DOI: 10.1073/Pnas.84.15.5202  0.532
1986 Ecker JR, Davis RW. Inhibition of gene expression in plant cells by expression of antisense RNA. Proceedings of the National Academy of Sciences of the United States of America. 83: 5372-6. PMID 16593734 DOI: 10.1073/Pnas.83.15.5372  0.535
1984 Ecker JR, Kudler L, Hyman RW. Variation in the structure of varicella-zoster virus DNA Intervirology. 21: 25-37. PMID 6321392 DOI: 10.1159/000149500  0.637
1983 Pichini B, Ecker JR, Grose C, Hyman RW. DNA mapping of paired varicella-zoster virus isolates from patients with shingles. Lancet (London, England). 2: 1223-5. PMID 6139571 DOI: 10.1016/S0140-6736(83)91271-0  0.625
1983 Hyman RW, Ecker JR, Tenser RB. Varicella-zoster virus RNA in human trigeminal ganglia. Lancet (London, England). 2: 814-6. PMID 6137648 DOI: 10.1016/S0140-6736(83)90736-5  0.601
1982 Ecker JR, Hyman RW. Varicella zoster virus DNA exists as two isomers Proceedings of the National Academy of Sciences of the United States of America. 79: 156-160. PMID 6275385 DOI: 10.1073/Pnas.79.1.156  0.625
1981 Ecker JR, Hyman RW. Varicella-zoster virus vaccine DNA differs from the parental virus DNA Journal of Virology. 40: 314-318. PMID 6270384 DOI: 10.1128/Jvi.40.1.314-318.1981  0.61
1981 Ecker JR, Hyman RW. Variables that may influence the alkaline sedimentation pattern of herpes simplex virus DNA Archives of Virology. 68: 221-228. PMID 6268021 DOI: 10.1007/Bf01314575  0.63
1981 Ecker JR, Hyman RW. Analysis of interruptions in the phosphodiester backbone of herpes simplex virus DNA Virology. 110: 213-216. PMID 6259830 DOI: 10.1016/0042-6822(81)90024-6  0.637
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