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. Exaptation of ancestral cell-identity networks enables C4 photosynthesis. Nature. 2024 Nov 20. Swift J, Luginbuehl LH, Hua L, Schreier TB, Donald RM, Stanley S, Wang N, Lee TA, Nery JR, Ecker JR, Hibberd JM. PMID: 39567684.
      View in: PubMed   Mentions:    Fields:    
    2. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature. 2024 Oct 09. Heffel MG, Zhou J, Zhang Y, Lee DS, Hou K, Pastor-Alonso O, Abuhanna KD, Galasso J, Kern C, Tai CY, Garcia-Padilla C, Nafisi M, Zhou Y, Schmitt AD, Li T, Haeussler M, Wick B, Zhang MJ, Xie F, Ziffra RS, Mukamel EA, Eskin E, Nowakowski TJ, Dixon JR, Pasaniuc B, Ecker JR, Zhu Q, Bintu B, Paredes MF, Luo C. PMID: 39385032.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    3. Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex. bioRxiv. 2024 Sep 20. Johansen NJ, Kempynck N, Zemke NR, Somasundaram S, De Winter S, Hooper M, Dwivedi D, Lohia R, Wehbe F, Li B, Abaffyová D, Armand EJ, De Man J, Eksi EC, Hecker N, Hulselmans G, Konstantakos V, Mauduit D, Mich JK, Partel G, Daigle TL, Levi BP, Zhang K, Tanaka Y, Gillis J, Ting JT, Ben-Simon Y, Miller J, Ecker JR, Ren B, Aerts S, Lein ES, Tasic B, Bakken TE. PMID: 39229027; PMCID: PMC11370467.
      View in: PubMed   Mentions:
    4. Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana. Genome Res. 2024 Aug 20; 34(7):1106-1120. Denyer T, Wu PJ, Colt K, Abramson BW, Pang Z, Solansky P, Mamerto A, Nobori T, Ecker JR, Lam E, Michael TP, Timmermans MCP. PMID: 38951025; PMCID: PMC11368201.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    5. BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data. Bioinformatics. 2024 07 01; 40(7). Tian W, Ding W, Shen J, Li D, Wang T, Ecker JR. PMID: 38905499; PMCID: PMC11216754.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Arabidopsis transcriptome responses to low water potential using high-throughput plate assays. Elife. 2024 Jun 21; 12. Gonzalez S, Swift J, Yaaran A, Xu J, Miller C, Illouz-Eliaz N, Nery JR, Busch W, Zait Y, Ecker JR. PMID: 38904663; PMCID: PMC11192529.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    7. Retraction Notice to: Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers. Cell. 2024 07 11; 187(14):3785. Brigidi GS, Hayes MGB, Delos Santos NP, Hartzell AL, Texari L, Lin PA, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL. PMID: 38870944; PMCID: PMC11346531.
      View in: PubMed   Mentions:    Fields:    
    8. Cell-type-specific effects of age and sex on human cortical neurons. Neuron. 2024 Aug 07; 112(15):2524-2539.e5. Chien JF, Liu H, Wang BA, Luo C, Bartlett A, Castanon R, Johnson ND, Nery JR, Osteen J, Li J, Altshul J, Kenworthy M, Valadon C, Liem M, Claffey N, O'Connor C, Seeker LA, Ecker JR, Behrens MM, Mukamel EA. PMID: 38838671.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    9. BAllC and BAllCools: Efficient Formatting and Operating for Single-Cell DNA Methylation Data. bioRxiv. 2024 May 15. Tian W, Ding W, Shen J, Li D, Wang T, Ecker JR. PMID: 37808734; PMCID: PMC10557610.
      View in: PubMed   Mentions:
    10. Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases. bioRxiv. 2024 May 14. Zhang S, Shu H, Zhou J, Rubin-Sigler J, Yang X, Liu Y, Cooper-Knock J, Monte E, Zhu C, Tu S, Li H, Tong M, Ecker JR, Ichida JK, Shen Y, Zeng J, Tsao PS, Snyder MP. PMID: 38798507; PMCID: PMC11118500.
      View in: PubMed   Mentions:
    11. scMeFormer: a transformer-based deep learning model for imputing DNA methylation states in single cells enhances the detection of epigenetic alterations in schizophrenia. bioRxiv. 2024 Jan 25. Zhou J, Luo C, Liu H, Heffel MG, Straub RE, Kleinman JE, Hyde TM, Ecker JR, Weinberger DR, Han S. PMID: 38328094; PMCID: PMC10849713.
      View in: PubMed   Mentions:
    12. Spatial IMA1 regulation restricts root iron acquisition on MAMP perception. Nature. 2024 Jan; 625(7996):750-759. Cao M, Platre MP, Tsai HH, Zhang L, Nobori T, Armengot L, Chen Y, He W, Brent L, Coll NS, Ecker JR, Geldner N, Busch W. PMID: 38200311; PMCID: PMC11181898.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    13. Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature. 2024 Jan; 625(7996):E26. 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, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. PMID: 38200319; PMCID: PMC10808050.
      View in: PubMed   Mentions: 1     Fields:    
    14. Cell type-specific enrichment of somatic aneuploidy in the mammalian brain. bioRxiv. 2023 Dec 19. Mukamel EA, Liu H, Behrens MM, Ecker JR. PMID: 38187559; PMCID: PMC10769240.
      View in: PubMed   Mentions:
    15. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature. 2023 Dec; 624(7991):366-377. 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, Wu Z, Stoica I, Yao Z, Smith KA, Tasic B, Luo C, Dixon JR, Zeng H, Ren B, Behrens MM, Ecker JR. PMID: 38092913; PMCID: PMC10719113.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    16. Brain-wide correspondence of neuronal epigenomics and distant projections. Nature. 2023 Dec; 624(7991):355-365. Zhou J, Zhang Z, Wu M, Liu H, Pang Y, Bartlett A, Peng Z, Ding W, Rivkin A, Lagos WN, Williams E, Lee CT, Miyazaki PA, Aldridge A, Zeng Q, Salinda JLA, Claffey N, Liem M, Fitzpatrick C, Boggeman L, Yao Z, Smith KA, Tasic B, Altshul J, Kenworthy MA, Valadon C, Nery JR, Castanon RG, Patne NS, Vu M, Rashid M, Jacobs M, Ito T, Osteen J, Emerson N, Lee J, Cho S, Rink J, Huang HH, Pinto-Duartec A, Dominguez B, Smith JB, O'Connor C, Zeng H, Chen S, Lee KF, Mukamel EA, Jin X, Margarita Behrens M, Ecker JR, Callaway EM. PMID: 38092919; PMCID: PMC10719087.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    17. Single-cell analysis of chromatin accessibility in the adult mouse brain. Nature. 2023 Dec; 624(7991):378-389. Zu S, Li YE, Wang K, Armand EJ, Mamde S, Amaral ML, Wang Y, Chu A, Xie Y, Miller M, Xu J, Wang Z, Zhang K, Jia B, Hou X, Lin L, Yang Q, Lee S, Li B, Kuan S, Liu H, Zhou J, Pinto-Duarte A, Lucero J, Osteen J, Nunn M, Smith KA, Tasic B, Yao Z, Zeng H, Wang Z, Shang J, Behrens MM, Ecker JR, Wang A, Preissl S, Ren B. PMID: 38092917; PMCID: PMC10719105.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    18. Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature. 2023 Dec; 624(7991):390-402. 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, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. PMID: 38092918; PMCID: PMC10719095.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    19. Single-cell DNA methylation and 3D genome architecture in the human brain. Science. 2023 10 13; 382(6667):eadf5357. Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li YE, Siletti K, Liem M, Claffey N, O'Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. PMID: 37824674; PMCID: PMC10572106.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    20. A comparative atlas of single-cell chromatin accessibility in the human brain. Science. 2023 10 13; 382(6667):eadf7044. Li YE, Preissl S, Miller M, Johnson ND, Wang Z, Jiao H, Zhu C, Wang Z, Xie Y, Poirion O, Kern C, Pinto-Duarte A, Tian W, Siletti K, Emerson N, Osteen J, Lucero J, Lin L, Yang Q, Zhu Q, Zemke N, Espinoza S, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Hodge RD, Linnarsson S, Bakken T, Levi B, Keene CD, Shang J, Lein E, Wang A, Behrens MM, Ecker JR, Ren B. PMID: 37824643; PMCID: PMC10852054.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    21. Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. Nat Commun. 2023 Sep 26; 14(1):5988. Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker JR. PMID: 37752105; PMCID: PMC10522763.
      View in: PubMed   Mentions:    Fields:    
    22. 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:    Fields:    Translation:AnimalsCells
    23. 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: 13     Fields:    Translation:HumansAnimalsCells
    24. 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:
    25. 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: 4     Fields:    
    26. 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: 16     Fields:    Translation:Animals
    27. 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:
    28. 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:
    29. 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, Saldierna Guzmán JP, 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:
    30. 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:    
    31. 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:    
    32. 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: 14     Fields:    Translation:AnimalsCells
    33. 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: 7     Fields:    Translation:AnimalsCells
    34. 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: 6     Fields:    
    35. 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: 2     Fields:    
    36. 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: 59     Fields:    
    37. 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: 8     Fields:    Translation:AnimalsCells
    38. 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: 5     Fields:    Translation:AnimalsCells
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    271. A reevaluation of the role of the heterotrimeric G protein in coupling light responses in Arabidopsis. Plant Physiol. 2003 Apr; 131(4):1623-7. Jones AM, Ecker JR, Chen JG. PMID: 12692321; PMCID: PMC166918.
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    272. 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. Alonso JM, Stepanova AN, Solano R, Wisman E, Ferrari S, Ausubel FM, Ecker JR. PMID: 12606727; PMCID: PMC151454.
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    273. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science. 2003 Feb 07; 299(5608):902-6. Larkin RM, Alonso JM, Ecker JR, Chory J. PMID: 12574634.
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    274. 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. Mackey D, Belkhadir Y, Alonso JM, Ecker JR, Dangl JL. PMID: 12581527.
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    275. 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. Ullah H, Chen JG, Temple B, Boyes DC, Alonso JM, Davis KR, Ecker JR, Jones AM. PMID: 12566580; PMCID: PMC141209.
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    276. Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature. 2003 Jan 02; 421(6918):79-83. Strand A, Asami T, Alonso J, Ecker JR, Chory J. PMID: 12511958.
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    277. ABA-activated SnRK2 protein kinase is required for dehydration stress signaling in Arabidopsis. Plant Cell Physiol. 2002 Dec; 43(12):1473-83. Yoshida R, Hobo T, Ichimura K, Mizoguchi T, Takahashi F, Aronso J, Ecker JR, Shinozaki K. PMID: 12514244.
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    278. Divergent perspectives on GM food. Nat Biotechnol. 2002 Dec; 20(12):1195-6; author reply 1197. Beachy R, Bennetzen JL, Chassy BM, Chrispeels M, Chory J, Ecker JR, Noel JP, Kay SA, Dean C, Lamb C, Jones J, Santerre CR, Schroeder JI, Umen J, Yanofsky M, Wessler S, Zhao Y, Parrott W. PMID: 12454665.
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    279. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Genes Dev. 2002 Dec 01; 16(23):3100-12. Zhao Y, Hull AK, Gupta NR, Goss KA, Alonso J, Ecker JR, Normanly J, Chory J, Celenza JL. PMID: 12464638; PMCID: PMC187496.
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    280. Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics. 2002 Nov; 162(3):1445-56. Friedrichsen DM, Nemhauser J, Muramitsu T, Maloof JN, Alonso J, Ecker JR, Furuya M, Chory J. PMID: 12454087; PMCID: PMC1462317.
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    281. De-etiolated 1 and damaged DNA binding protein 1 interact to regulate Arabidopsis photomorphogenesis. Curr Biol. 2002 Sep 03; 12(17):1462-72. Schroeder DF, Gahrtz M, Maxwell BB, Cook RK, Kan JM, Alonso JM, Ecker JR, Chory J. PMID: 12225661.
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    282. HIV-1 integration in the human genome favors active genes and local hotspots. Cell. 2002 Aug 23; 110(4):521-9. Schröder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F. PMID: 12202041.
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    283. A role for peroxisomes in photomorphogenesis and development of Arabidopsis. Science. 2002 Jul 19; 297(5580):405-9. Hu J, Aguirre M, Peto C, Alonso J, Ecker J, Chory J. PMID: 12130786.
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    284. NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE. Plant Physiol. 2002 Jun; 129(2):530-9. Zheng H, Bednarek SY, Sanderfoot AA, Alonso J, Ecker JR, Raikhel NV. PMID: 12068098; PMCID: PMC161670.
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    285. Ethylene biosynthesis and signaling networks. Plant Cell. 2002; 14 Suppl:S131-51. Wang KL, Li H, Ecker JR. PMID: 12045274; PMCID: PMC151252.
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    286. Phototropin-related NPL1 controls chloroplast relocation induced by blue light. Nature. 2001 Apr 19; 410(6831):952-4. Jarillo JA, Gabrys H, Capel J, Alonso JM, Ecker JR, Cashmore AR. PMID: 11309623.
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    287. An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature. 2001 Mar 22; 410(6827):487-90. Jarillo JA, Capel J, Tang RH, Yang HQ, Alonso JM, Ecker JR, Cashmore AR. PMID: 11260718.
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    288. The ethylene pathway: a paradigm for plant hormone signaling and interaction. Sci STKE. 2001 Feb 20; 2001(70):re1. Alonso JM, Ecker JR. PMID: 11752640.
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    289. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature. 2000 Dec 14; 408(6814):816-20. Theologis A, Ecker JR, Palm CJ, Federspiel NA, Kaul S, White O, Alonso J, Altafi H, Araujo R, Bowman CL, Brooks SY, Buehler E, Chan A, Chao Q, Chen H, Cheuk RF, Chin CW, Chung MK, Conn L, Conway AB, Conway AR, Creasy TH, Dewar K, Dunn P, Etgu P, Feldblyum TV, Feng J, Fong B, Fujii CY, Gill JE, Goldsmith AD, Haas B, Hansen NF, Hughes B, Huizar L, Hunter JL, Jenkins J, Johnson-Hopson C, Khan S, Khaykin E, Kim CJ, Koo HL, Kremenetskaia I, Kurtz DB, Kwan A, Lam B, Langin-Hooper S, Lee A, Lee JM, Lenz CA, Li JH, Li Y, Lin X, Liu SX, Liu ZA, Luros JS, Maiti R, Marziali A, Militscher J, Miranda M, Nguyen M, Nierman WC, Osborne BI, Pai G, Peterson J, Pham PK, Rizzo M, Rooney T, Rowley D, Sakano H, Salzberg SL, Schwartz JR, Shinn P, Southwick AM, Sun H, Tallon LJ, Tambunga G, Toriumi MJ, Town CD, Utterback T, Van Aken S, Vaysberg M, Vysotskaia VS, Walker M, Wu D, Yu G, Fraser CM, Venter JC, Davis RW. PMID: 11130712.
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    290. Ethylene signaling: from mutants to molecules. Curr Opin Plant Biol. 2000 Oct; 3(5):353-60. Stepanova AN, Ecker JR. PMID: 11019801.
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    291. National Science Foundation-Sponsored Workshop Report: "The 2010 Project" functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol. 2000 Jun; 123(2):423-6. Chory J, Ecker JR, Briggs S, Caboche M, Coruzzi GM, Cook D, Dangl J, Grant S, Guerinot ML, Henikoff S, Martienssen R, Okada K, Raikhel NV, Somerville CR, Weigel D. PMID: 10859172; PMCID: PMC1539254.
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    292. Involvement of NRAMP1 from Arabidopsis thaliana in iron transport. Biochem J. 2000 May 01; 347 Pt 3:749-55. Curie C, Alonso JM, Le Jean M, Ecker JR, Briat JF. PMID: 10769179; PMCID: PMC1221012.
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    293. Regulation of differential growth in the apical hook of Arabidopsis. Development. 1999 Aug; 126(16):3661-8. Raz V, Ecker JR. PMID: 10409511.
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    294. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet. 1999 Jul; 22(3):271-5. Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, Altmann T. PMID: 10391215.
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    295. EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. Science. 1999 Jun 25; 284(5423):2148-52. Alonso JM, Hirayama T, Roman G, Nourizadeh S, Ecker JR. PMID: 10381874.
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    296. RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson disease-related copper transporter, is required for ethylene signaling in Arabidopsis. Cell. 1999 Apr 30; 97(3):383-93. Hirayama T, Kieber JJ, Hirayama N, Kogan M, Guzman P, Nourizadeh S, Alonso JM, Dailey WP, Dancis A, Ecker JR. PMID: 10319818.
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    297. Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev. 1998 Dec 01; 12(23):3703-14. Solano R, Stepanova A, Chao Q, Ecker JR. PMID: 9851977; PMCID: PMC317251.
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    298. Arabidopsis homologs of a c-Jun coactivator are present both in monomeric form and in the COP9 complex, and their abundance is differentially affected by the pleiotropic cop/det/fus mutations. Plant Cell. 1998 Nov; 10(11):1779-90. Kwok SF, Solano R, Tsuge T, Chamovitz DA, Ecker JR, Matsui M, Deng XW. PMID: 9811788; PMCID: PMC143959.
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    299. Ethylene gas: perception, signaling and response. Curr Opin Plant Biol. 1998 Oct; 1(5):393-8. Solano R, Ecker JR. PMID: 10066624.
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    300. EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis. Plant Cell. 1998 Aug; 10(8):1321-32. Hua J, Sakai H, Nourizadeh S, Chen QG, Bleecker AB, Ecker JR, Meyerowitz EM. PMID: 9707532; PMCID: PMC144061.
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    301. Genome sequencing. Genes blossom from a weed. Nature. 1998 Jan 29; 391(6666):438-9. Ecker JR. PMID: 9461207.
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    302. The ethylene gas signal transduction pathway: a molecular perspective. Annu Rev Genet. 1998; 32:227-54. Johnson PR, Ecker JR. PMID: 9928480.
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    303. [The "Inpatient Vaccination" Project in upper Austria. Technical report]. Wien Med Wochenschr. 1998; 148(8-9):198-203. Süss G, Aigner K, Bolitschek J, Forstner B, Dejaco R, Dorninger HP, Dovjak P, Ecker J, Hochreiter K, Knaus W, Kühn P, Mayer K, Mayrhofer E, Mori M, Schinko H, Wimberger F, Kunze M. PMID: 9677676.
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    304. BRI-ghtening the pathway to steroid hormone signaling events in plants. Cell. 1997 Sep 05; 90(5):825-7. Ecker JR. PMID: 9298893.
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    305. Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins. Cell. 1997 Jun 27; 89(7):1133-44. Chao Q, Rothenberg M, Solano R, Roman G, Terzaghi W, Ecker JR. PMID: 9215635.
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    306. Signaling in plants. Proc Natl Acad Sci U S A. 1997 Apr 01; 94(7):2793-5. Mulligan RM, Chory J, Ecker JR. PMID: 9096297; PMCID: PMC34151.
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    307. HOOKLESS1, an ethylene response gene, is required for differential cell elongation in the Arabidopsis hypocotyl. Cell. 1996 Apr 19; 85(2):183-94. Lehman A, Black R, Ecker JR. PMID: 8612271.
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    308. The genome of Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1995 Nov 21; 92(24):10831-5. Goodman HM, Ecker JR, Dean C. PMID: 7479893; PMCID: PMC40525.
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    309. 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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    310. The ethylene signal transduction pathway in plants. Science. 1995 May 05; 268(5211):667-75. Ecker JR. PMID: 7732375.
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    311. 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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    312. 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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    313. 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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    314. 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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    315. 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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    316. 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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    317. 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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    318. 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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    319. 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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    320. 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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    321. 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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    322. 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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    323. 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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