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    Joseph Ecker

    TitleAdjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentCell and Developmental Biology
    Address9500 Gilman Drive #0932
    CA La Jolla 92093
    Phone858-453-4100
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      Collapse Research 
      Collapse Research Activities and Funding
      The role of DNA methylation dynamics and patterning in postmitotic neuronal-maturation
      NIH/NIMH R01MH112763Mar 16, 2017 - Jan 31, 2022
      Role: Co-Principal Investigator
      Multidimensional Epigenomic Single Cell Analyses
      NIH/NHGRI R21HG009274Sep 28, 2016 - Jul 31, 2019
      Role: Principal Investigator
      Epigenomic Approaches for Unbiased Single Human-Neuron Subtype Census
      NIH/NIMH R21MH112161Sep 28, 2016 - Aug 31, 2018
      Role: Principal Investigator
      Environmental contribution to neuronal-methylome dynamics in animal models of autism spectrum disorders
      NIH/NIEHS R01ES025585Aug 1, 2015 - Jun 30, 2020
      Role: Co-Principal Investigator
      Epigenomic mapping approaches for cell-type classification in the brain
      NIH/NIMH U01MH105985Sep 26, 2014 - Jun 30, 2017
      Role: Principal Investigator
      Epigenetic Alterations of the Developing Brain in Animal Models of Schizophrenia
      NIH/NIMH R01MH094670Sep 7, 2011 - Apr 30, 2016
      Role: Co-Principal Investigator
      The Arabidopsis Transcription Factor ORFeome and downstream genomic application
      NIH/NIGMS RC2GM092412Sep 30, 2009 - Dec 31, 2011
      Role: Principal Investigator
      Genome Wide Analysis of DNA Methylation
      NIH/NHGRI R01HG003523Sep 29, 2004 - Jun 30, 2007
      Role: Principal Investigator
      DEVELOPMENT OF LARGE DNA METHODS FOR ARABIDOPSIS
      NIH/NIGMS R01GM042471Jul 1, 1989 - Jun 30, 1992
      Role: Principal Investigator
      DEVELOPMENT OF LARGE DNA METHODS FOR ARABIDOPSIS
      NIH/NHGRI R01HG000322Jul 1, 1989 - Jun 30, 1992
      Role: Principal Investigator
      MOLECULAR GENETICS OF STRESS-RESPONSES IN ARABIDOPSIS
      NIH/NIGMS R29GM038894Jul 1, 1987 - Jun 30, 1993
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. 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 J. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science. 2017 Aug 11; 357(6351):600-604. PMID: 28798132.
        View in: PubMed
      2. Bartlett A, O'Malley RC, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker J. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat Protoc. 2017 Aug; 12(8):1659-1672. PMID: 28726847.
        View in: PubMed
      3. 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 J. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2017 Aug; 14(8):819-825. PMID: 28650476.
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      4. 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 J, Gu Y, Vogel JP. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. Plant J. 2017 Aug; 91(3):361-370. PMID: 28432803.
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      5. Keown CL, Berletch JB, Castanon R, Nery JR, Disteche CM, Ecker J, Mukamel EA. Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain. Proc Natl Acad Sci U S A. 2017 Apr 04; 114(14):E2882-E2890. PMID: 28320934.
        View in: PubMed
      6. He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker J. Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc Natl Acad Sci U S A. 2017 Feb 13. PMID: 28193886.
        View in: PubMed
      7. 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 J, Stacey G. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. New Phytol. 2017 Jan 20. PMID: 28106918.
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      8. Shani E, Salehin M, Zhang Y, Sanchez SE, Doherty C, Wang R, Mangado CC, Song L, Tal I, Pisanty O, Ecker J, Kay SA, Pruneda-Paz J, Estelle M. Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. Curr Biol. 2017 Jan 18. PMID: 28111153.
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      9. Gimenez-Ibanez S, Boter M, Ortigosa A, García-Casado G, Chini A, Lewsey MG, Ecker J, Ntoukakis V, Solano R. JAZ2 controls stomata dynamics during bacterial invasion. New Phytol. 2016 Dec 22. PMID: 28005270.
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      10. Luo C, Lancaster MA, Castanon R, Nery JR, Knoblich JA, Ecker J. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain. Cell Rep. 2016 Dec 20; 17(12):3369-3384. PMID: 28009303.
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      11. Narsai R, Secco D, Schultz MD, Ecker J, 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. Plant J. 2016 Nov 12. PMID: 27859855.
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      12. Song L, Huang SC, Wise A, Castanon R, Nery JR, Chen H, Watanabe M, Thomas J, Bar-Joseph Z, Ecker J. A transcription factor hierarchy defines an environmental stress response network. Science. 2016 Nov 04; 354(6312). PMID: 27811239.
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      13. 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, Ahmed R, Van Dyken C, Li Y, Olson S, Battaglia D, Lee DM, Wu DH, Amato P, Wolf DP, Ecker J, Mitalipov S. Functional Human Oocytes Generated by Transfer of Polar Body Genomes. Cell Stem Cell. 2016 Oct 20. PMID: 27840020.
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      14. 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 J, Cantu D, Rank DR, Schatz MC. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016 Oct 17. PMID: 27749838.
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      15. Zhang F, Qi B, Wang L, Zhao B, Rode S, Riggan ND, Ecker J, Qiao H. EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling. Nat Commun. 2016 Oct 03; 7:13018. PMID: 27694846.
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      16. O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker J. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 2016 Sep 8; 166(6):1598. PMID: 27610578.
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      17. Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker J, Briggs SP. Integration of omic networks in a developmental atlas of maize. Science. 2016 Aug 19; 353(6301):814-8. PMID: 27540173.
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      18. Kawakatsu T, Huang SS, 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, Becker C, O'Neil R, O'Malley RC, Quarless DX. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 2016 Jul 14; 166(2):492-505. PMID: 27419873.
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      19. 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, Huang Y, Nery JR, Drotar J, Lungjangwa T, Trono D, Ecker J, Jaenisch R. Molecular Criteria for Defining the Naive Human Pluripotent State. Cell Stem Cell. 2016 Oct 6; 19(4):502-515. PMID: 27424783.
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      20. Aleman F, Yazaki J, Lee M, Takahashi Y, Kim AY, Li Z, Kinoshita T, Ecker J, Schroeder JI. An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling. Sci Rep. 2016; 6:28941. PMID: 27357749.
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      21. Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SS, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroeder JI, Chory J, LaBaer J, Vidal M, Braun P, Ecker J. Mapping transcription factor interactome networks using HaloTag protein arrays. Proc Natl Acad Sci U S A. 2016 Jul 19; 113(29):E4238-47. PMID: 27357687.
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      22. Song L, Koga Y, Ecker J. Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq). Curr Protoc Plant Biol. 2016; 1(2):293-306. PMID: 28782043.
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      23. O'Malley RC, Huang SS, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker J. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 2016 May 19; 165(5):1280-92. PMID: 27203113.
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      24. Prigge MJ, Greenham K, Zhang Y, Santner A, Castillejo C, Mutka AM, O'Malley RC, Ecker J, 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). 2016; 6(5):1383-90. PMID: 26976444.
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      25. Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker J. Unique cell-type-specific patterns of DNA methylation in the root meristem. Nat Plants. 2016; 2(5):16058. PMID: 27243651.
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      26. Bergelson J, Buckler ES, Ecker J, Nordborg M, Weigel D. A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants. Plant Cell. 2016 Mar; 28(3):606-9. PMID: 26956491.
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      27. Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker J, Nathans J. Epigenomic landscapes of retinal rods and cones. Elife. 2016; 5. PMID: 26949250.
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      28. Bogdanovic 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, Sauka-Spengler T, Ecker J, Vermeulen M, Gómez-Skarmeta JL, Lister R. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016 Apr; 48(4):417-26. PMID: 26928226.
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      29. Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker J. Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A. 2016 Feb 9; 113(6):E801-10. PMID: 26787884.
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      30. 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, Lott I, Ferrer I, Ecker J, Esteller M. Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. Transl Psychiatry. 2016; 6:e718. PMID: 26784972.
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      31. Pedmale UV, Huang SS, Zander M, Cole BJ, Hetzel J, Ljung K, Reis PA, Sridevi P, Nito K, Nery JR, Ecker J, Chory J. Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light. Cell. 2016 Jan 14; 164(1-2):233-45. PMID: 26724867.
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      32. 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, Ren B, Sejnowski TJ, Wang W, Ecker J. Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2016 Feb 11; 530(7589):242. PMID: 26605523.
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      33. Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker J, Pelizzola M. methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. BMC Bioinformatics. 2015; 16(1):313. PMID: 26415965.
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      34. 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 J, Chen X. Correction: DNA Topoisomerase 1a Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis. PLoS Genet. 2015 Sep; 11(9):e1005452. PMID: 26379054.
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      35. Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker J, Kay SA. Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci U S A. 2015 Aug 25; 112(34):E4802-10. PMID: 26261339.
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      36. Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker J, Whelan J, Lister R. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife. 2015; 4. PMID: 26196146.
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      37. Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker J, Nathans J. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron. 2015 Jun 17; 86(6):1369-84. PMID: 26087164.
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      38. Luo C, Ecker J. Epigenetics. Exceptional epigenetics in the brain. Science. 2015 Jun 5; 348(6239):1094-5. PMID: 26045424.
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      39. He Y, Ecker J. Non-CG Methylation in the Human Genome. Annu Rev Genomics Hum Genet. 2015 Aug 24; 16:55-77. PMID: 26077819.
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      40. 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, Ren B, Sejnowski TJ, Wang W, Ecker J. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2015 Jul 9; 523(7559):212-6. PMID: 26030523.
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      41. 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, Takahashi Y, Aizawa E, Kim NY, Lajara J, Guillen P, Campistol JM, Esteban CR, Ross PJ, Saghatelian A, Ren B, Ecker J, Izpisua Belmonte JC. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 2015 May 21; 521(7552):316-21. PMID: 25945737.
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      42. Kida YS, Kawamura T, Wei Z, Sogo T, Jacinto S, Shigeno A, Kushige H, Yoshihara E, Liddle C, Ecker J, Yu RT, Atkins AR, Downes M, Evans RM. ERRs Mediate a Metabolic Switch Required for Somatic Cell Reprogramming to Pluripotency. Cell Stem Cell. 2015 May 7; 16(5):547-55. PMID: 25865501.
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      43. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563.
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      44. 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 J, Thomson JA, Ren B. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015 Feb 19; 518(7539):331-6. PMID: 25693564.
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      45. Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker J. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc. 2015 Mar; 10(3):475-83. PMID: 25692984.
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      46. O'Malley RC, Barragan CC, Ecker J. A User's Guide to the Arabidopsis T-DNA Insertion Mutant Collections. Methods Mol Biol. 2015; 1284:323-42. PMID: 25757780.
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      47. Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker J, Snyder MP. Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci U S A. 2014 Dec 2; 111(48):17224-9. PMID: 25413365.
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      48. 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, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker J, Hughes TR. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014 Sep 11; 158(6):1431-43. PMID: 25215497.
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      49. Weßling R, Epple P, Altmann S, He Y, Yang L, Henz SR, McDonald N, Wiley K, Bader KC, Gläßer C, Mukhtar MS, Haigis S, Ghamsari L, Stephens AE, Ecker J, Vidal M, Jones JD, Mayer KF, Ver Loren van Themaat E, Weigel D, Schulze-Lefert P, Dangl JL, Panstruga R, Braun P. Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe. 2014 Sep 10; 16(3):364-75. PMID: 25211078.
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      50. 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, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker J, Xiao A, Young RA, Lansdorp PM, Jaenisch R. The Developmental Potential of iPSCs Is Greatly Influenced by Reprogramming Factor Selection. Cell Stem Cell. 2014 Sep 4; 15(3):295-309. PMID: 25192464.
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      51. Yu W, McIntosh C, Lister R, Zhu I, Han Y, Ren J, Landsman D, Lee E, Briones V, Terashima M, Leighty R, Ecker J, Muegge K. Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways. Genome Res. 2014 Oct; 24(10):1613-23. PMID: 25170028.
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      52. Catalá R, López-Cobollo R, Mar Castellano M, Angosto T, Alonso JM, Ecker J, 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. Plant Cell. 2014 Aug; 26(8):3326-42. PMID: 25122152.
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      53. Pruneda-Paz JL, Breton G, Nagel DH, Kang SE, Bonaldi K, Doherty CJ, Ravelo S, Galli M, Ecker J, Kay SA. A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Rep. 2014 Jul 24; 8(2):622-32. PMID: 25043187.
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      54. Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker J, Chen X. DNA Topoisomerase 1a Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis. PLoS Genet. 2014 Jul; 10(7):e1004446. PMID: 24992598.
        View in: PubMed
      55. 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, Gutierrez NM, Van Dyken C, Polat A, Sugawara A, Sparman M, Gokhale S, Amato P, Wolf DP, Ecker J, Laurent LC, Mitalipov S. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature. 2014 Jul 10; 511(7508):177-83. PMID: 25008523.
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      56. Yu W, Briones V, Lister R, McIntosh C, Han Y, Lee EY, Ren J, Terashima M, Leighty RM, Ecker J, Muegge K. CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity. Proc Natl Acad Sci U S A. 2014 Apr 22; 111(16):5890-5. PMID: 24711395.
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      57. 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, Li WQ, Vallender EJ, Wagner U, Qin JY, Michelini KJ, Bugarija B, Park D, Aryee E, Stricker T, Zhou J, White KP, Ren B, Schroth GP, Ecker J, Xiang AP, Lahn BT. Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Genome Res. 2014 Feb; 24(2):267-80. PMID: 24310002.
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      58. Hua Z, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker J, Vierstra RD. Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis. Proc Natl Acad Sci U S A. 2013 Oct 15; 110(42):16927-32. PMID: 24082131.
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      59. Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker J, Millar AH, Ren B, Wang W. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics. 2013 Dec 15; 29(24):3204-10. PMID: 24078702.
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      60. Schweizer F, Fernández-Calvo P, Zander M, Diez-Diaz M, Fonseca S, Glauser G, Lewsey MG, Ecker J, Solano R, Reymond P. Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. Plant Cell. 2013 Aug; 25(8):3117-32. PMID: 23943862.
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      61. 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, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker J. Global epigenomic reconfiguration during mammalian brain development. Science. 2013 Aug 9; 341(6146):1237905. PMID: 23828890.
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      62. 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, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker J. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2013; 2:e00675. PMID: 23795294.
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      63. Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker J. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 2013 Oct; 23(10):1663-74. PMID: 23739894.
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      64. Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker J. Response to Perspective : "Separation anxiety: An analysis of ethylene-induced cleavage of EIN2". Plant Signal Behav. 2013 Aug 1; 8(8). PMID: 23733051.
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      65. 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, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker J, Ren B. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 2013 May 23; 153(5):1134-48. PMID: 23664764.
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      66. Hill K, Mathews DE, Kim HJ, Street IH, Wildes SL, Chiang YH, Mason MG, Alonso JM, Ecker J, Kieber JJ, Schaller GE. Functional characterization of type-B response regulators in the Arabidopsis cytokinin response. Plant Physiol. 2013 May; 162(1):212-24. PMID: 23482873.
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      67. Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker J. Patterns of population epigenomic diversity. Nature. 2013 Mar 14; 495(7440):193-8. PMID: 23467092.
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      68. Ecker J. Epigenetic trigger for tomato ripening. Nat Biotechnol. 2013 Feb; 31(2):119-20. PMID: 23392509.
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      154. Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker J, Emerson B, Hogenesch JB, Unterman T, Young RA, Montminy M. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci U S A. 2005 Mar 22; 102(12):4459-64. PMID: 15753290.
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      155. Ryu JS, Kim JI, Kunkel T, Kim BC, Cho DS, Hong SH, Kim SH, Fernández AP, Kim Y, Alonso JM, Ecker J, Nagy F, Lim PO, Song PS, Schäfer E, Nam HG. Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer. Cell. 2005 Feb 11; 120(3):395-406. PMID: 15707897.
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      156. Werner JD, Borevitz JO, Warthmann N, Trainer GT, Ecker J, Chory J, Weigel D. Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation. Proc Natl Acad Sci U S A. 2005 Feb 15; 102(7):2460-5. PMID: 15695584.
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      157. Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker J, 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. Plant Cell. 2005 Feb; 17(2):444-63. PMID: 15659631.
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      158. Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker J. Applications of DNA tiling arrays for whole-genome analysis. Genomics. 2005 Jan; 85(1):1-15. PMID: 15607417.
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      159. Liu G, Holub EB, Alonso JM, Ecker J, Fobert PR. An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance. Plant J. 2005 Jan; 41(2):304-18. PMID: 15634206.
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      160. Prigge MJ, Otsuga D, Alonso JM, Ecker J, Drews GN, Clark SE. Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. Plant Cell. 2005 Jan; 17(1):61-76. PMID: 15598805.
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      161. Monte E, Tepperman JM, Al-Sady B, Kaczorowski KA, Alonso JM, Ecker J, Li X, Zhang Y, Quail PH. The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Proc Natl Acad Sci U S A. 2004 Nov 16; 101(46):16091-8. PMID: 15505214.
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      162. Binder BM, Mortimore LA, Stepanova AN, Ecker J, Bleecker AB. Short-term growth responses to ethylene in Arabidopsis seedlings are EIN3/EIL1 independent. Plant Physiol. 2004 Oct; 136(2):2921-7. PMID: 15466219.
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      163. Shibuya K, Barry KG, Ciardi JA, Loucas HM, Underwood BA, Nourizadeh S, Ecker J, Klee HJ, Clark DG. The central role of PhEIN2 in ethylene responses throughout plant development in petunia. Plant Physiol. 2004 Oct; 136(2):2900-12. PMID: 15466231.
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      164. Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry CC, Ecker J, Bushman FD. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2004 Aug; 2(8):E234. PMID: 15314653.
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      165. Mockler TC, Yu X, Shalitin D, Parikh D, Michael TP, Liou J, Huang J, Smith Z, Alonso JM, Ecker J, Chory J, Lin C. Regulation of flowering time in Arabidopsis by K homology domain proteins. Proc Natl Acad Sci U S A. 2004 Aug 24; 101(34):12759-64. PMID: 15310842.
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      166. Li H, Johnson P, Stepanova A, Alonso JM, Ecker J. Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. Dev Cell. 2004 Aug; 7(2):193-204. PMID: 15296716.
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      167. Chen JG, Pandey S, Huang J, Alonso JM, Ecker J, Assmann SM, Jones AM. GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination. Plant Physiol. 2004 Jun; 135(2):907-15. PMID: 15181210.
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      168. Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker J, Berry CC, Chory J. Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics. 2004 Jun; 167(2):907-17. PMID: 15238539.
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      169. Pfund C, Tans-Kersten J, Dunning FM, Alonso JM, Ecker J, Allen C, Bent AF. Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana. Mol Plant Microbe Interact. 2004 Jun; 17(6):696-706. PMID: 15195952.
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      170. Tyler L, Thomas SG, Hu J, Dill A, Alonso JM, Ecker J, Sun TP. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol. 2004 Jun; 135(2):1008-19. PMID: 15173565.
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      171. Page ML, Hamel PP, Gabilly ST, Zegzouti H, Perea JV, Alonso JM, Ecker J, 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. J Biol Chem. 2004 Jul 30; 279(31):32474-82. PMID: 15159384.
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      172. Wang KL, Yoshida H, Lurin C, Ecker J. Regulation of ethylene gas biosynthesis by the Arabidopsis ETO1 protein. Nature. 2004 Apr 29; 428(6986):945-50. PMID: 15118728.
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      173. Novillo F, Alonso JM, Ecker J, 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. Proc Natl Acad Sci U S A. 2004 Mar 16; 101(11):3985-90. PMID: 15004278.
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      174. To JP, Haberer G, Ferreira FJ, Deruère J, Mason MG, Schaller GE, Alonso JM, Ecker J, Kieber JJ. Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling. Plant Cell. 2004 Mar; 16(3):658-71. PMID: 14973166.
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      175. Guo H, Ecker J. The ethylene signaling pathway: new insights. Curr Opin Plant Biol. 2004 Feb; 7(1):40-9. PMID: 14732440.
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      176. Borevitz JO, Ecker J. Plant genomics: the third wave. Annu Rev Genomics Hum Genet. 2004; 5:443-77. PMID: 15485356.
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      177. Guo H, Ecker J. Plant responses to ethylene gas are mediated by SCF(EBF1/EBF2)-dependent proteolysis of EIN3 transcription factor. Cell. 2003 Dec 12; 115(6):667-77. PMID: 14675532.
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      178. Catala R, Santos E, Alonso JM, Ecker J, Martinez-Zapater JM, Salinas J. Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis. Plant Cell. 2003 Dec; 15(12):2940-51. PMID: 14630965.
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      179. Lariguet P, Boccalandro HE, Alonso JM, Ecker J, Chory J, Casal JJ, Fankhauser C. A growth regulatory loop that provides homeostasis to phytochrome a signaling. Plant Cell. 2003 Dec; 15(12):2966-78. PMID: 14615593.
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      180. Michael TP, Salomé PA, Yu HJ, Spencer TR, Sharp EL, McPeek MA, Alonso JM, Ecker J, McClung CR. Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science. 2003 Nov 7; 302(5647):1049-53. PMID: 14605371.
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      181. 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, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker J. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 2003 Oct 31; 302(5646):842-6. PMID: 14593172.
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      182. Monte E, Alonso JM, Ecker J, 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. Plant Cell. 2003 Sep; 15(9):1962-80. PMID: 12953104.
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      183. 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, 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 DE, Marchand T, Risseeuw E, Brogden D, Zeko A, Crosby WL, Berry CC, Ecker J. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science. 2003 Aug 1; 301(5633):653-7. PMID: 12893945.
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      184. Jones AM, Ecker J, Chen JG. A reevaluation of the role of the heterotrimeric G protein in coupling light responses in Arabidopsis. Plant Physiol. 2003 Apr; 131(4):1623-7. PMID: 12692321.
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      185. Alonso JM, Stepanova AN, Solano R, Wisman E, Ferrari S, Ausubel FM, Ecker J. Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. Proc Natl Acad Sci U S A. 2003 Mar 4; 100(5):2992-7. PMID: 12606727.
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      186. Larkin RM, Alonso JM, Ecker J, Chory J. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science. 2003 Feb 7; 299(5608):902-6. PMID: 12574634.
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      187. Mackey D, Belkhadir Y, Alonso JM, Ecker J, Dangl JL. Arabidopsis RIN4 is a target of the type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance. Cell. 2003 Feb 7; 112(3):379-89. PMID: 12581527.
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      188. Ullah H, Chen JG, Temple B, Boyes DC, Alonso JM, Davis KR, Ecker J, Jones AM. The beta-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes. Plant Cell. 2003 Feb; 15(2):393-409. PMID: 12566580.
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      189. Strand A, Asami T, Alonso J, Ecker J, Chory J. Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature. 2003 Jan 2; 421(6918):79-83. PMID: 12511958.
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      190. Beachy R, Bennetzen JL, Chassy BM, Chrispeels M, Chory J, Ecker J, Noel JP, Kay SA, Dean C, Lamb C, Jones J, Santerre CR, Schroeder JI, Umen J, Yanofsky M, Wessler S, Zhao Y, Parrott W. Divergent perspectives on GM food. Nat Biotechnol. 2002 Dec; 20(12):1195-6; author reply 1197. PMID: 12454665.
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      191. Yoshida R, Hobo T, Ichimura K, Mizoguchi T, Takahashi F, Aronso J, Ecker J, Shinozaki K. ABA-activated SnRK2 protein kinase is required for dehydration stress signaling in Arabidopsis. Plant Cell Physiol. 2002 Dec; 43(12):1473-83. PMID: 12514244.
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      192. Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker J, Normanly J, Chory J, Celenza JL. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev. 2002 Dec 1; 16(23):3100-12. PMID: 12464638.
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      193. Friedrichsen DM, Nemhauser J, Muramitsu T, Maloof JN, Alonso J, Ecker J, Furuya M, Chory J. Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics. 2002 Nov; 162(3):1445-56. PMID: 12454087.
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      194. Schroeder DF, Gahrtz M, Maxwell BB, Cook RK, Kan JM, Alonso JM, Ecker J, Chory J. De-etiolated 1 and damaged DNA binding protein 1 interact to regulate Arabidopsis photomorphogenesis. Curr Biol. 2002 Sep 3; 12(17):1462-72. PMID: 12225661.
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      195. Schröder AR, Shinn P, Chen H, Berry C, Ecker J, Bushman F. HIV-1 integration in the human genome favors active genes and local hotspots. Cell. 2002 Aug 23; 110(4):521-9. PMID: 12202041.
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      196. Hu J, Aguirre M, Peto C, Alonso J, Ecker J, Chory J. A role for peroxisomes in photomorphogenesis and development of Arabidopsis. Science. 2002 Jul 19; 297(5580):405-9. PMID: 12130786.
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      197. Zheng H, Bednarek SY, Sanderfoot AA, Alonso J, Ecker J, Raikhel NV. NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE. Plant Physiol. 2002 Jun; 129(2):530-9. PMID: 12068098.
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      198. Wang KL, Li H, Ecker J. Ethylene biosynthesis and signaling networks. Plant Cell. 2002; 14 Suppl:S131-51. PMID: 12045274.
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      199. Jarillo JA, Gabrys H, Capel J, Alonso JM, Ecker J, Cashmore AR. Phototropin-related NPL1 controls chloroplast relocation induced by blue light. Nature. 2001 Apr 19; 410(6831):952-4. PMID: 11309623.
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      200. Jarillo JA, Capel J, Tang RH, Yang HQ, Alonso JM, Ecker J, Cashmore AR. An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature. 2001 Mar 22; 410(6827):487-90. PMID: 11260718.
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      201. Alonso JM, Ecker J. The ethylene pathway: a paradigm for plant hormone signaling and interaction. Sci STKE. 2001 Feb 20; 2001(70):re1. PMID: 11752640.
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      202. Theologis A, Ecker J, 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, Cheuk RF, Chin CW, Chung MK, Conn L, Conway AB, Conway AR, Creasy TH, Dewar K, Dunn P, Etgu P, Feldblyum TV, Feng J, Fong B, Fujii CY, Gill JE, Goldsmith AD, Haas B, Hansen NF, Hughes B, Huizar L, Hunter JL, Jenkins J, Johnson-Hopson C, Khan S, Khaykin E, Kim CJ, Koo HL, Kremenetskaia I, Kurtz DB, Kwan A, Lam B, Langin-Hooper S, Lee A, Lee JM, Lenz CA, Li JH, Li Y, Lin X, Liu SX, Liu ZA, Luros JS, Maiti R, Marziali A, Militscher J, Miranda M, Nguyen M, Nierman WC, Osborne BI, Pai G, Peterson J, Pham PK, Rizzo M, Rooney T, Rowley D, Sakano H, Salzberg SL, Schwartz JR, Shinn P, Southwick AM, Sun H, Tallon LJ, Tambunga G, Toriumi MJ, Town CD, Utterback T, Van Aken S, Vaysberg M, Vysotskaia VS, Walker M, Wu D, Yu G, Fraser CM, Venter JC, Davis RW. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature. 2000 Dec 14; 408(6814):816-20. PMID: 11130712.
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      203. Stepanova AN, Ecker J. Ethylene signaling: from mutants to molecules. Curr Opin Plant Biol. 2000 Oct; 3(5):353-60. PMID: 11019801.
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      204. Chory J, Ecker J, 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 Physiol. 2000 Jun; 123(2):423-6. PMID: 10859172.
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      205. Curie C, Alonso JM, Le Jean M, Ecker J, Briat JF. Involvement of NRAMP1 from Arabidopsis thaliana in iron transport. Biochem J. 2000 May 1; 347 Pt 3:749-55. PMID: 10769179.
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      206. Raz V, Ecker J. Regulation of differential growth in the apical hook of Arabidopsis. Development. 1999 Aug; 126(16):3661-8. PMID: 10409511.
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      207. Mozo T, Dewar K, Dunn P, Ecker J, 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. Nat Genet. 1999 Jul; 22(3):271-5. PMID: 10391215.
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      208. Alonso JM, Hirayama T, Roman G, Nourizadeh S, Ecker J. EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. Science. 1999 Jun 25; 284(5423):2148-52. PMID: 10381874.
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      209. Hirayama T, Kieber JJ, Hirayama N, Kogan M, Guzman P, Nourizadeh S, Alonso JM, Dailey WP, Dancis A, Ecker J. RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson disease-related copper transporter, is required for ethylene signaling in Arabidopsis. Cell. 1999 Apr 30; 97(3):383-93. PMID: 10319818.
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      210. Solano R, Stepanova A, Chao Q, Ecker J. Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev. 1998 Dec 1; 12(23):3703-14. PMID: 9851977.
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      211. Kwok SF, Solano R, Tsuge T, Chamovitz DA, Ecker J, 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. 1998 Nov; 10(11):1779-90. PMID: 9811788.
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      212. Solano R, Ecker J. Ethylene gas: perception, signaling and response. Curr Opin Plant Biol. 1998 Oct; 1(5):393-8. PMID: 10066624.
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      213. Hua J, Sakai H, Nourizadeh S, Chen QG, Bleecker AB, Ecker J, Meyerowitz EM. EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis. Plant Cell. 1998 Aug; 10(8):1321-32. PMID: 9707532.
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      214. Ecker J. Genome sequencing. Genes blossom from a weed. Nature. 1998 Jan 29; 391(6666):438-9. PMID: 9461207.
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      215. Johnson PR, Ecker J. The ethylene gas signal transduction pathway: a molecular perspective. Annu Rev Genet. 1998; 32:227-54. PMID: 9928480.
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      216. Süss G, Aigner K, Bolitschek J, Forstner B, Dejaco R, Dorninger HP, Dovjak P, Ecker J, Hochreiter K, Knaus W, Kühn P, Mayer K, Mayrhofer E, Mori M, Schinko H, Wimberger F, Kunze M. [The "Inpatient Vaccination" Project in upper Austria. Technical report]. Wien Med Wochenschr. 1998; 148(8-9):198-203. PMID: 9677676.
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      217. Ecker J. BRI-ghtening the pathway to steroid hormone signaling events in plants. Cell. 1997 Sep 5; 90(5):825-7. PMID: 9298893.
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      218. Chao Q, Rothenberg M, Solano R, Roman G, Terzaghi W, Ecker J. Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins. Cell. 1997 Jun 27; 89(7):1133-44. PMID: 9215635.
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      219. Mulligan RM, Chory J, Ecker J. Signaling in plants. Proc Natl Acad Sci U S A. 1997 Apr 1; 94(7):2793-5. PMID: 9096297.
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      220. Lehman A, Black R, Ecker J. HOOKLESS1, an ethylene response gene, is required for differential cell elongation in the Arabidopsis hypocotyl. Cell. 1996 Apr 19; 85(2):183-94. PMID: 8612271.
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      221. Goodman HM, Ecker J, Dean C. The genome of Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1995 Nov 21; 92(24):10831-5. PMID: 7479893.
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      222. Roman G, Ecker J. Genetic analysis of a seedling stress response to ethylene in Arabidopsis. Philos Trans R Soc Lond B Biol Sci. 1995 Oct 30; 350(1331):75-81. PMID: 8577853.
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      223. Ecker J. The ethylene signal transduction pathway in plants. Science. 1995 May 5; 268(5211):667-75. PMID: 7732375.
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      224. Roman G, Lubarsky B, Kieber JJ, Rothenberg M, Ecker J. Genetic analysis of ethylene signal transduction in Arabidopsis thaliana: five novel mutant loci integrated into a stress response pathway. Genetics. 1995 Mar; 139(3):1393-409. PMID: 7768447.
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      225. Bell CJ, Ecker J. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics. 1994 Jan 1; 19(1):137-44. PMID: 8188214.
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      226. Kieber JJ, Ecker J. Ethylene gas: it's not just for ripening any more! Trends Genet. 1993 Oct; 9(10):356-62. PMID: 8273151.
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      227. Ecker J, Sherman R. Soft-tissue coverage of the distal third of the leg and ankle. Orthop Clin North Am. 1993 Jul; 24(3):481-8. PMID: 8101985.
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      228. Kieber JJ, Rothenberg M, Roman G, Feldmann KA, Ecker J. CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell. 1993 Feb 12; 72(3):427-41. PMID: 8431946.
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      229. Bent AF, Innes RW, Ecker J, Staskawicz BJ. Disease development in ethylene-insensitive Arabidopsis thaliana infected with virulent and avirulent Pseudomonas and Xanthomonas pathogens. Mol Plant Microbe Interact. 1992 Sep-Oct; 5(5):372-8. PMID: 1472714.
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      230. Schindler U, Menkens AE, Beckmann H, Ecker J, Cashmore AR. Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF bZIP proteins. EMBO J. 1992 Apr; 11(4):1261-73. PMID: 1373374.
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      231. Ewens WJ, Bell CJ, Donnelly PJ, Dunn P, Matallana E, Ecker J. Genome mapping with anchored clones: theoretical aspects. Genomics. 1991 Dec; 11(4):799-805. PMID: 1686019.
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      232. Lehman TA, Bennett WP, Metcalf RA, Welsh JA, Ecker J, Modali RV, Ullrich S, Romano JW, Appella E, Testa JR. p53 mutations, ras mutations, and p53-heat shock 70 protein complexes in human lung carcinoma cell lines. Cancer Res. 1991 Aug 1; 51(15):4090-6. PMID: 1855224.
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      233. Bindiger A, Ecker J, Kuschner S, Sherman R. External fixation of extremity flaps and grafts. Ann Plast Surg. 1991 Feb; 26(2):198-9. PMID: 2006850.
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      234. Schindler U, Ecker J, Cashmore AR. An Arabidopsis thaliana G-box-binding protein similar to the wheat leucine zipper protein identified as HBP-1. Symp Soc Exp Biol. 1991; 45:211-8. PMID: 1843410.
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      235. Guzmán P, Ecker J. Exploiting the triple response of Arabidopsis to identify ethylene-related mutants. Plant Cell. 1990 Jun; 2(6):513-23. PMID: 2152173.
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      236. Monia BP, Haskell KM, Ecker J, Ecker DJ, Crooke ST. Chromosomal mapping of the ubiquitin gene family in Saccharomyces cerevisiae by pulsed field gel electrophoresis. Nucleic Acids Res. 1989 May 11; 17(9):3611-2. PMID: 2542906.
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      237. Ecker J, Davis RW. Plant defense genes are regulated by ethylene. Proc Natl Acad Sci U S A. 1987 Aug; 84(15):5202-6. PMID: 16593860.
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      238. Ecker J, Davis RW. Inhibition of gene expression in plant cells by expression of antisense RNA. Proc Natl Acad Sci U S A. 1986 Aug; 83(15):5372-6. PMID: 16593734.
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