Joseph Ecker

Title(s)Adjunct Professor, Cell and Developmental Biology
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0001-5799-5895 Additional info
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    Collapse Biography 
    Collapse Awards and Honors
    National Academy of Sciences2007John J. Carty Award for the Advancement of Science
    National Academy of Sciences2006Elected member

    Collapse Research 
    Collapse Research Activities and Funding
    Epigenome-based Cell Census and Regulatory Element Discovery in the Aging Mouse Brain
    NIH R01AG066018Sep 30, 2019 - Jun 30, 2024
    Role: Principal Investigator
    Epigenomic cell-type classification and regulatory element identification in the human brain
    NIH U01MH121282Sep 16, 2019 - Aug 31, 2022
    Role: Principal Investigator
    Development of methods for multi-omic analysis of DNA methylation and chromatin architecture in single cells
    NIH R01HG010634Sep 6, 2019 - Jun 30, 2023
    Role: Principal Investigator
    Unbiased Epigenomic and Transcriptomic Profiling of Non-Neuronal Cells in the Mouse Brain
    NIH RF1DA048816Aug 15, 2019 - Aug 14, 2022
    Role: Co-Principal Investigator
    Center for Epigenomics of the Mouse Brain Atlas (CEMBA)
    NIH U19MH114831Sep 20, 2017 - Jun 30, 2022
    Role: Principal Investigator
    The role of DNA methylation dynamics and patterning in postmitotic neuronal-maturation
    NIH R01MH112763Mar 16, 2017 - Jan 31, 2022
    Role: Co-Principal Investigator
    Multidimensional Epigenomic Single Cell Analyses
    NIH R21HG009274Sep 28, 2016 - Jul 31, 2019
    Role: Principal Investigator
    Epigenomic Approaches for Unbiased Single Human-Neuron Subtype Census
    NIH R21MH112161Sep 28, 2016 - Aug 31, 2018
    Role: Principal Investigator
    Environmental contribution to neuronal-methylome dynamics in animal models of autism spectrum disorders
    NIH R01ES025585Aug 1, 2015 - Jun 30, 2021
    Role: Co-Principal Investigator
    Epigenomic mapping approaches for cell-type classification in the brain
    NIH U01MH105985Sep 26, 2014 - Nov 30, 2017
    Role: Principal Investigator
    Epigenetic Alterations of the Developing Brain in Animal Models of Schizophrenia
    NIH R01MH094670Sep 7, 2011 - Apr 30, 2017
    Role: Co-Principal Investigator
    The Arabidopsis Transcription Factor ORFeome and downstream genomic application
    NIH RC2GM092412Sep 30, 2009 - Dec 31, 2011
    Role: Principal Investigator
    Genome Wide Analysis of DNA Methylation
    NIH R01HG003523Sep 29, 2004 - Jun 30, 2007
    Role: Principal Investigator
    DEVELOPMENT OF LARGE DNA METHODS FOR ARABIDOPSIS
    NIH R01GM042471Jul 1, 1989 - Jun 30, 1992
    Role: Principal Investigator
    DEVELOPMENT OF LARGE DNA METHODS FOR ARABIDOPSIS
    NIH R01HG000322Jul 1, 1989 - Jun 30, 1992
    Role: Principal Investigator
    MOLECULAR GENETICS OF STRESS-RESPONSES IN ARABIDOPSIS
    NIH 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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Yet uninfected? Resolving cell states of plants under pathogen attack. Cell Rep Methods. 2023 07 24; 3(7):100538. Nobori T, Ecker JR. PMID: 37533641; PMCID: PMC10391557.
      View in: PubMed   Mentions:
    2. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol. 2023 Jun; 21(6):e3002133. Hawrylycz M, Martone ME, Ascoli GA, Bjaalie JG, Dong HW, Ghosh SS, Gillis J, Hertzano R, Haynor DR, Hof PR, Kim Y, Lein E, Liu Y, Miller JA, Mitra PP, Mukamel E, Ng L, Osumi-Sutherland D, Peng H, Ray PL, Sanchez R, Regev A, Ropelewski A, Scheuermann RH, Tan SZK, Thompson CL, Tickle T, Tilgner H, Varghese M, Wester B, White O, Zeng H, Aevermann B, Allemang D, Ament S, Athey TL, Baker C, Baker KS, Baker PM, Bandrowski A, Banerjee S, Bishwakarma P, Carr A, Chen M, Choudhury R, Cool J, Creasy H, D'Orazi F, Degatano K, Dichter B, Ding SL, Dolbeare T, Ecker JR, Fang R, Fillion-Robin JC, Fliss TP, Gee J, Gillespie T, Gouwens N, Zhang GQ, Halchenko YO, Harris NL, Herb BR, Hintiryan H, Hood G, Horvath S, Huo B, Jarecka D, Jiang S, Khajouei F, Kiernan EA, Kir H, Kruse L, Lee C, Lelieveldt B, Li Y, Liu H, Liu L, Markuhar A, Mathews J, Mathews KL, Mezias C, Miller MI, Mollenkopf T, Mufti S, Mungall CJ, Orvis J, Puchades MA, Qu L, Receveur JP, Ren B, Sjoquist N, Staats B, Tward D, van Velthoven CTJ, Wang Q, Xie F, Xu H, Yao Z, Yun Z, Zhang YR, Zheng WJ, Zingg B. PMID: 37390046; PMCID: PMC10313015.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    3. Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures. bioRxiv. 2023 Jun 30. Wang W, Hariharan M, Bartlett A, Barragan C, Castanon R, Rothenberg V, Song H, Nery J, Aldridge A, Altshul J, Kenworthy M, Ding W, Liu H, Tian W, Zhou J, Chen H, Wei B, Gündüz IB, Norell T, Broderick TJ, McClain MT, Satterwhite LL, Burke TW, Petzold EA, Shen X, Woods CW, Fowler VG, Ruffin F, Panuwet P, Barr DB, Beare JL, Smith AK, Spurbeck RR, Vangeti S, Ramos I, Nudelman G, Sealfon SC, Castellino F, Walley AM, Evans T, Müller F, Greenleaf WJ, Ecker JR. PMID: 37425926; PMCID: PMC10327221.
      View in: PubMed   Mentions:
    4. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. Cell Genom. 2023 Jul 12; 3(7):100342. Xie F, Armand EJ, Yao Z, Liu H, Bartlett A, Behrens MM, Li YE, Lucero JD, Luo C, Nery JR, Pinto-Duarte A, Poirion OB, Preissl S, Rivkin AC, Tasic B, Zeng H, Ren B, Ecker JR, Mukamel EA. PMID: 37492103; PMCID: PMC10363915.
      View in: PubMed   Mentions: 1  
    5. Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap. Nat Plants. 2023 07; 9(7):1026-1033. Nobori T, Oliva M, Lister R, Ecker JR. PMID: 37308583; PMCID: PMC10356616.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    6. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. bioRxiv. 2023 Apr 18. Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, Osteen JK, Pinto-Duarte A, Lee J, Rink J, Cho S, Emerson N, Nunn M, O'Connor C, Yao Z, Smith KA, Tasic B, Zeng H, Luo C, Dixon JR, Ren B, Behrens MM, Ecker JR. PMID: 37131654; PMCID: PMC10153407.
      View in: PubMed   Mentions:
    7. Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex. bioRxiv. 2023 Apr 08. Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Behrens MM, Lein ES, Ecker JR, Ren B. PMID: 37066152; PMCID: PMC10104177.
      View in: PubMed   Mentions:
    8. Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways. bioRxiv. 2023 Mar 09. Yin L, Zander M, Huang SC, Xie M, Song L, Guzm N JPS, Hann E, Shanbhag BK, Ng S, Jain S, Janssen BJ, Clark NM, Walley JW, Beddoe T, Bar-Joseph Z, Lewsey MG, Ecker JR. PMID: 36945593; PMCID: PMC10028877.
      View in: PubMed   Mentions:
    9. Author Correction: CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2023 Mar; 20(3):469. Wanamaker SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR. PMID: 36690743.
      View in: PubMed   Mentions:    Fields:    
    10. Author Correction: PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. Nat Genet. 2023 Feb; 55(2):355. Willige BC, Zander M, Yoo CY, Phan A, Garza RM, Wanamaker SA, He Y, Nery JR, Chen H, Chen M, Ecker JR, Chory J. PMID: 36690790.
      View in: PubMed   Mentions: 1     Fields:    
    11. Leaf cell-specific and single-cell transcriptional profiling reveals a role for the palisade layer in UV light protection. Plant Cell. 2022 08 25; 34(9):3261-3279. Procko C, Lee T, Borsuk A, Bargmann BOR, Dabi T, Nery JR, Estelle M, Baird L, O'Connor C, Brodersen C, Ecker JR, Chory J. PMID: 35666176; PMCID: PMC9421592.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    12. Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. Elife. 2022 05 23; 11. Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, Ecker JR, Mukamel EA, Behrens MM. PMID: 35604009; PMCID: PMC9170249.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    13. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2022 May; 605(7909):E3. ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. PMID: 35474001; PMCID: PMC9095460.
      View in: PubMed   Mentions: 1     Fields:    
    14. Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 2022 Apr; 604(7904):E8. Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preiss S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES. PMID: 35319013; PMCID: PMC8986536.
      View in: PubMed   Mentions: 1     Fields:    
    15. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genom. 2022 Mar 09; 2(3). Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, Zhou J, Niu SY, Castanon R, Bartlett A, Rivkin A, Wang X, Lucero J, Nery JR, Davis DA, Mash DC, Satija R, Dixon JR, Linnarsson S, Lein E, Behrens MM, Ren B, Mukamel EA, Ecker JR. PMID: 35419551; PMCID: PMC9004682.
      View in: PubMed   Mentions: 21  
    16. The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis. Proc Natl Acad Sci U S A. 2022 01 18; 119(3). Potok ME, Zhong Z, Picard CL, Liu Q, Do T, Jacobsen CE, Sakr O, Naranbaatar B, Thilakaratne R, Khnkoyan Z, Purl M, Cheng H, Vervaet H, Feng S, Rayatpisheh S, Wohlschlegel JA, O'Malley RC, Ecker JR, Jacobsen SE. PMID: 35027454; PMCID: PMC8784105.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    17. The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues. Plant J. 2022 02; 109(4):764-778. Swift J, Greenham K, Ecker JR, Coruzzi GM, Robertson McClung C. PMID: 34797944; PMCID: PMC9215356.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    18. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 2021 10; 598(7879):103-110. Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA. PMID: 34616066; PMCID: PMC8494649.
      View in: PubMed   Mentions: 65     Fields:    Translation:AnimalsCells
    19. DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 2021 10; 598(7879):120-128. Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, Poirion OB, Preissl S, Pinto-Duarte A, O'Connor C, Boggeman L, Fitzpatrick C, Nunn M, Mukamel EA, Zhang Z, Callaway EM, Ren B, Dixon JR, Behrens MM, Ecker JR. PMID: 34616061; PMCID: PMC8494641.
      View in: PubMed   Mentions: 57     Fields:    Translation:AnimalsCells
    20. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature. 2021 10; 598(7879):111-119. Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES. PMID: 34616062; PMCID: PMC8494640.
      View in: PubMed   Mentions: 128     Fields:    Translation:HumansAnimalsCells
    21. Epigenomic diversity of cortical projection neurons in the mouse brain. Nature. 2021 10; 598(7879):167-173. Zhang Z, Zhou J, Tan P, Pang Y, Rivkin AC, Kirchgessner MA, Williams E, Lee CT, Liu H, Franklin AD, Miyazaki PA, Bartlett A, Aldridge AI, Vu M, Boggeman L, Fitzpatrick C, Nery JR, Castanon RG, Rashid M, Jacobs MW, Ito-Cole T, O'Connor C, Pinto-Duartec A, Dominguez B, Smith JB, Niu SY, Lee KF, Jin X, Mukamel EA, Behrens MM, Ecker JR, Callaway EM. PMID: 34616065; PMCID: PMC8494636.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    22. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 2021 10; 598(7879):129-136. Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, Han JY, Lucero J, Yan Y, Miller M, Kuan S, Gorkin D, Gaulton KJ, Shen Y, Nunn M, Mukamel EA, Behrens MM, Ecker JR, Ren B. PMID: 34616068; PMCID: PMC8494637.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansAnimalsCells
    23. Activity-dependent modulation of synapse-regulating genes in astrocytes. Elife. 2021 09 08; 10. Farhy-Tselnicker I, Boisvert MM, Liu H, Dowling C, Erikson GA, Blanco-Suarez E, Farhy C, Shokhirev MN, Ecker JR, Allen NJ. PMID: 34494546; PMCID: PMC8497060.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    24. A plant-specific syntaxin-6 protein contributes to the intracytoplasmic route for the begomovirus CabLCV. Plant Physiol. 2021 09 04; 187(1):158-173. Gouveia-Mageste BC, Martins LGC, Dal-Bianco M, Machado JPB, da Silva JCF, Kim AY, Yazaki J, Dos Santos AA, Ecker JR, Fontes EPB. PMID: 34618135; PMCID: PMC8418432.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    25. PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. Nat Genet. 2021 07; 53(7):955-961. Willige BC, Zander M, Yoo CY, Phan A, Garza RM, Wanamaker SA, He Y, Nery JR, Chen H, Chen M, Ecker JR, Chory J. PMID: 34140685; PMCID: PMC9169284.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    26. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat Commun. 2021 05 11; 12(1):2677. Ruf-Zamojski F, Zhang Z, Zamojski M, Smith GR, Mendelev N, Liu H, Nudelman G, Moriwaki M, Pincas H, Castanon RG, Nair VD, Seenarine N, Amper MAS, Zhou X, Ongaro L, Toufaily C, Schang G, Nery JR, Bartlett A, Aldridge A, Jain N, Childs GV, Troyanskaya OG, Ecker JR, Turgeon JL, Welt CK, Bernard DJ, Sealfon SC. PMID: 33976139; PMCID: PMC8113460.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    27. Iterative single-cell multi-omic integration using online learning. Nat Biotechnol. 2021 08; 39(8):1000-1007. Gao C, Liu J, Kriebel AR, Preissl S, Luo C, Castanon R, Sandoval J, Rivkin A, Nery JR, Behrens MM, Ecker JR, Ren B, Welch JD. PMID: 33875866; PMCID: PMC8355612.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
    28. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nat Commun. 2021 02 26; 12(1):1337. Fang R, Preissl S, Li Y, Hou X, Lucero J, Wang X, Motamedi A, Shiau AK, Zhou X, Xie F, Mukamel EA, Zhang K, Zhang Y, Behrens MM, Ecker JR, Ren B. PMID: 33637727; PMCID: PMC7910485.
      View in: PubMed   Mentions: 112     Fields:    Translation:AnimalsCells
    29. The emergence of the brain non-CpG methylation system in vertebrates. Nat Ecol Evol. 2021 03; 5(3):369-378. de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O, Lister R. PMID: 33462491; PMCID: PMC7116863.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    30. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 2021 Jan; 589(7842):E4. Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. PMID: 33398137; PMCID: PMC8064906.
      View in: PubMed   Mentions: 3     Fields:    
    31. Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Res. 2020 Dec 23. Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe F, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JR, Martienssen RA, Lam E. PMID: 33361111; PMCID: PMC7849404.
      View in: PubMed   Mentions: 25     Fields:    
    32. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 2020 Oct; 586(7831):E31. Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. PMID: 33037424; PMCID: PMC7962567.
      View in: PubMed   Mentions:    Fields:    
    33. Pluripotent stem cells with low differentiation potential contain incompletely reprogrammed DNA replication. J Cell Biol. 2020 09 07; 219(9). Paniza T, Deshpande M, Wang N, O'Neil R, Zuccaro MV, Smith ME, Madireddy A, James D, Ecker J, Rosenwaks Z, Egli D, Gerhardt J. PMID: 32673399; PMCID: PMC7480103.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    34. Publisher Correction: Integrated multi-omics framework of the plant response to jasmonic acid. Nat Plants. 2020 Aug; 6(8):1065. Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, Ecker JR. PMID: 32694625.
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    283. Genetic analysis of a seedling stress response to ethylene in Arabidopsis. Philos Trans R Soc Lond B Biol Sci. 1995 Oct 30; 350(1331):75-81. Roman G, Ecker JR. PMID: 8577853.
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    284. The ethylene signal transduction pathway in plants. Science. 1995 May 05; 268(5211):667-75. Ecker JR. PMID: 7732375.
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    285. 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. Roman G, Lubarsky B, Kieber JJ, Rothenberg M, Ecker JR. PMID: 7768447; PMCID: PMC1206465.
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    286. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics. 1994 Jan 01; 19(1):137-44. Bell CJ, Ecker JR. PMID: 8188214.
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    287. Ethylene gas: it's not just for ripening any more! Trends Genet. 1993 Oct; 9(10):356-62. Kieber JJ, Ecker JR. PMID: 8273151.
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    288. 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. Kieber JJ, Rothenberg M, Roman G, Feldmann KA, Ecker JR. PMID: 8431946.
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    289. 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. Bent AF, Innes RW, Ecker JR, Staskawicz BJ. PMID: 1472714.
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    290. Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF bZIP proteins. EMBO J. 1992 Apr; 11(4):1261-73. Schindler U, Menkens AE, Beckmann H, Ecker JR, Cashmore AR. PMID: 1373374; PMCID: PMC556574.
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    291. Genome mapping with anchored clones: theoretical aspects. Genomics. 1991 Dec; 11(4):799-805. Ewens WJ, Bell CJ, Donnelly PJ, Dunn P, Matallana E, Ecker JR. PMID: 1686019.
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    292. 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. Lehman TA, Bennett WP, Metcalf RA, Welsh JA, Ecker J, Modali RV, Ullrich S, Romano JW, Appella E, Testa JR, et al. PMID: 1855224.
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    293. External fixation of extremity flaps and grafts. Ann Plast Surg. 1991 Feb; 26(2):198-9. Bindiger A, Ecker J, Kuschner S, Sherman R. PMID: 2006850.
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    294. 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. Schindler U, Ecker JR, Cashmore AR. PMID: 1843410.
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    295. Exploiting the triple response of Arabidopsis to identify ethylene-related mutants. Plant Cell. 1990 Jun; 2(6):513-23. Guzmán P, Ecker JR. PMID: 2152173; PMCID: PMC159907.
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    296. Plant defense genes are regulated by ethylene. Proc Natl Acad Sci U S A. 1987 Aug; 84(15):5202-6. Ecker JR, Davis RW. PMID: 16593860; PMCID: PMC298822.
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    297. 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. Ecker JR, Davis RW. PMID: 16593734; PMCID: PMC386288.
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