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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
      Center for Epigenomics of the Mouse Brain Atlas (CEMBA)
      NIH/NIMH U19MH114831Sep 20, 2017 - Jun 30, 2022
      Role: Principal Investigator
      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.
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      1. Kawakatsu T, Nery JR, Castanon R, Ecker J. Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biol. 2017 Sep 15; 18(1):171. PMID: 28911331.
        View in: PubMed
      2. 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
      3. 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
      4. 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.
        View in: PubMed
      5. 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.
        View in: PubMed
      6. 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
      7. 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 28; 114(9):E1633-E1640. PMID: 28193886.
        View in: PubMed
      8. 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. 2017 Feb; 89(4):805-824. PMID: 27859855.
        View in: PubMed
      9. Hossain MS, Kawakatsu T, Kim KD, Zhang N, 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 Apr; 214(2):808-819. PMID: 28106918.
        View in: PubMed
      10. 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 Feb 06; 27(3):437-444. PMID: 28111153.
        View in: PubMed
      11. 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. 2017 Feb; 213(3):1378-1392. PMID: 28005270.
        View in: PubMed
      12. 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.
        View in: PubMed
      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. 2017 Jan 05; 20(1):112-119. PMID: 27840020.
        View in: PubMed
      14. 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 11 04; 354(6312). PMID: 27811239.
        View in: PubMed
      15. 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 Dec; 13(12):1050-1054. PMID: 27749838.
        View in: PubMed
      16. 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.
        View in: PubMed
      17. 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 08; 166(6):1598. PMID: 27610578.
        View in: PubMed
      18. 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.
        View in: PubMed
      19. 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, Becker C, O'Neil R, O'Malley RC, Quarless DX, Schork NJ, Weigel D, Nordborg M, Ecker J. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 2016 Jul 14; 166(2):492-505. PMID: 27419873.
        View in: PubMed
      20. 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 06; 19(4):502-515. PMID: 27424783.
        View in: PubMed
      21. 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 Jun 30; 6:28941. PMID: 27357749; PMCID: PMC4928087.
      22. 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; PMCID: PMC4961138.
      23. 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.
        View in: PubMed
      24. 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 May 19; 165(5):1280-1292. PMID: 27203113; PMCID: PMC4907330 [Available on 05/19/17].
      25. 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 May 03; 6(5):1383-90. PMID: 26976444; PMCID: PMC4856089.
      26. 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 04 29; 2(5):16058. PMID: 27243651; PMCID: PMC4855458 [Available on 10/29/16].
      27. 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; PMCID: PMC4826003.
      28. 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 Mar 07; 5:e11613. PMID: 26949250; PMCID: PMC4798964.
      29. 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.
        View in: PubMed
      30. 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 09; 113(6):E801-10. PMID: 26787884; PMCID: PMC4760824.
      31. 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 Jan 19; 6:e718. PMID: 26784972.
        View in: PubMed
      32. Pedmale UV, Huang SC, Zander M, Cole BJ, Hetzel J, Ljung K, Reis PAB, 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):233-245. PMID: 26724867; PMCID: PMC4721562 [Available on 01/14/17].
      33. 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.
        View in: PubMed
      34. 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 Sep 29; 16:313. PMID: 26415965; PMCID: PMC4587815.
      35. 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; PMCID: PMC4574932.
      36. 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; PMCID: PMC4553765.
      37. 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 Jul 21; 4. PMID: 26196146; PMCID: PMC4534844.
      38. 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; PMCID: PMC4499463.
      39. Luo C, Ecker J. Epigenetics. Exceptional epigenetics in the brain. Science. 2015 Jun 05; 348(6239):1094-5. PMID: 26045424; PMCID: PMC4880990.
      40. He Y, Ecker J. Non-CG Methylation in the Human Genome. Annu Rev Genomics Hum Genet. 2015; 16:55-77. PMID: 26077819; PMCID: PMC4729449.
      41. 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 09; 523(7559):212-6. PMID: 26030523; PMCID: PMC4499021.
      42. 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.
        View in: PubMed
      43. 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 07; 16(5):547-55. PMID: 25865501; PMCID: PMC4427539.
      44. 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, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker J, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
      45. 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; PMCID: PMC4515363.
      46. 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; PMCID: PMC4465251.
      47. 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.
        View in: PubMed
      48. 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 02; 111(48):17224-9. PMID: 25413365; PMCID: PMC4260565.
      49. 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 AJM, 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):1431-1443. PMID: 25215497; PMCID: PMC4163041.
      50. 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; PMCID: PMC4191710.
      51. 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 04; 15(3):295-309. PMID: 25192464; PMCID: PMC4170792.
      52. 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; PMCID: PMC4199375.
      53. 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; PMCID: PMC4371832.
      54. 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; PMCID: PMC4125603.
      55. Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella PA, 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; PMCID: PMC4080997.
      56. 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; PMCID: PMC4898064.
      57. 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; PMCID: PMC4000807.
      58. 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; PMCID: PMC3912417.
      59. 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; PMCID: PMC3801079.
      60. 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; PMCID: PMC3842760.
      61. 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; PMCID: PMC3784603.
      62. 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 09; 341(6146):1237905. PMID: 23828890; PMCID: PMC3785061.
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      225. 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; PMCID: PMC1206465.
      226. Bell CJ, Ecker J. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics. 1994 Jan 01; 19(1):137-44. PMID: 8188214.
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      227. 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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      228. 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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      229. 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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      230. 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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      231. 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; PMCID: PMC556574.
      232. 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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      233. 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 01; 51(15):4090-6. PMID: 1855224.
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      234. 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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      235. 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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      236. 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; PMCID: PMC159907.
      237. 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; PMCID: PMC317823.
      238. 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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      239. 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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