Loading...

Joseph Ecker

TitleAdjunct Professor
InstitutionUniversity of California San Diego
DepartmentCell and Developmental Biology
Address9500 Gilman Drive #0932
La Jolla CA 92093
Phone858-453-4100
vCardDownload vCard

    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.
    List All   |   Timeline
    1. Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker J. Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. Nat Commun. 2018 May 22; 9(1):2075. PMID: 29789609.
      View in: PubMed
    2. Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker J. A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. Nat Commun. 2018 Apr 23; 9(1):1604. PMID: 29686312.
      View in: PubMed
    3. Michael TP, Jupe F, Bemm F, Motley ST, Sandoval JP, Lanz C, Loudet O, Weigel D, Ecker J. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat Commun. 2018 02 07; 9(1):541. PMID: 29416032.
      View in: PubMed
    4. Carter AC, Chang HY, Church G, Dombkowski A, Ecker J, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, Palmer M, Snyder MP, Tung J, Urban A, Vidal M, Wong W. Challenges and recommendations for epigenomics in precision health. Nat Biotechnol. 2017 Dec 08; 35(12):1128-1132. PMID: 29220033.
      View in: PubMed
    5. Huang SC, Ecker J. Piecing together cis-regulatory networks: insights from epigenomics studies in plants. Wiley Interdiscip Rev Syst Biol Med. 2018 05; 10(3):e1411. PMID: 29194997.
      View in: PubMed
    6. Ecker J, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron. 2017 Nov 01; 96(3):542-557. PMID: 29096072.
      View in: PubMed
    7. 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
    8. 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 08 11; 357(6351):600-604. PMID: 28798132.
      View in: PubMed
    9. 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
    10. 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
    11. 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
    12. 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 04 04; 114(14):E2882-E2890. PMID: 28320934.
      View in: PubMed
    13. 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 02 28; 114(9):E1633-E1640. PMID: 28193886.
      View in: PubMed
    14. 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
    15. 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
    16. 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
    17. 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
    18. 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 12 20; 17(12):3369-3384. PMID: 28009303.
      View in: PubMed
    19. 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 01 05; 20(1):112-119. PMID: 27840020.
      View in: PubMed
    20. 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
    21. 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
    22. 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
    23. 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
    24. 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
    25. 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. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 2016 Jul 14; 166(2):492-505. PMID: 27419873.
      View in: PubMed
    26. 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 10 06; 19(4):502-515. PMID: 27424783.
      View in: PubMed
    27. 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 06 30; 6:28941. PMID: 27357749.
      View in: PubMed
    28. 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 07 19; 113(29):E4238-47. PMID: 27357687; PMCID: PMC4961138.
      View in: PubMed, PubMed Central
    29. 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
    30. 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].
      View in: PubMed, PubMed Central
    31. 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 05 03; 6(5):1383-90. PMID: 26976444; PMCID: PMC4856089.
      View in: PubMed, PubMed Central
    32. 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].
      View in: PubMed, PubMed Central
    33. 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.
      View in: PubMed, PubMed Central
    34. 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.
      View in: PubMed, PubMed Central
    35. 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
    36. 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.
      View in: PubMed, PubMed Central
    37. 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].
      View in: PubMed, PubMed Central
    38. 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
    39. 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.
      View in: PubMed, PubMed Central
    40. 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.
      View in: PubMed, PubMed Central
    41. 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.
      View in: PubMed, PubMed Central
    42. 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.
      View in: PubMed, PubMed Central
    43. 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.
      View in: PubMed, PubMed Central
    44. Luo C, Ecker J. Epigenetics. Exceptional epigenetics in the brain. Science. 2015 Jun 05; 348(6239):1094-5. PMID: 26045424; PMCID: PMC4880990.
      View in: PubMed, PubMed Central
    45. He Y, Ecker J. Non-CG Methylation in the Human Genome. Annu Rev Genomics Hum Genet. 2015; 16:55-77. PMID: 26077819; PMCID: PMC4729449.
      View in: PubMed, PubMed Central
    46. 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.
      View in: PubMed, PubMed Central
    47. 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
    48. 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.
      View in: PubMed, PubMed Central
    49. 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.
      View in: PubMed, PubMed Central
    50. 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, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker J, Ren B. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 2015 Feb 19; 518(7539):350-354. PMID: 25693566; PMCID: PMC4449149.
      View in: PubMed, PubMed Central
    51. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563; PMCID: PMC4530010.
      View in: PubMed, PubMed Central
    52. 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.
      View in: PubMed, PubMed Central
    53. 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
    54. 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.
      View in: PubMed
    55. 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.
      View in: PubMed, PubMed Central
    56. 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.
      View in: PubMed, PubMed Central
    57. 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.
      View in: PubMed, PubMed Central
    58. 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.
      View in: PubMed, PubMed Central
    59. 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.
      View in: PubMed, PubMed Central
    60. 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.
      View in: PubMed, PubMed Central
    61. 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.
      View in: PubMed, PubMed Central
    62. 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.
      View in: PubMed, PubMed Central
    63. 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.
      View in: PubMed, PubMed Central
    64. 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.
      View in: PubMed, PubMed Central
    65. 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.
      View in: PubMed, PubMed Central
    66. 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.
      View in: PubMed, PubMed Central
    67. 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.
      View in: PubMed, PubMed Central
    68. 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.
      View in: PubMed, PubMed Central
    69. 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 Jun 11; 2:e00675. PMID: 23795294; PMCID: PMC3679525.
      View in: PubMed, PubMed Central
    70. 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; PMCID: PMC3787263.
      View in: PubMed, PubMed Central
    71. 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; 8(8). PMID: 23733051; PMCID: PMC3999072.
      View in: PubMed, PubMed Central
    72. 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; PMCID: PMC3786220.
      View in: PubMed, PubMed Central
    73. 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; PMCID: PMC3641203.
      View in: PubMed, PubMed Central
    74. 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; PMCID: PMC3798000.
      View in: PubMed, PubMed Central
    75. Ecker J. Epigenetic trigger for tomato ripening. Nat Biotechnol. 2013 Feb; 31(2):119-20. PMID: 23392509.
      View in: PubMed
    76. Vollmers C, Schmitz RJ, Nathanson J, Yeo G, Ecker J, Panda S. Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metab. 2012 Dec 05; 16(6):833-45. PMID: 23217262; PMCID: PMC3541940.
      View in: PubMed, PubMed Central
    77. Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker J, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Res. 2012 Dec 15; 72(24):6319-24. PMID: 23188507.
      View in: PubMed
    78. Woodson JD, Perez-Ruiz JM, Schmitz RJ, Ecker J, Chory J. Sigma factor-mediated plastid retrograde signals control nuclear gene expression. Plant J. 2013 Jan; 73(1):1-13. PMID: 22950756; PMCID: PMC3605210.
      View in: PubMed, PubMed Central
    79. Schultz MD, Schmitz RJ, Ecker J. 'Leveling' the playing field for analyses of single-base resolution DNA methylomes. Trends Genet. 2012 Dec; 28(12):583-5. PMID: 23131467; PMCID: PMC3523709.
      View in: PubMed, PubMed Central
    80. Ecker J, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature. 2012 Sep 06; 489(7414):52-5. PMID: 22955614.
      View in: PubMed
    81. Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker J. Processing and subcellular trafficking of ER-tethered EIN2 control response to ethylene gas. Science. 2012 Oct 19; 338(6105):390-3. PMID: 22936567; PMCID: PMC3523706.
      View in: PubMed, PubMed Central
    82. Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, Ecker J, 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 Dev. 2012 Aug 15; 26(16):1825-36. PMID: 22855789; PMCID: PMC3426761.
      View in: PubMed, PubMed Central
    83. Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker J. Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A. 2012 Aug 07; 109(32):E2183-91. PMID: 22733782; PMCID: PMC3420206.
      View in: PubMed, PubMed Central
    84. Peng Q, Ecker J. Detection of allele-specific methylation through a generalized heterogeneous epigenome model. Bioinformatics. 2012 Jun 15; 28(12):i163-71. PMID: 22689757; PMCID: PMC3371863.
      View in: PubMed, PubMed Central
    85. Johnson DB, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker J, Wang L. Release factor one is nonessential in Escherichia coli. ACS Chem Biol. 2012 Aug 17; 7(8):1337-44. PMID: 22662873; PMCID: PMC3423824.
      View in: PubMed, PubMed Central
    86. Li L, Ljung K, Breton G, Schmitz RJ, Pruneda-Paz J, Cowing-Zitron C, Cole BJ, Ivans LJ, Pedmale UV, Jung HS, Ecker J, Kay SA, Chory J. Linking photoreceptor excitation to changes in plant architecture. Genes Dev. 2012 Apr 15; 26(8):785-90. PMID: 22508725; PMCID: PMC3337452.
      View in: PubMed, PubMed Central
    87. Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Okubo-Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker J. Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis. G3 (Bethesda). 2012 Apr; 2(4):487-98. PMID: 22540040; PMCID: PMC3337477.
      View in: PubMed, PubMed Central
    88. Schmitz RJ, Ecker J. Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci. 2012 Mar; 17(3):149-54. PMID: 22342533; PMCID: PMC3645451.
      View in: PubMed, PubMed Central
    89. 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 J, Bafna V, Strausberg RL, Simpson AJ, Ren B. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012 Feb; 22(2):246-58. PMID: 22156296; PMCID: PMC3266032.
      View in: PubMed, PubMed Central
    90. 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 J, Stanford WL, Zuber J, Stark A, Penninger JM. Forward and reverse genetics through derivation of haploid mouse embryonic stem cells. Cell Stem Cell. 2011 Dec 02; 9(6):563-74. PMID: 22136931; PMCID: PMC4008724.
      View in: PubMed, PubMed Central
    91. Hotto AM, Schmitz RJ, Fei Z, Ecker J, Stern DB. Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome. G3 (Bethesda). 2011 Dec; 1(7):559-70. PMID: 22384367; PMCID: PMC3276175.
      View in: PubMed, PubMed Central
    92. Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD, Schmitz RJ, Xiang Z, Ecker J, Briggs SP, Wang L. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat Chem Biol. 2011 Sep 18; 7(11):779-86. PMID: 21926996; PMCID: PMC3201715.
      View in: PubMed, PubMed Central
    93. Schmitz RJ, Schultz MD, Lewsey MG, O'Malley RC, Urich MA, Libiger O, Schork NJ, Ecker J. Transgenerational epigenetic instability is a source of novel methylation variants. Science. 2011 Oct 21; 334(6054):369-73. PMID: 21921155; PMCID: PMC3210014.
      View in: PubMed, PubMed Central
    94. 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, Poulin MM, Gebreab F, Gutierrez BJ, Tam S, Monachello D, Boxem M, Harbort CJ, McDonald N, Gai L, Chen H, He Y. Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science. 2011 Jul 29; 333(6042):596-601. PMID: 21798943; PMCID: PMC3170753.
      View in: PubMed, PubMed Central
    95. 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 J, Milos PM, Agarwal S, Rao A. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 2011 May 19; 473(7347):394-7. PMID: 21552279.
      View in: PubMed
    96. 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, Evans RM, Ecker J. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011 Mar 03; 471(7336):68-73. PMID: 21289626; PMCID: PMC3100360.
      View in: PubMed, PubMed Central
    97. Pelizzola M, Ecker J. The DNA methylome. FEBS Lett. 2011 Jul 07; 585(13):1994-2000. PMID: 21056564; PMCID: PMC3129437.
      View in: PubMed, PubMed Central
    98. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker J, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct; 28(10):1045-8. PMID: 20944595; PMCID: PMC3607281.
      View in: PubMed, PubMed Central
    99. 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, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker J, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. PMID: 20852635; PMCID: PMC2955169.
      View in: PubMed, PubMed Central
    100. Boutrot F, Segonzac C, Chang KN, Qiao H, Ecker J, Zipfel C, Rathjen JP. Direct transcriptional control of the Arabidopsis immune receptor FLS2 by the ethylene-dependent transcription factors EIN3 and EIL1. Proc Natl Acad Sci U S A. 2010 Aug 10; 107(32):14502-7. PMID: 20663954; PMCID: PMC2922558.
      View in: PubMed, PubMed Central
    101. An F, Zhao Q, Ji Y, Li W, Jiang Z, Yu X, Zhang C, Han Y, He W, Liu Y, Zhang S, Ecker J, 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. 2010 Jul; 22(7):2384-401. PMID: 20647342; PMCID: PMC2929093.
      View in: PubMed, PubMed Central
    102. Ecker J. Zeroing in on DNA methylomes with no BS. Nat Methods. 2010 Jun; 7(6):435-7. PMID: 20508637.
      View in: PubMed
    103. 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, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker J, Ren B. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 2010 May 07; 6(5):479-91. PMID: 20452322; PMCID: PMC2867844.
      View in: PubMed, PubMed Central
    104. 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, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker J, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010 Jun 03; 465(7298):627-31. PMID: 20336072; PMCID: PMC3023908.
      View in: PubMed, PubMed Central
    105. O'Malley RC, Ecker J. Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J. 2010 Mar; 61(6):928-40. PMID: 20409268.
      View in: PubMed
    106. Endres MW, Gregory BD, Gao Z, Foreman AW, Mlotshwa S, Ge X, Pruss GJ, Ecker J, Bowman LH, Vance V. Two plant viral suppressors of silencing require the ethylene-inducible host transcription factor RAV2 to block RNA silencing. PLoS Pathog. 2010 Jan 15; 6(1):e1000729. PMID: 20084269; PMCID: PMC2800190.
      View in: PubMed, PubMed Central
    107. 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, Thomson JA, Ren B, Ecker J. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009 Nov 19; 462(7271):315-22. PMID: 19829295; PMCID: PMC2857523.
      View in: PubMed, PubMed Central
    108. Tsuchisaka A, Yu G, Jin H, Alonso JM, Ecker J, Zhang X, Gao S, Theologis A. A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana. Genetics. 2009 Nov; 183(3):979-1003. PMID: 19752216; PMCID: PMC2778992.
      View in: PubMed, PubMed Central
    109. Prepublication data sharing. Nature. 2009 Sep 10; 461(7261):168-70. PMID: 19741685.
      View in: PubMed
    110. Liljegren SJ, Leslie ME, Darnielle L, Lewis MW, Taylor SM, Luo R, Geldner N, Chory J, Randazzo PA, Yanofsky MF, Ecker J. Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein. Development. 2009 Jun; 136(11):1909-18. PMID: 19429787; PMCID: PMC2680113.
      View in: PubMed, PubMed Central
    111. Dowen RH, Engel JL, Shao F, Ecker J, Dixon JE. A family of bacterial cysteine protease type III effectors utilizes acylation-dependent and -independent strategies to localize to plasma membranes. J Biol Chem. 2009 Jun 05; 284(23):15867-79. PMID: 19346252; PMCID: PMC2708883.
      View in: PubMed, PubMed Central
    112. Lister R, Ecker J. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res. 2009 Jun; 19(6):959-66. PMID: 19273618; PMCID: PMC3807530.
      View in: PubMed, PubMed Central
    113. Li H, Wong WS, Zhu L, Guo HW, 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. 2009 Mar; 9(6):1646-61. PMID: 19253305.
      View in: PubMed
    114. Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker J, Borevitz JO, Kay SA. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol. 2009 Feb 11; 10(2):R17. PMID: 19210792.
      View in: PubMed
    115. Qiao H, Chang KN, Yazaki J, Ecker J. Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis. Genes Dev. 2009 Feb 15; 23(4):512-21. PMID: 19196655; PMCID: PMC2648649.
      View in: PubMed, PubMed Central
    116. Lister R, Gregory BD, Ecker J. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol. 2009 Apr; 12(2):107-18. PMID: 19157957; PMCID: PMC2723731.
      View in: PubMed, PubMed Central
    117. 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 J, Roth FP, Vidal M. Literature-curated protein interaction datasets. Nat Methods. 2009 Jan; 6(1):39-46. PMID: 19116613; PMCID: PMC2683745.
      View in: PubMed, PubMed Central
    118. 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, Poethig S, Raikhel N, Schmitt J, Schnittger A, Vidal M. 2020 vision for biology: the role of plants in addressing grand challenges in biology. Mol Plant. 2008 Jul; 1(4):561-3. PMID: 19825561.
      View in: PubMed
    119. Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker J. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell. 2008 Jun; 14(6):854-66. PMID: 18486559.
      View in: PubMed
    120. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker J. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008 May 02; 133(3):523-36. PMID: 18423832; PMCID: PMC2723732.
      View in: PubMed, PubMed Central
    121. Hu J, Mitchum MG, Barnaby N, Ayele BT, Ogawa M, Nam E, Lai WC, Hanada A, Alonso JM, Ecker J, Swain SM, Yamaguchi S, Kamiya Y, Sun TP. Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. Plant Cell. 2008 Feb; 20(2):320-36. PMID: 18310462; PMCID: PMC2276448.
      View in: PubMed, PubMed Central
    122. Leivar P, Monte E, Al-Sady B, Carle C, Storer A, Alonso JM, Ecker J, Quail PH. The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. Plant Cell. 2008 Feb; 20(2):337-52. PMID: 18252845; PMCID: PMC2276449.
      View in: PubMed, PubMed Central
    123. Gregory BD, Yazaki J, Ecker J. Utilizing tiling microarrays for whole-genome analysis in plants. Plant J. 2008 Feb; 53(4):636-44. PMID: 18269573.
      View in: PubMed
    124. 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 J, Belostotsky DA. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell. 2007 Dec 28; 131(7):1340-53. PMID: 18160042.
      View in: PubMed
    125. Yazaki J, Gregory BD, Ecker J. Mapping the genome landscape using tiling array technology. Curr Opin Plant Biol. 2007 Oct; 10(5):534-42. PMID: 17703988; PMCID: PMC2665186.
      View in: PubMed, PubMed Central
    126. Li H, He Z, Lu G, Lee SC, Alonso J, Ecker J, Luan S. A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. Plant Cell. 2007 Aug; 19(8):2403-16. PMID: 17704213; PMCID: PMC2002612.
      View in: PubMed, PubMed Central
    127. Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker J, Weigel D, Nordborg M. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet. 2007 Sep; 39(9):1151-5. PMID: 17676040.
      View in: PubMed
    128. Gentry MS, Dowen RH, Worby CA, Mattoo S, Ecker J, Dixon JE. The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease. J Cell Biol. 2007 Jul 30; 178(3):477-88. PMID: 17646401; PMCID: PMC2064834.
      View in: PubMed, PubMed Central
    129. 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, Rätsch G, Ecker J, Weigel D. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science. 2007 Jul 20; 317(5836):338-42. PMID: 17641193.
      View in: PubMed
    130. 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 J. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2007 Jul 17; 104(29):12057-62. PMID: 17626786; PMCID: PMC1914337.
      View in: PubMed, PubMed Central
    131. Swiezewski S, Crevillen P, Liu F, Ecker J, Jerzmanowski A, Dean C. Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC. Proc Natl Acad Sci U S A. 2007 Feb 27; 104(9):3633-8. PMID: 17360694; PMCID: PMC1805594.
      View in: PubMed, PubMed Central
    132. Puig S, Mira H, Dorcey E, Sancenón V, Andrés-Colás N, Garcia-Molina A, Burkhead JL, Gogolin KA, Abdel-Ghany SE, Thiele DJ, Ecker J, Pilon M, Peñarrubia L. Higher plants possess two different types of ATX1-like copper chaperones. Biochem Biophys Res Commun. 2007 Mar 09; 354(2):385-90. PMID: 17223078.
      View in: PubMed
    133. O'Malley RC, Alonso JM, Kim CJ, Leisse TJ, Ecker J. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. Nat Protoc. 2007; 2(11):2910-7. PMID: 18007627.
      View in: PubMed
    134. Chilley PM, Casson SA, Tarkowski P, Hawkins N, Wang KL, Hussey PJ, Beale M, Ecker J, Sandberg GK, Lindsey K. The POLARIS peptide of Arabidopsis regulates auxin transport and root growth via effects on ethylene signaling. Plant Cell. 2006 Nov; 18(11):3058-72. PMID: 17138700; PMCID: PMC1693943.
      View in: PubMed, PubMed Central
    135. Hutchison CE, Li J, Argueso C, Gonzalez M, Lee E, Lewis MW, Maxwell BB, Perdue TD, Schaller GE, Alonso JM, Ecker J, Kieber JJ. The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling. Plant Cell. 2006 Nov; 18(11):3073-87. PMID: 17122069; PMCID: PMC1693944.
      View in: PubMed, PubMed Central
    136. Kim SA, Punshon T, Lanzirotti A, Li L, Alonso JM, Ecker J, Kaplan J, Guerinot ML. Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1. Science. 2006 Nov 24; 314(5803):1295-8. PMID: 17082420.
      View in: PubMed
    137. Mori IC, Murata Y, Yang Y, Munemasa S, Wang YF, Andreoli S, Tiriac H, Alonso JM, Harper JF, Ecker J, 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 Biol. 2006 Oct; 4(10):e327. PMID: 17032064; PMCID: PMC1592316.
      View in: PubMed, PubMed Central
    138. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker J. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 2006 Sep 22; 126(6):1189-201. PMID: 16949657.
      View in: PubMed
    139. Olmedo G, Guo H, Gregory BD, Nourizadeh SD, Aguilar-Henonin L, Li H, An F, Guzman P, Ecker J. ETHYLENE-INSENSITIVE5 encodes a 5'-->3' exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2. Proc Natl Acad Sci U S A. 2006 Sep 05; 103(36):13286-93. PMID: 16920797; PMCID: PMC1550774.
      View in: PubMed, PubMed Central
    140. Yoshida H, Wang KL, Chang CM, Mori K, Uchida E, Ecker J. The ACC synthase TOE sequence is required for interaction with ETO1 family proteins and destabilization of target proteins. Plant Mol Biol. 2006 Oct; 62(3):427-37. PMID: 16897471.
      View in: PubMed
    141. Chen JG, Ullah H, Temple B, Liang J, Guo J, Alonso JM, Ecker J, Jones AM. RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis. J Exp Bot. 2006; 57(11):2697-708. PMID: 16829549.
      View in: PubMed
    142. Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker J, Bushman FD. Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog. 2006 Jun; 2(6):e60. PMID: 16789841; PMCID: PMC1480600.
      View in: PubMed, PubMed Central
    143. Lariguet P, Schepens I, Hodgson D, Pedmale UV, Trevisan M, Kami C, de Carbonnel M, Alonso JM, Ecker J, Liscum E, Fankhauser C. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism. Proc Natl Acad Sci U S A. 2006 Jun 27; 103(26):10134-9. PMID: 16777956; PMCID: PMC1502518.
      View in: PubMed, PubMed Central
    144. Rudella A, Friso G, Alonso JM, Ecker J, van Wijk KJ. Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis. Plant Cell. 2006 Jul; 18(7):1704-21. PMID: 16766689; PMCID: PMC1488914.
      View in: PubMed, PubMed Central
    145. Alonso JM, Ecker J. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet. 2006 Jul; 7(7):524-36. PMID: 16755288.
      View in: PubMed
    146. Barr SD, Ciuffi A, Leipzig J, Shinn P, Ecker J, Bushman FD. HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry. Mol Ther. 2006 Aug; 14(2):218-25. PMID: 16647883.
      View in: PubMed
    147. Andrés-Colás N, Sancenón V, Rodríguez-Navarro S, Mayo S, Thiele DJ, Ecker J, Puig S, Peñarrubia L. The Arabidopsis heavy metal P-type ATPase HMA5 interacts with metallochaperones and functions in copper detoxification of roots. Plant J. 2006 Jan; 45(2):225-36. PMID: 16367966.
      View in: PubMed
    148. Ciuffi A, Mitchell RS, Hoffmann C, Leipzig J, Shinn P, Ecker J, Bushman FD. Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts. Mol Ther. 2006 Feb; 13(2):366-73. PMID: 16325473.
      View in: PubMed
    149. Ciuffi A, Llano M, Poeschla E, Hoffmann C, Leipzig J, Shinn P, Ecker J, Bushman F. A role for LEDGF/p75 in targeting HIV DNA integration. Nat Med. 2005 Dec; 11(12):1287-9. PMID: 16311605.
      View in: PubMed
    150. Overvoorde PJ, Okushima Y, Alonso JM, Chan A, Chang C, Ecker J, 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. Plant Cell. 2005 Dec; 17(12):3282-300. PMID: 16284307; PMCID: PMC1315369.
      View in: PubMed, PubMed Central
    151. Mason MG, Mathews DE, Argyros DA, Maxwell BB, Kieber JJ, Alonso JM, Ecker J, Schaller GE. Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. Plant Cell. 2005 Nov; 17(11):3007-18. PMID: 16227453; PMCID: PMC1276026.
      View in: PubMed, PubMed Central
    152. Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker J, Reed JW. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development. 2005 Sep; 132(18):4107-18. PMID: 16107481.
      View in: PubMed
    153. Yoshida H, Nagata M, Saito K, Wang KL, Ecker J. Arabidopsis ETO1 specifically interacts with and negatively regulates type 2 1-aminocyclopropane-1-carboxylate synthases. BMC Plant Biol. 2005 Aug 10; 5:14. PMID: 16091151; PMCID: PMC1199607.
      View in: PubMed, PubMed Central
    154. Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker J, Kay SA. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci U S A. 2005 Jul 19; 102(29):10387-92. PMID: 16006522; PMCID: PMC1177380.
      View in: PubMed, PubMed Central
    155. Wilmoth JC, Wang S, Tiwari SB, Joshi AD, Hagen G, Guilfoyle TJ, Alonso JM, Ecker J, Reed JW. NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. Plant J. 2005 Jul; 43(1):118-30. PMID: 15960621.
      View in: PubMed
    156. Werner JD, Borevitz JO, Uhlenhaut NH, Ecker J, Chory J, Weigel D. FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions. Genetics. 2005 Jul; 170(3):1197-207. PMID: 15911588; PMCID: PMC1451178.
      View in: PubMed, PubMed Central
    157. Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker J, Kay SA. Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. Plant Physiol. 2005 Jun; 138(2):990-7. PMID: 15908595; PMCID: PMC1150413.
      View in: PubMed, PubMed Central
    158. 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; PMCID: PMC555478.
      View in: PubMed, PubMed Central
    159. 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.
      View in: PubMed
    160. 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; PMCID: PMC548991.
      View in: PubMed, PubMed Central
    161. 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; PMCID: PMC548818.
      View in: PubMed, PubMed Central
    162. 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.
      View in: PubMed
    163. 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.
      View in: PubMed
    164. 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; PMCID: PMC544490.
      View in: PubMed, PubMed Central
    165. 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; PMCID: PMC528976.
      View in: PubMed, PubMed Central
    166. 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; PMCID: PMC523352.
      View in: PubMed, PubMed Central
    167. 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; PMCID: PMC523354.
      View in: PubMed, PubMed Central
    168. 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; PMCID: PMC509299.
      View in: PubMed, PubMed Central
    169. 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; PMCID: PMC515126.
      View in: PubMed, PubMed Central
    170. 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.
      View in: PubMed
    171. 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; PMCID: PMC514125.
      View in: PubMed, PubMed Central
    172. 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; PMCID: PMC1470895.
      View in: PubMed, PubMed Central
    173. 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.
      View in: PubMed
    174. 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; PMCID: PMC514135.
      View in: PubMed, PubMed Central
    175. 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.
      View in: PubMed
    176. 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.
      View in: PubMed
    177. 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; PMCID: PMC374356.
      View in: PubMed, PubMed Central
    178. 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; PMCID: PMC385279.
      View in: PubMed, PubMed Central
    179. Guo H, Ecker J. The ethylene signaling pathway: new insights. Curr Opin Plant Biol. 2004 Feb; 7(1):40-9. PMID: 14732440.
      View in: PubMed
    180. Borevitz JO, Ecker J. Plant genomics: the third wave. Annu Rev Genomics Hum Genet. 2004; 5:443-77. PMID: 15485356.
      View in: PubMed
    181. 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.
      View in: PubMed
    182. 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; PMCID: PMC282833.
      View in: PubMed, PubMed Central
    183. 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; PMCID: PMC282841.
      View in: PubMed, PubMed Central
    184. 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 07; 302(5647):1049-53. PMID: 14605371.
      View in: PubMed
    185. 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.
      View in: PubMed
    186. 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; PMCID: PMC181324.
      View in: PubMed, PubMed Central
    187. 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 01; 301(5633):653-7. PMID: 12893945.
      View in: PubMed
    188. 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; PMCID: PMC166918.
      View in: PubMed, PubMed Central
    189. 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 04; 100(5):2992-7. PMID: 12606727; PMCID: PMC151454.
      View in: PubMed, PubMed Central
    190. Larkin RM, Alonso JM, Ecker J, Chory J. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science. 2003 Feb 07; 299(5608):902-6. PMID: 12574634.
      View in: PubMed
    191. 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 07; 112(3):379-89. PMID: 12581527.
      View in: PubMed
    192. 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; PMCID: PMC141209.
      View in: PubMed, PubMed Central
    193. Strand A, Asami T, Alonso J, Ecker J, Chory J. Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature. 2003 Jan 02; 421(6918):79-83. PMID: 12511958.
      View in: PubMed
    194. 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.
      View in: PubMed
    195. 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.
      View in: PubMed
    196. 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 01; 16(23):3100-12. PMID: 12464638; PMCID: PMC187496.
      View in: PubMed, PubMed Central
    197. 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; PMCID: PMC1462317.
      View in: PubMed, PubMed Central
    198. 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 03; 12(17):1462-72. PMID: 12225661.
      View in: PubMed
    199. 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.
      View in: PubMed
    200. 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.
      View in: PubMed
    201. 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; PMCID: PMC161670.
      View in: PubMed, PubMed Central
    202. Wang KL, Li H, Ecker J. Ethylene biosynthesis and signaling networks. Plant Cell. 2002; 14 Suppl:S131-51. PMID: 12045274; PMCID: PMC151252.
      View in: PubMed, PubMed Central
    Joseph's Networks
    Concepts
    Derived automatically from this person's publications.
    See all (653) concept(s)
    _
    Co-Authors
    People in Profiles who have published with this person.
    See all (59) people
    _
    Related Authors
    People who share related concepts with this person.
    See all (60) people
    _
    ↑