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 selected 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. Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex. Cell Genom. 2025 May 19; 100879. 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: 40403730.
      View in: PubMed   Mentions:    Fields:    
    2. Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina. bioRxiv. 2025 Apr 02. Yuan Y, Biswas P, Zemke NR, Dang K, Wu Y, D'Antonio M, Xie Y, Yang Q, Dong K, Lau PK, Li D, Seng C, Bartosik W, Buchanan J, Lin L, Lancione R, Wang K, Lee S, Gibbs Z, Ecker J, Frazer K, Wang T, Preissl S, Wang A, Ayyagari R, Ren B. PMID: 39764062; PMCID: PMC11703273.
      View in: PubMed   Mentions:
    3. Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex. bioRxiv. 2025 Mar 25. 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. Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation. bioRxiv. 2025 Mar 24. Zhou J, Wu Y, Liu H, Tian W, Castanon RG, Bartlett A, Zhang Z, Yao G, Shi D, Clock B, Marcotte S, Nery JR, Liem M, Claffey N, Boggeman L, Barragan C, Drigo RAE, Weimer AK, Shi M, Cooper-Knock J, Zhang S, Snyder MP, Preissl S, Ren B, O'Connor C, Chen S, Luo C, Dixon JR, Ecker JR. PMID: 40196612; PMCID: PMC11974725.
      View in: PubMed   Mentions:
    5. Deep learning imputes DNA methylation states in single cells and enhances the detection of epigenetic alterations in schizophrenia. Cell Genom. 2025 Mar 12; 5(3):100774. Zhou J, Luo C, Liu H, Heffel MG, Straub RE, Kleinman JE, Hyde TM, Ecker JR, Weinberger DR, Han S. PMID: 39986279; PMCID: PMC11960545.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    6. A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation. Dev Cell. 2025 05 05; 60(9):1377-1391.e7. Miller CN, Jarrell-Hurtado S, Haag MV, Sara Ye Y, Simenc M, Alvarez-Maldonado P, Behnami S, Zhang L, Swift J, Papikian A, Yu J, Colt K, Ecker JR, Michael TP, Law JA, Busch W. PMID: 39793584.
      View in: PubMed   Mentions:    Fields:    
    7. A rare PRIMER cell state in plant immunity. Nature. 2025 Feb; 638(8049):197-205. Nobori T, Monell A, Lee TA, Sakata Y, Shirahama S, Zhou J, Nery JR, Mine A, Ecker JR. PMID: 39779856; PMCID: PMC11798839.
      View in: PubMed   Mentions:    Fields:    
    8. Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome. bioRxiv. 2025 Jan 04. Wang W, Hariharan M, Ding W, Bartlett A, Barragan C, Castanon R, Rothenberg V, Song H, Nery J, Aldridge A, Altshul J, Kenworthy M, Liu H, Tian W, Zhou J, Zeng Q, 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:
    9. Exaptation of ancestral cell-identity networks enables C4 photosynthesis. Nature. 2024 Dec; 636(8041):143-150. Swift J, Luginbuehl LH, Hua L, Schreier TB, Donald RM, Stanley S, Wang N, Lee TA, Nery JR, Ecker JR, Hibberd JM. PMID: 39567684; PMCID: PMC11618092.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    10. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature. 2024 Nov; 635(8038):481-489. 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; PMCID: PMC11560841.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    11. 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: 1     Fields:    Translation:AnimalsCells
    12. 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
    13. 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
    14. 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:    
    15. 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: 7     Fields:    Translation:HumansCells
    16. 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:
    17. 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:
    18. 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:
    19. 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: 7     Fields:    Translation:AnimalsCells
    20. 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:    
    21. 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:
    22. 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: 36     Fields:    Translation:AnimalsCells
    23. 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: 15     Fields:    Translation:HumansAnimalsCells
    24. 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: 18     Fields:    Translation:HumansAnimalsCells
    25. 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: 14     Fields:    Translation:AnimalsCells
    26. 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: 38     Fields:    Translation:HumansAnimalsCells
    27. 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: 40     Fields:    
    28. 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:    
    29. 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: 1     Fields:    Translation:AnimalsCells
    30. A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biol. 2023 06; 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: 19     Fields:    
    31. 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: 5     Fields:    
    32. 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: 23     Fields:    Translation:Animals
    33. 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:
    34. 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:
    35. 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:
    36. 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:    
    37. 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:    Fields:    
    38. 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: 20     Fields:    Translation:AnimalsCells
    39. 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: 12     Fields:    Translation:AnimalsCells
    40. 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: 5     Fields:    
    41. 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: 3     Fields:    
    42. 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: 66     Fields:    
    43. 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: 10     Fields:    Translation:AnimalsCells
    44. 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: 7     Fields:    Translation:AnimalsCells
    45. 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: 110     Fields:    Translation:AnimalsCells
    46. 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: 280     Fields:    Translation:HumansAnimalsCells
    47. 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: 34     Fields:    Translation:AnimalsCells
    48. 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: 139     Fields:    Translation:AnimalsCells
    49. 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: 76     Fields:    Translation:HumansAnimalsCells
    50. 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: 49     Fields:    Translation:HumansAnimalsCells
    51. 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: 7     Fields:    Translation:AnimalsCells
    52. 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: 42     Fields:    Translation:Cells
    53. 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: 27     Fields:    Translation:AnimalsCells
    54. 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: 45     Fields:    Translation:AnimalsCells
    55. 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: 180     Fields:    Translation:AnimalsCells
    56. 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: 44     Fields:    
    57. 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:    
    58. Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Res. 2021 Feb; 31(2):225-238. 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: 35     Fields:    
    59. 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: 2     Fields:    
    60. 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: 8     Fields:    Translation:HumansAnimalsCells
    61. 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.
      View in: PubMed   Mentions:    Fields:    
    62. An atlas of dynamic chromatin landscapes in mouse fetal development. Nature. 2020 07; 583(7818):744-751. 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: 32728240; PMCID: PMC7398618.
      View in: PubMed   Mentions: 159     Fields:    Translation:HumansAnimalsCells
    63. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature. 2020 07; 583(7818):752-759. He Y, Hariharan M, Gorkin DU, Dickel DE, Luo C, Castanon RG, Nery JR, Lee AY, Zhao Y, Huang H, Williams BA, Trout D, Amrhein H, Fang R, Chen H, Li B, Visel A, Pennacchio LA, Ren B, Ecker JR. PMID: 32728242; PMCID: PMC7398276.
      View in: PubMed   Mentions: 67     Fields:    
    64. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710. 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: 32728249; PMCID: PMC7410828.
      View in: PubMed   Mentions: 904     Fields:    Translation:HumansAnimalsCells
    65. A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proc Natl Acad Sci U S A. 2020 05 26; 117(21):11836-11842. Wierbowski SD, Vo TV, Falter-Braun P, Jobe TO, Kruse LH, Wei X, Liang J, Meyer MJ, Akturk N, Rivera-Erick CA, Cordero NA, Paramo MI, Shayhidin EE, Bertolotti M, Tippens ND, Akther K, Sharma R, Katayose Y, Salehi-Ashtiani K, Hao T, Ronald PC, Ecker JR, Schweitzer PA, Kikuchi S, Mizuno H, Hill DE, Vidal M, Moghe GD, McCouch SR, Yu H. PMID: 32398372; PMCID: PMC7260977.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    66. Extraction of Distinct Neuronal Cell Types from within a Genetically Continuous Population. Neuron. 2020 07 22; 107(2):274-282.e6. Kim EJ, Zhang Z, Huang L, Ito-Cole T, Jacobs MW, Juavinett AL, Senturk G, Hu M, Ku M, Ecker JR, Callaway EM. PMID: 32396852; PMCID: PMC7381365.
      View in: PubMed   Mentions: 53     Fields:    Translation:AnimalsCells
    67. Integrated multi-omics framework of the plant response to jasmonic acid. Nat Plants. 2020 03; 6(3):290-302. 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: 32170290; PMCID: PMC7094030.
      View in: PubMed   Mentions: 75     Fields:    
    68. Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome. Elife. 2020 03 11; 9. Lavery LA, Ure K, Wan YW, Luo C, Trostle AJ, Wang W, Jin H, Lopez J, Lucero J, Durham MA, Castanon R, Nery JR, Liu Z, Goodell M, Ecker JR, Behrens MM, Zoghbi HY. PMID: 32159514; PMCID: PMC7065908.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    69. Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism. Plant Cell. 2020 04; 32(4):967-983. Burko Y, Seluzicki A, Zander M, Pedmale UV, Ecker JR, Chory J. PMID: 32086365; PMCID: PMC7145465.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    70. The JA-pathway MYC transcription factors regulate photomorphogenic responses by targeting HY5 gene expression. Plant J. 2020 04; 102(1):138-152. Ortigosa A, Fonseca S, Franco-Zorrilla JM, Fernández-Calvo P, Zander M, Lewsey MG, García-Casado G, Fernández-Barbero G, Ecker JR, Solano R. PMID: 31755159.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    71. Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana. PLoS Genet. 2019 12; 15(12):e1008492. Sasaki E, Kawakatsu T, Ecker JR, Nordborg M. PMID: 31887137; PMCID: PMC6953882.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    72. A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels. Proc Natl Acad Sci U S A. 2019 11 12; 116(46):23345-23356. Van Moerkercke A, Duncan O, Zander M, Šimura J, Broda M, Vanden Bossche R, Lewsey MG, Lama S, Singh KB, Ljung K, Ecker JR, Goossens A, Millar AH, Van Aken O. PMID: 31662474; PMCID: PMC6859355.
      View in: PubMed   Mentions: 54     Fields:    Translation:AnimalsCells
    73. Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers. Cell. 2019 10 03; 179(2):373-391.e27. Brigidi GS, Hayes MGB, Delos Santos NP, Hartzell AL, Texari L, Lin PA, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL. PMID: 31585079; PMCID: PMC6800120.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    74. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nat Methods. 2019 10; 16(10):999-1006. Lee DS, Luo C, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR. PMID: 31501549; PMCID: PMC6765423.
      View in: PubMed   Mentions: 145     Fields:    
    75. Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels. Nat Commun. 2019 09 06; 10(1):4021. Salehin M, Li B, Tang M, Katz E, Song L, Ecker JR, Kliebenstein DJ, Estelle M. PMID: 31492889; PMCID: PMC6731224.
      View in: PubMed   Mentions: 88     Fields:    Translation:Animals
    76. Epigenetic silencing of a multifunctional plant stress regulator. Elife. 2019 08 16; 8. Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nery JR, Chen H, Zhang Z, Jupe F, Stepanova A, Schmitz RJ, Lewsey MG, Chory J, Ecker JR. PMID: 31418686; PMCID: PMC6739875.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    77. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. Proc Natl Acad Sci U S A. 2019 07 09; 116(28):14011-14018. Zhou J, Ma J, Chen Y, Cheng C, Bao B, Peng J, Sejnowski TJ, Dixon JR, Ecker JR. PMID: 31235599; PMCID: PMC6628819.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansCells
    78. Diversity and dynamics of DNA methylation: epigenomic resources and tools for crop breeding. Breed Sci. 2019 Jun; 69(2):191-204. Kawakatsu T, Ecker JR. PMID: 31481828; PMCID: PMC6711733.
      View in: PubMed   Mentions: 22  
    79. The complex architecture and epigenomic impact of plant T-DNA insertions. PLoS Genet. 2019 01; 15(1):e1007819. Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, Slotkin RK, Chen H, Castanon R, Nery JR, Ecker JR. PMID: 30657772; PMCID: PMC6338467.
      View in: PubMed   Mentions: 71     Fields:    Translation:AnimalsCells
    80. Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons. Elife. 2019 01 15; 8. Luo C, Lee QY, Wapinski O, Castanon R, Nery JR, Mall M, Kareta MS, Cullen SM, Goodell MA, Chang HY, Wernig M, Ecker JR. PMID: 30644360; PMCID: PMC6333439.
      View in: PubMed   Mentions: 46     Fields:    Translation:AnimalsCells
    81. OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. Elife. 2018 10 16; 7. Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, Ecker JR, Goll M, Panning B. PMID: 30325306; PMCID: PMC6214653.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansAnimalsCells
    82. Dynamic DNA methylation: In the right place at the right time. Science. 2018 09 28; 361(6409):1336-1340. Luo C, Hajkova P, Ecker JR. PMID: 30262495; PMCID: PMC6197482.
      View in: PubMed   Mentions: 299     Fields:    
    83. Robust single-cell DNA methylome profiling with snmC-seq2. Nat Commun. 2018 09 20; 9(1):3824. Luo C, Rivkin A, Zhou J, Sandoval JP, Kurihara L, Lucero J, Castanon R, Nery JR, Pinto-Duarte A, Bui B, Fitzpatrick C, O'Connor C, Ruga S, Van Eden ME, Davis DA, Mash DC, Behrens MM, Ecker JR. PMID: 30237449; PMCID: PMC6147798.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansAnimalsCells
    84. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. Elife. 2018 09 06; 7. Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J. PMID: 30188322; PMCID: PMC6126923.
      View in: PubMed   Mentions: 124     Fields:    Translation:AnimalsCells
    85. Profiling Interactome Networks with the HaloTag-NAPPA In Situ Protein Array. Curr Protoc Plant Biol. 2018 09; 3(3):e20071. Yazaki J, Galli M, Kim AY, Ecker JR. PMID: 30106517.
      View in: PubMed   Mentions: 5     Fields:    
    86. Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. Nat Commun. 2018 05 22; 9(1):2075. Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker JR. PMID: 29789609; PMCID: PMC5964099.
      View in: PubMed   Mentions: 2     Fields:    
    87. A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. Nat Commun. 2018 04 23; 9(1):1604. Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker JR. PMID: 29686312; PMCID: PMC5913131.
      View in: PubMed   Mentions: 80     Fields:    Translation:AnimalsCells
    88. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat Commun. 2018 02 07; 9(1):541. Michael TP, Jupe F, Bemm F, Motley ST, Sandoval JP, Lanz C, Loudet O, Weigel D, Ecker JR. PMID: 29416032; PMCID: PMC5803254.
      View in: PubMed   Mentions: 141     Fields:    Translation:AnimalsCells
    89. Challenges and recommendations for epigenomics in precision health. Nat Biotechnol. 2017 12 08; 35(12):1128-1132. Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, 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. PMID: 29220033; PMCID: PMC5821229.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    90. Piecing together cis-regulatory networks: insights from epigenomics studies in plants. Wiley Interdiscip Rev Syst Biol Med. 2018 05; 10(3):e1411. Huang SC, Ecker JR. PMID: 29194997.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    91. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron. 2017 Nov 01; 96(3):542-557. Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. PMID: 29096072; PMCID: PMC5689454.
      View in: PubMed   Mentions: 129     Fields:    Translation:HumansAnimals
    92. Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biol. 2017 09 15; 18(1):171. Kawakatsu T, Nery JR, Castanon R, Ecker JR. PMID: 28911331; PMCID: PMC5599895.
      View in: PubMed   Mentions: 106     Fields:    Translation:AnimalsCells
    93. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science. 2017 08 11; 357(6351):600-604. 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 JR. PMID: 28798132; PMCID: PMC5570439.
      View in: PubMed   Mentions: 236     Fields:    
    94. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat Protoc. 2017 Aug; 12(8):1659-1672. Bartlett A, O'Malley RC, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker JR. PMID: 28726847; PMCID: PMC5576341.
      View in: PubMed   Mentions: 211     Fields:    
    95. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2017 08; 14(8):819-825. 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: 28650476; PMCID: PMC5564216.
      View in: PubMed   Mentions: 71     Fields:    
    96. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. Plant J. 2017 Aug; 91(3):361-370. 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 JR, Gu Y, Vogel JP. PMID: 28432803.
      View in: PubMed   Mentions: 20     Fields:    Translation:Animals
    97. 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. Keown CL, Berletch JB, Castanon R, Nery JR, Disteche CM, Ecker JR, Mukamel EA. PMID: 28320934; PMCID: PMC5389278.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    98. 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. He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR. PMID: 28193886; PMCID: PMC5338528.
      View in: PubMed   Mentions: 39     Fields:    
    99. 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. Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J. PMID: 27859855.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    100. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. New Phytol. 2017 Apr; 214(2):808-819. 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 JR, Stacey G. PMID: 28106918.
      View in: PubMed   Mentions: 30     Fields:    Translation:AnimalsCells
    101. Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors. Curr Biol. 2017 Feb 06; 27(3):437-444. Shani E, Salehin M, Zhang Y, Sanchez SE, Doherty C, Wang R, Mangado CC, Song L, Tal I, Pisanty O, Ecker JR, Kay SA, Pruneda-Paz J, Estelle M. PMID: 28111153; PMCID: PMC5296222.
      View in: PubMed   Mentions: 70     Fields:    
    102. JAZ2 controls stomata dynamics during bacterial invasion. New Phytol. 2017 Feb; 213(3):1378-1392. Gimenez-Ibanez S, Boter M, Ortigosa A, García-Casado G, Chini A, Lewsey MG, Ecker JR, Ntoukakis V, Solano R. PMID: 28005270.
      View in: PubMed   Mentions: 57     Fields:    
    103. Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain. Cell Rep. 2016 12 20; 17(12):3369-3384. Luo C, Lancaster MA, Castanon R, Nery JR, Knoblich JA, Ecker JR. PMID: 28009303; PMCID: PMC5495578.
      View in: PubMed   Mentions: 173     Fields:    
    104. Functional Human Oocytes Generated by Transfer of Polar Body Genomes. Cell Stem Cell. 2017 01 05; 20(1):112-119. 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 JR, Mitalipov S. PMID: 27840020; PMCID: PMC5218919.
      View in: PubMed   Mentions: 34     Fields:    
    105. A transcription factor hierarchy defines an environmental stress response network. Science. 2016 11 04; 354(6312). Song L, Huang SC, Wise A, Castanon R, Nery JR, Chen H, Watanabe M, Thomas J, Bar-Joseph Z, Ecker JR. PMID: 27811239; PMCID: PMC5217750.
      View in: PubMed   Mentions: 213     Fields:    
    106. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods. 2016 Dec; 13(12):1050-1054. 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 JR, Cantu D, Rank DR, Schatz MC. PMID: 27749838; PMCID: PMC5503144.
      View in: PubMed   Mentions: 911     Fields:    Translation:HumansAnimals
    107. EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling. Nat Commun. 2016 10 03; 7:13018. Zhang F, Qi B, Wang L, Zhao B, Rode S, Riggan ND, Ecker JR, Qiao H. PMID: 27694846; PMCID: PMC5063967.
      View in: PubMed   Mentions: 64     Fields:    Translation:AnimalsCells
    108. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 2016 Sep 08; 166(6):1598. O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. PMID: 27610578.
      View in: PubMed   Mentions: 102     Fields:    
    109. Integration of omic networks in a developmental atlas of maize. Science. 2016 Aug 19; 353(6301):814-8. Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP. PMID: 27540173; PMCID: PMC5808982.
      View in: PubMed   Mentions: 211     Fields:    Translation:AnimalsCells
    110. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 2016 Jul 14; 166(2):492-505. 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, 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR. PMID: 27419873; PMCID: PMC5172462.
      View in: PubMed   Mentions: 298     Fields:    
    111. Molecular Criteria for Defining the Naive Human Pluripotent State. Cell Stem Cell. 2016 10 06; 19(4):502-515. 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 JR, Jaenisch R. PMID: 27424783; PMCID: PMC5065525.
      View in: PubMed   Mentions: 233     Fields:    
    112. 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. Aleman F, Yazaki J, Lee M, Takahashi Y, Kim AY, Li Z, Kinoshita T, Ecker JR, Schroeder JI. PMID: 27357749; PMCID: PMC4928087.
      View in: PubMed   Mentions: 75     Fields:    Translation:AnimalsCells
    113. Mapping transcription factor interactome networks using HaloTag protein arrays. Proc Natl Acad Sci U S A. 2016 07 19; 113(29):E4238-47. 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 JR. PMID: 27357687; PMCID: PMC4961138.
      View in: PubMed   Mentions: 29     Fields:    Translation:Animals
    114. Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq). Curr Protoc Plant Biol. 2016; 1(2):293-306. Song L, Koga Y, Ecker JR. PMID: 28782043; PMCID: PMC5544034.
      View in: PubMed   Mentions: 9     Fields:    
    115. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 2016 May 19; 165(5):1280-1292. O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. PMID: 27203113; PMCID: PMC4907330.
      View in: PubMed   Mentions: 535     Fields:    
    116. 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. Prigge MJ, Greenham K, Zhang Y, Santner A, Castillejo C, Mutka AM, O'Malley RC, Ecker JR, Kunkel BN, Estelle M. PMID: 26976444; PMCID: PMC4856089.
      View in: PubMed   Mentions: 50     Fields:    Translation:AnimalsCells
    117. Unique cell-type-specific patterns of DNA methylation in the root meristem. Nat Plants. 2016 04 29; 2(5):16058. Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. PMID: 27243651; PMCID: PMC4855458.
      View in: PubMed   Mentions: 87     Fields:    Translation:AnimalsCells
    118. 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. Bergelson J, Buckler ES, Ecker JR, Nordborg M, Weigel D. PMID: 26956491; PMCID: PMC4826003.
      View in: PubMed   Mentions: 18     Fields:    Translation:Animals
    119. Epigenomic landscapes of retinal rods and cones. Elife. 2016 Mar 07; 5:e11613. Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J. PMID: 26949250; PMCID: PMC4798964.
      View in: PubMed   Mentions: 71     Fields:    Translation:AnimalsCells
    120. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016 Apr; 48(4):417-26. 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 JR, Vermeulen M, Gómez-Skarmeta JL, Lister R. PMID: 26928226; PMCID: PMC5912259.
      View in: PubMed   Mentions: 101     Fields:    
    121. Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. Transl Psychiatry. 2016 Jan 19; 6:e718. Sanchez-Mut JV, Heyn H, Vidal E, Moran S, Sayols S, Delgado-Morales R, Schultz MD, Ansoleaga B, Garcia-Esparcia P, Pons-Espinal M, de Lagran MM, Dopazo J, Rabano A, Avila J, Dierssen M, Lott I, Ferrer I, Ecker JR, Esteller M. PMID: 26784972; PMCID: PMC5068885.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansCells
    122. Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A. 2016 Feb 09; 113(6):E801-10. Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR. PMID: 26787884; PMCID: PMC4760824.
      View in: PubMed   Mentions: 81     Fields:    
    123. Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light. Cell. 2016 Jan 14; 164(1-2):233-245. Pedmale UV, Huang SC, Zander M, Cole BJ, Hetzel J, Ljung K, Reis PAB, Sridevi P, Nito K, Nery JR, Ecker JR, Chory J. PMID: 26724867; PMCID: PMC4721562.
      View in: PubMed   Mentions: 210     Fields:    
    124. Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2016 Feb 11; 530(7589):242. 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 JR. PMID: 26605523.
      View in: PubMed   Mentions: 4     Fields:    
    125. methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. BMC Bioinformatics. 2015 Sep 29; 16:313. Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M. PMID: 26415965; PMCID: PMC4587815.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    126. Correction: DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis. PLoS Genet. 2015 Sep; 11(9):e1005452. 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 JR, Chen X. PMID: 26379054; PMCID: PMC4574932.
      View in: PubMed   Mentions: 1     Fields:    
    127. 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. Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker JR, Kay SA. PMID: 26261339; PMCID: PMC4553765.
      View in: PubMed   Mentions: 121     Fields:    Translation:AnimalsCells
    128. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife. 2015 Jul 21; 4. Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. PMID: 26196146; PMCID: PMC4534844.
      View in: PubMed   Mentions: 151     Fields:    Translation:AnimalsCells
    129. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron. 2015 Jun 17; 86(6):1369-84. Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J. PMID: 26087164; PMCID: PMC4499463.
      View in: PubMed   Mentions: 362     Fields:    
    130. Epigenetics. Exceptional epigenetics in the brain. Science. 2015 Jun 05; 348(6239):1094-5. Luo C, Ecker JR. PMID: 26045424; PMCID: PMC4880990.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    131. Non-CG Methylation in the Human Genome. Annu Rev Genomics Hum Genet. 2015; 16:55-77. He Y, Ecker JR. PMID: 26077819; PMCID: PMC4729449.
      View in: PubMed   Mentions: 112     Fields:    Translation:HumansCells
    132. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2015 Jul 09; 523(7559):212-6. 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 JR. PMID: 26030523; PMCID: PMC4499021.
      View in: PubMed   Mentions: 328     Fields:    Translation:HumansCells
    133. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 2015 May 21; 521(7552):316-21. 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 JR, Izpisua Belmonte JC. PMID: 25945737; PMCID: PMC5278765.
      View in: PubMed   Mentions: 107     Fields:    
    134. ERRs Mediate a Metabolic Switch Required for Somatic Cell Reprogramming to Pluripotency. Cell Stem Cell. 2015 May 07; 16(5):547-55. Kida YS, Kawamura T, Wei Z, Sogo T, Jacinto S, Shigeno A, Kushige H, Yoshihara E, Liddle C, Ecker JR, Yu RT, Atkins AR, Downes M, Evans RM. PMID: 25865501; PMCID: PMC4427539.
      View in: PubMed   Mentions: 69     Fields:    
    135. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. PMID: 25693563; PMCID: PMC4530010.
      View in: PubMed   Mentions: 2818     Fields:    Translation:HumansCells
    136. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015 Feb 19; 518(7539):331-6. 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 JR, Thomson JA, Ren B. PMID: 25693564; PMCID: PMC4515363.
      View in: PubMed   Mentions: 751     Fields:    Translation:HumansCells
    137. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 2015 Feb 19; 518(7539):350-354. 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 JR, Ren B. PMID: 25693566; PMCID: PMC4449149.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansCells
    138. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc. 2015 Mar; 10(3):475-83. Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. PMID: 25692984; PMCID: PMC4465251.
      View in: PubMed   Mentions: 121     Fields:    Translation:Cells
    139. A user's guide to the Arabidopsis T-DNA insertion mutant collections. Methods Mol Biol. 2015; 1284:323-42. O'Malley RC, Barragan CC, Ecker JR. PMID: 25757780; PMCID: PMC5215775.
      View in: PubMed   Mentions: 52     Fields:    
    140. Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):17224-9. Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. PMID: 25413365; PMCID: PMC4260565.
      View in: PubMed   Mentions: 203     Fields:    
    141. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014 Sep 11; 158(6):1431-1443. 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 JR, Hughes TR. PMID: 25215497; PMCID: PMC4163041.
      View in: PubMed   Mentions: 901     Fields:    
    142. 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. 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 JR, Vidal M, Jones JD, Mayer KF, Ver Loren van Themaat E, Weigel D, Schulze-Lefert P, Dangl JL, Panstruga R, Braun P. PMID: 25211078; PMCID: PMC4191710.
      View in: PubMed   Mentions: 140     Fields:    
    143. The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. Cell Stem Cell. 2014 Sep 04; 15(3):295-309. 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 JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R. PMID: 25192464; PMCID: PMC4170792.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansAnimalsCells
    144. 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. Yu W, McIntosh C, Lister R, Zhu I, Han Y, Ren J, Landsman D, Lee E, Briones V, Terashima M, Leighty R, Ecker JR, Muegge K. PMID: 25170028; PMCID: PMC4199375.
      View in: PubMed   Mentions: 55     Fields:    Translation:AnimalsCells
    145. 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. Catalá R, López-Cobollo R, Mar Castellano M, Angosto T, Alonso JM, Ecker JR, Salinas J. PMID: 25122152; PMCID: PMC4371832.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
    146. A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Rep. 2014 Jul 24; 8(2):622-32. Pruneda-Paz JL, Breton G, Nagel DH, Kang SE, Bonaldi K, Doherty CJ, Ravelo S, Galli M, Ecker JR, Kay SA. PMID: 25043187; PMCID: PMC4125603.
      View in: PubMed   Mentions: 83     Fields:    Translation:Animals
    147. DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet. 2014 Jul; 10(7):e1004446. 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 JR, Chen X. PMID: 24992598; PMCID: PMC4080997.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    148. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature. 2014 Jul 10; 511(7508):177-83. 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 JR, Laurent LC, Mitalipov S. PMID: 25008523; PMCID: PMC4898064.
      View in: PubMed   Mentions: 147     Fields:    
    149. 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. Yu W, Briones V, Lister R, McIntosh C, Han Y, Lee EY, Ren J, Terashima M, Leighty RM, Ecker JR, Muegge K. PMID: 24711395; PMCID: PMC4000807.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    150. 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. 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 JR, Xiang AP, Lahn BT. PMID: 24310002; PMCID: PMC3912417.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    151. 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. Hua Z, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR, Vierstra RD. PMID: 24082131; PMCID: PMC3801079.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    152. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics. 2013 Dec 15; 29(24):3204-10. Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W. PMID: 24078702; PMCID: PMC3842760.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    153. 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. Schweizer F, Fernández-Calvo P, Zander M, Diez-Diaz M, Fonseca S, Glauser G, Lewsey MG, Ecker JR, Solano R, Reymond P. PMID: 23943862; PMCID: PMC3784603.
      View in: PubMed   Mentions: 232     Fields:    Translation:AnimalsCells
    154. Global epigenomic reconfiguration during mammalian brain development. Science. 2013 Aug 09; 341(6146):1237905. 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 JR. PMID: 23828890; PMCID: PMC3785061.
      View in: PubMed   Mentions: 943     Fields:    
    155. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2013 Jun 11; 2:e00675. 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 JR. PMID: 23795294; PMCID: PMC3679525.
      View in: PubMed   Mentions: 198     Fields:    Translation:AnimalsCells
    156. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res. 2013 Oct; 23(10):1663-74. Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. PMID: 23739894; PMCID: PMC3787263.
      View in: PubMed   Mentions: 121     Fields:    Translation:AnimalsCells
    157. Response to perspective: "separation anxiety: an analysis of ethylene-induced cleavage of EIN2". Plant Signal Behav. 2013 Aug; 8(8). Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. PMID: 23733051; PMCID: PMC3999072.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    158. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 2013 May 23; 153(5):1134-48. 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 JR, Ren B. PMID: 23664764; PMCID: PMC3786220.
      View in: PubMed   Mentions: 411     Fields:    Translation:HumansAnimalsCells
    159. Functional characterization of type-B response regulators in the Arabidopsis cytokinin response. Plant Physiol. 2013 May; 162(1):212-24. Hill K, Mathews DE, Kim HJ, Street IH, Wildes SL, Chiang YH, Mason MG, Alonso JM, Ecker JR, Kieber JJ, Schaller GE. PMID: 23482873; PMCID: PMC3641203.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
    160. Patterns of population epigenomic diversity. Nature. 2013 Mar 14; 495(7440):193-8. Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR. PMID: 23467092; PMCID: PMC3798000.
      View in: PubMed   Mentions: 254     Fields:    Translation:AnimalsCells
    161. Epigenetic trigger for tomato ripening. Nat Biotechnol. 2013 Feb; 31(2):119-20. Ecker JR. PMID: 23392509; PMCID: PMC5215857.
      View in: PubMed   Mentions: 11     Fields:    
    162. Epiallelic variation in Arabidopsis thaliana. Cold Spring Harb Symp Quant Biol. 2012; 77:135-45. O'Malley RC, Ecker JR. PMID: 23223383; PMCID: PMC5241134.
      View in: PubMed   Mentions: 4     Fields:    
    163. Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metab. 2012 Dec 05; 16(6):833-45. Vollmers C, Schmitz RJ, Nathanson J, Yeo G, Ecker JR, Panda S. PMID: 23217262; PMCID: PMC3541940.
      View in: PubMed   Mentions: 130     Fields:    Translation:AnimalsCells
    164. 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. Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA, AACR Cancer Epigenome Task Force. PMID: 23188507.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    165. Sigma factor-mediated plastid retrograde signals control nuclear gene expression. Plant J. 2013 Jan; 73(1):1-13. Woodson JD, Perez-Ruiz JM, Schmitz RJ, Ecker JR, Chory J. PMID: 22950756; PMCID: PMC3605210.
      View in: PubMed   Mentions: 91     Fields:    
    166. 'Leveling' the playing field for analyses of single-base resolution DNA methylomes. Trends Genet. 2012 Dec; 28(12):583-5. Schultz MD, Schmitz RJ, Ecker JR. PMID: 23131467; PMCID: PMC3523709.
      View in: PubMed   Mentions: 164     Fields:    Translation:Cells
    167. Genomics: ENCODE explained. Nature. 2012 Sep 06; 489(7414):52-5. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. PMID: 22955614.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansCells
    168. Processing and subcellular trafficking of ER-tethered EIN2 control response to ethylene gas. Science. 2012 Oct 19; 338(6105):390-3. Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. PMID: 22936567; PMCID: PMC3523706.
      View in: PubMed   Mentions: 218     Fields:    Translation:AnimalsCells
    169. 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. Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS. PMID: 22855789; PMCID: PMC3426761.
      View in: PubMed   Mentions: 71     Fields:    Translation:AnimalsCells
    170. Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A. 2012 Aug 07; 109(32):E2183-91. Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. PMID: 22733782; PMCID: PMC3420206.
      View in: PubMed   Mentions: 403     Fields:    Translation:AnimalsCells
    171. Detection of allele-specific methylation through a generalized heterogeneous epigenome model. Bioinformatics. 2012 Jun 15; 28(12):i163-71. Peng Q, Ecker JR. PMID: 22689757; PMCID: PMC3371863.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    172. Release factor one is nonessential in Escherichia coli. ACS Chem Biol. 2012 Aug 17; 7(8):1337-44. Johnson DB, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker JR, Wang L. PMID: 22662873; PMCID: PMC3423824.
      View in: PubMed   Mentions: 52     Fields:    Translation:Cells
    173. Linking photoreceptor excitation to changes in plant architecture. Genes Dev. 2012 Apr 15; 26(8):785-90. Li L, Ljung K, Breton G, Schmitz RJ, Pruneda-Paz J, Cowing-Zitron C, Cole BJ, Ivans LJ, Pedmale UV, Jung HS, Ecker JR, Kay SA, Chory J. PMID: 22508725; PMCID: PMC3337452.
      View in: PubMed   Mentions: 221     Fields:    Translation:Animals
    174. Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis. G3 (Bethesda). 2012 Apr; 2(4):487-98. Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Okubo-Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker JR. PMID: 22540040; PMCID: PMC3337477.
      View in: PubMed   Mentions: 28     Fields:    
    175. Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci. 2012 Mar; 17(3):149-54. Schmitz RJ, Ecker JR. PMID: 22342533; PMCID: PMC3645451.
      View in: PubMed   Mentions: 43     Fields:    
    176. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012 Feb; 22(2):246-58. 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 JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. PMID: 22156296; PMCID: PMC3266032.
      View in: PubMed   Mentions: 278     Fields:    Translation:HumansCells
    177. Forward and reverse genetics through derivation of haploid mouse embryonic stem cells. Cell Stem Cell. 2011 Dec 02; 9(6):563-74. 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 JR, Stanford WL, Zuber J, Stark A, Penninger JM. PMID: 22136931; PMCID: PMC4008724.
      View in: PubMed   Mentions: 116     Fields:    
    178. Unexpected Diversity of Chloroplast Noncoding RNAs as Revealed by Deep Sequencing of the Arabidopsis Transcriptome. G3 (Bethesda). 2011 Dec; 1(7):559-70. Hotto AM, Schmitz RJ, Fei Z, Ecker JR, Stern DB. PMID: 22384367; PMCID: PMC3276175.
      View in: PubMed   Mentions: 37     Fields:    
    179. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat Chem Biol. 2011 Sep 18; 7(11):779-86. Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD, Schmitz RJ, Xiang Z, Ecker JR, Briggs SP, Wang L. PMID: 21926996; PMCID: PMC3201715.
      View in: PubMed   Mentions: 143     Fields:    
    180. Transgenerational epigenetic instability is a source of novel methylation variants. Science. 2011 Oct 21; 334(6054):369-73. Schmitz RJ, Schultz MD, Lewsey MG, O'Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. PMID: 21921155; PMCID: PMC3210014.
      View in: PubMed   Mentions: 291     Fields:    
    181. Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science. 2011 Jul 29; 333(6042):596-601. 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, European Union Effectoromics Consortium, Vandenhaute J, Roth FP, Hill DE, Ecker JR, Vidal M, Beynon J, Braun P, Dangl JL. PMID: 21798943; PMCID: PMC3170753.
      View in: PubMed   Mentions: 328     Fields:    
    182. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 2011 May 19; 473(7347):394-7. 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 JR, Milos PM, Agarwal S, Rao A. PMID: 21552279; PMCID: PMC3124347.
      View in: PubMed   Mentions: 385     Fields:    
    183. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011 Mar 03; 471(7336):68-73. 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 JR. PMID: 21289626; PMCID: PMC3100360.
      View in: PubMed   Mentions: 706     Fields:    
    184. The DNA methylome. FEBS Lett. 2011 Jul 07; 585(13):1994-2000. Pelizzola M, Ecker JR. PMID: 21056564; PMCID: PMC3129437.
      View in: PubMed   Mentions: 45     Fields:    
    185. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct; 28(10):1045-8. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. PMID: 20944595; PMCID: PMC3607281.
      View in: PubMed   Mentions: 897     Fields:    Translation:HumansCells
    186. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. 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 JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. PMID: 20852635; PMCID: PMC2955169.
      View in: PubMed   Mentions: 320     Fields:    
    187. 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. Boutrot F, Segonzac C, Chang KN, Qiao H, Ecker JR, Zipfel C, Rathjen JP. PMID: 20663954; PMCID: PMC2922558.
      View in: PubMed   Mentions: 103     Fields:    
    188. 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. An F, Zhao Q, Ji Y, Li W, Jiang Z, Yu X, Zhang C, Han Y, He W, Liu Y, Zhang S, Ecker JR, Guo H. PMID: 20647342; PMCID: PMC2929093.
      View in: PubMed   Mentions: 196     Fields:    Translation:AnimalsCells
    189. Zeroing in on DNA methylomes with no BS. Nat Methods. 2010 Jun; 7(6):435-7. Ecker JR. PMID: 20508637.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    190. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 2010 May 07; 6(5):479-91. 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 JR, Ren B. PMID: 20452322; PMCID: PMC2867844.
      View in: PubMed   Mentions: 395     Fields:    
    191. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010 Jun 03; 465(7298):627-31. 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 JR, 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. PMID: 20336072; PMCID: PMC3023908.
      View in: PubMed   Mentions: 772     Fields:    
    192. Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J. 2010 Mar; 61(6):928-40. O'Malley RC, Ecker JR. PMID: 20409268.
      View in: PubMed   Mentions: 74     Fields:    Translation:Animals
    193. 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. Endres MW, Gregory BD, Gao Z, Foreman AW, Mlotshwa S, Ge X, Pruss GJ, Ecker JR, Bowman LH, Vance V. PMID: 20084269; PMCID: PMC2800190.
      View in: PubMed   Mentions: 68     Fields:    Translation:AnimalsCells
    194. The biceps brachii muscle and its distal insertion: observations of surgical and evolutionary relevance. Surg Radiol Anat. 2010 Apr; 32(4):371-5. Cucca YY, McLay SV, Okamoto T, Ecker J, McMenamin PG. PMID: 19847376.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    195. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009 Nov 19; 462(7271):315-22. 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 JR. PMID: 19829295; PMCID: PMC2857523.
      View in: PubMed   Mentions: 2066     Fields:    
    196. A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana. Genetics. 2009 Nov; 183(3):979-1003. Tsuchisaka A, Yu G, Jin H, Alonso JM, Ecker JR, Zhang X, Gao S, Theologis A. PMID: 19752216; PMCID: PMC2778992.
      View in: PubMed   Mentions: 131     Fields:    Translation:Animals
    197. Prepublication data sharing. Nature. 2009 Sep 10; 461(7261):168-70. Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J. PMID: 19741685; PMCID: PMC3073843.
      View in: PubMed   Mentions: 89     Fields:    
    198. Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein. Development. 2009 Jun; 136(11):1909-18. Liljegren SJ, Leslie ME, Darnielle L, Lewis MW, Taylor SM, Luo R, Geldner N, Chory J, Randazzo PA, Yanofsky MF, Ecker JR. PMID: 19429787; PMCID: PMC2680113.
      View in: PubMed   Mentions: 57     Fields:    Translation:AnimalsCells
    199. 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. Dowen RH, Engel JL, Shao F, Ecker JR, Dixon JE. PMID: 19346252; PMCID: PMC2708883.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    200. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res. 2009 Jun; 19(6):959-66. Lister R, Ecker JR. PMID: 19273618; PMCID: PMC3807530.
      View in: PubMed   Mentions: 156     Fields:    
    201. 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. Li H, Wong WS, Zhu L, Guo HW, Ecker J, Li N. PMID: 19253305.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    202. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol. 2009 Feb 11; 10(2):R17. Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA. PMID: 19210792; PMCID: PMC2688271.
      View in: PubMed   Mentions: 53     Fields:    Translation:AnimalsCells
    203. 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. Qiao H, Chang KN, Yazaki J, Ecker JR. PMID: 19196655; PMCID: PMC2648649.
      View in: PubMed   Mentions: 137     Fields:    Translation:AnimalsCells
    204. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol. 2009 Apr; 12(2):107-18. Lister R, Gregory BD, Ecker JR. PMID: 19157957; PMCID: PMC2723731.
      View in: PubMed   Mentions: 91     Fields:    
    205. Literature-curated protein interaction datasets. Nat Methods. 2009 Jan; 6(1):39-46. 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 JR, Roth FP, Vidal M. PMID: 19116613; PMCID: PMC2683745.
      View in: PubMed   Mentions: 123     Fields:    
    206. 2020 vision for biology: the role of plants in addressing grand challenges in biology. Mol Plant. 2008 Jul; 1(4):561-3. 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. PMID: 19825561.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    207. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell. 2008 Jun; 14(6):854-66. Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR. PMID: 18486559.
      View in: PubMed   Mentions: 203     Fields:    Translation:AnimalsCells
    208. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008 May 02; 133(3):523-36. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. PMID: 18423832; PMCID: PMC2723732.
      View in: PubMed   Mentions: 1050     Fields:    
    209. Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. Plant Cell. 2008 Feb; 20(2):320-36. Hu J, Mitchum MG, Barnaby N, Ayele BT, Ogawa M, Nam E, Lai WC, Hanada A, Alonso JM, Ecker JR, Swain SM, Yamaguchi S, Kamiya Y, Sun TP. PMID: 18310462; PMCID: PMC2276448.
      View in: PubMed   Mentions: 94     Fields:    Translation:Animals
    210. 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. Leivar P, Monte E, Al-Sady B, Carle C, Storer A, Alonso JM, Ecker JR, Quail PH. PMID: 18252845; PMCID: PMC2276449.
      View in: PubMed   Mentions: 182     Fields:    Translation:AnimalsCells
    211. Utilizing tiling microarrays for whole-genome analysis in plants. Plant J. 2008 Feb; 53(4):636-44. Gregory BD, Yazaki J, Ecker JR. PMID: 18269573.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    212. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell. 2007 Dec 28; 131(7):1340-53. 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 JR, Belostotsky DA. PMID: 18160042.
      View in: PubMed   Mentions: 163     Fields:    Translation:AnimalsCells
    213. Mapping the genome landscape using tiling array technology. Curr Opin Plant Biol. 2007 Oct; 10(5):534-42. Yazaki J, Gregory BD, Ecker JR. PMID: 17703988; PMCID: PMC2665186.
      View in: PubMed   Mentions: 21     Fields:    
    214. 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. Li H, He Z, Lu G, Lee SC, Alonso J, Ecker JR, Luan S. PMID: 17704213; PMCID: PMC2002612.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    215. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet. 2007 Sep; 39(9):1151-5. Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D, Nordborg M. PMID: 17676040.
      View in: PubMed   Mentions: 230     Fields:    Translation:AnimalsCells
    216. The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease. J Cell Biol. 2007 Jul 30; 178(3):477-88. Gentry MS, Dowen RH, Worby CA, Mattoo S, Ecker JR, Dixon JE. PMID: 17646401; PMCID: PMC2064834.
      View in: PubMed   Mentions: 60     Fields:    
    217. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science. 2007 Jul 20; 317(5836):338-42. 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 JR, Weigel D. PMID: 17641193.
      View in: PubMed   Mentions: 328     Fields:    Translation:AnimalsCells
    218. Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2007 Jul 17; 104(29):12057-62. 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 JR. PMID: 17626786; PMCID: PMC1914337.
      View in: PubMed   Mentions: 74     Fields:    Translation:AnimalsCells
    219. 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. Swiezewski S, Crevillen P, Liu F, Ecker JR, Jerzmanowski A, Dean C. PMID: 17360694; PMCID: PMC1805594.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    220. Higher plants possess two different types of ATX1-like copper chaperones. Biochem Biophys Res Commun. 2007 Mar 09; 354(2):385-90. Puig S, Mira H, Dorcey E, Sancenón V, Andrés-Colás N, Garcia-Molina A, Burkhead JL, Gogolin KA, Abdel-Ghany SE, Thiele DJ, Ecker JR, Pilon M, Peñarrubia L. PMID: 17223078.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    221. 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. O'Malley RC, Alonso JM, Kim CJ, Leisse TJ, Ecker JR. PMID: 18007627.
      View in: PubMed   Mentions: 48     Fields:    Translation:Animals
    222. The POLARIS peptide of Arabidopsis regulates auxin transport and root growth via effects on ethylene signaling. Plant Cell. 2006 Nov; 18(11):3058-72. Chilley PM, Casson SA, Tarkowski P, Hawkins N, Wang KL, Hussey PJ, Beale M, Ecker JR, Sandberg GK, Lindsey K. PMID: 17138700; PMCID: PMC1693943.
      View in: PubMed   Mentions: 41     Fields:    
    223. The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling. Plant Cell. 2006 Nov; 18(11):3073-87. Hutchison CE, Li J, Argueso C, Gonzalez M, Lee E, Lewis MW, Maxwell BB, Perdue TD, Schaller GE, Alonso JM, Ecker JR, Kieber JJ. PMID: 17122069; PMCID: PMC1693944.
      View in: PubMed   Mentions: 195     Fields:    
    224. Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1. Science. 2006 Nov 24; 314(5803):1295-8. Kim SA, Punshon T, Lanzirotti A, Li L, Alonso JM, Ecker JR, Kaplan J, Guerinot ML. PMID: 17082420.
      View in: PubMed   Mentions: 225     Fields:    Translation:AnimalsCells
    225. 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. Mori IC, Murata Y, Yang Y, Munemasa S, Wang YF, Andreoli S, Tiriac H, Alonso JM, Harper JF, Ecker JR, Kwak JM, Schroeder JI. PMID: 17032064; PMCID: PMC1592316.
      View in: PubMed   Mentions: 236     Fields:    Translation:AnimalsCells
    226. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 2006 Sep 22; 126(6):1189-201. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. PMID: 16949657.
      View in: PubMed   Mentions: 740     Fields:    Translation:AnimalsCells
    227. 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. Olmedo G, Guo H, Gregory BD, Nourizadeh SD, Aguilar-Henonin L, Li H, An F, Guzman P, Ecker JR. PMID: 16920797; PMCID: PMC1550774.
      View in: PubMed   Mentions: 53     Fields:    Translation:AnimalsCells
    228. 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. Yoshida H, Wang KL, Chang CM, Mori K, Uchida E, Ecker JR. PMID: 16897471.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    229. RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis. J Exp Bot. 2006; 57(11):2697-708. Chen JG, Ullah H, Temple B, Liang J, Guo J, Alonso JM, Ecker JR, Jones AM. PMID: 16829549.
      View in: PubMed   Mentions: 71     Fields:    Translation:AnimalsCells
    230. Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog. 2006 Jun; 2(6):e60. Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, Crawford G, Collins F, Shinn P, Leipzig J, Hannenhalli S, Berry CC, Ecker JR, Bushman FD. PMID: 16789841; PMCID: PMC1480600.
      View in: PubMed   Mentions: 165     Fields:    Translation:HumansCells
    231. 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. Lariguet P, Schepens I, Hodgson D, Pedmale UV, Trevisan M, Kami C, de Carbonnel M, Alonso JM, Ecker JR, Liscum E, Fankhauser C. PMID: 16777956; PMCID: PMC1502518.
      View in: PubMed   Mentions: 68     Fields:    Translation:AnimalsCells
    232. 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. Rudella A, Friso G, Alonso JM, Ecker JR, van Wijk KJ. PMID: 16766689; PMCID: PMC1488914.
      View in: PubMed   Mentions: 47     Fields:    Translation:AnimalsCells
    233. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet. 2006 Jul; 7(7):524-36. Alonso JM, Ecker JR. PMID: 16755288.
      View in: PubMed   Mentions: 74     Fields:    Translation:Animals
    234. HIV integration site selection: targeting in macrophages and the effects of different routes of viral entry. Mol Ther. 2006 Aug; 14(2):218-25. Barr SD, Ciuffi A, Leipzig J, Shinn P, Ecker JR, Bushman FD. PMID: 16647883.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    235. 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. Andrés-Colás N, Sancenón V, Rodríguez-Navarro S, Mayo S, Thiele DJ, Ecker JR, Puig S, Peñarrubia L. PMID: 16367966.
      View in: PubMed   Mentions: 98     Fields:    Translation:AnimalsCells
    236. Integration site selection by HIV-based vectors in dividing and growth-arrested IMR-90 lung fibroblasts. Mol Ther. 2006 Feb; 13(2):366-73. Ciuffi A, Mitchell RS, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman FD. PMID: 16325473.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    237. A role for LEDGF/p75 in targeting HIV DNA integration. Nat Med. 2005 Dec; 11(12):1287-9. Ciuffi A, Llano M, Poeschla E, Hoffmann C, Leipzig J, Shinn P, Ecker JR, Bushman F. PMID: 16311605.
      View in: PubMed   Mentions: 314     Fields:    Translation:HumansCells
    238. Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana. Plant Cell. 2005 Dec; 17(12):3282-300. Overvoorde PJ, Okushima Y, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Liu A, Onodera C, Quach H, Smith A, Yu G, Theologis A. PMID: 16284307; PMCID: PMC1315369.
      View in: PubMed   Mentions: 156     Fields:    Translation:AnimalsCells
    239. Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. Plant Cell. 2005 Nov; 17(11):3007-18. Mason MG, Mathews DE, Argyros DA, Maxwell BB, Kieber JJ, Alonso JM, Ecker JR, Schaller GE. PMID: 16227453; PMCID: PMC1276026.
      View in: PubMed   Mentions: 215     Fields:    Translation:AnimalsCells
    240. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development. 2005 Sep; 132(18):4107-18. Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker JR, Reed JW. PMID: 16107481.
      View in: PubMed   Mentions: 311     Fields:    Translation:Animals
    241. Arabidopsis ETO1 specifically interacts with and negatively regulates type 2 1-aminocyclopropane-1-carboxylate synthases. BMC Plant Biol. 2005 Aug 10; 5:14. Yoshida H, Nagata M, Saito K, Wang KL, Ecker JR. PMID: 16091151; PMCID: PMC1199607.
      View in: PubMed   Mentions: 72     Fields:    Translation:AnimalsCells
    242. 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. Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA. PMID: 16006522; PMCID: PMC1177380.
      View in: PubMed   Mentions: 180     Fields:    Translation:Animals
    243. NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. Plant J. 2005 Jul; 43(1):118-30. Wilmoth JC, Wang S, Tiwari SB, Joshi AD, Hagen G, Guilfoyle TJ, Alonso JM, Ecker JR, Reed JW. PMID: 15960621.
      View in: PubMed   Mentions: 170     Fields:    Translation:AnimalsCells
    244. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. J Virol. 2005 Jun; 79(11):6610-9. Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, Verdin E, Berry CC, Ecker JR, Bushman FD. PMID: 15890899; PMCID: PMC1112149.
      View in: PubMed   Mentions: 132     Fields:    Translation:HumansCells
    245. FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions. Genetics. 2005 Jul; 170(3):1197-207. Werner JD, Borevitz JO, Uhlenhaut NH, Ecker JR, Chory J, Weigel D. PMID: 15911588; PMCID: PMC1451178.
      View in: PubMed   Mentions: 72     Fields:    Translation:AnimalsCells
    246. Rapid array mapping of circadian clock and developmental mutations in Arabidopsis. Plant Physiol. 2005 Jun; 138(2):990-7. Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker JR, Kay SA. PMID: 15908595; PMCID: PMC1150413.
      View in: PubMed   Mentions: 44     Fields:    Translation:AnimalsCells
    247. 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. Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker JR, Emerson B, Hogenesch JB, Unterman T, Young RA, Montminy M. PMID: 15753290; PMCID: PMC555478.
      View in: PubMed   Mentions: 413     Fields:    Translation:HumansCells
    248. 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. Ryu JS, Kim JI, Kunkel T, Kim BC, Cho DS, Hong SH, Kim SH, Fernández AP, Kim Y, Alonso JM, Ecker JR, Nagy F, Lim PO, Song PS, Schäfer E, Nam HG. PMID: 15707897.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    249. 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. Werner JD, Borevitz JO, Warthmann N, Trainer GT, Ecker JR, Chory J, Weigel D. PMID: 15695584; PMCID: PMC548991.
      View in: PubMed   Mentions: 86     Fields:    Translation:AnimalsCells
    250. 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. Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D, Onodera C, Quach H, Smith A, Yu G, Theologis A. PMID: 15659631; PMCID: PMC548818.
      View in: PubMed   Mentions: 452     Fields:    Translation:AnimalsCells
    251. Applications of DNA tiling arrays for whole-genome analysis. Genomics. 2005 Jan; 85(1):1-15. Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR. PMID: 15607417.
      View in: PubMed   Mentions: 85     Fields:    Translation:HumansAnimalsCells
    252. An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance. Plant J. 2005 Jan; 41(2):304-18. Liu G, Holub EB, Alonso JM, Ecker JR, Fobert PR. PMID: 15634206.
      View in: PubMed   Mentions: 54     Fields:    
    253. 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. Prigge MJ, Otsuga D, Alonso JM, Ecker JR, Drews GN, Clark SE. PMID: 15598805; PMCID: PMC544490.
      View in: PubMed   Mentions: 288     Fields:    Translation:AnimalsCells
    254. 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. Monte E, Tepperman JM, Al-Sady B, Kaczorowski KA, Alonso JM, Ecker JR, Li X, Zhang Y, Quail PH. PMID: 15505214; PMCID: PMC528976.
      View in: PubMed   Mentions: 135     Fields:    Translation:AnimalsCells
    255. Short-term growth responses to ethylene in Arabidopsis seedlings are EIN3/EIL1 independent. Plant Physiol. 2004 Oct; 136(2):2921-7. Binder BM, Mortimore LA, Stepanova AN, Ecker JR, Bleecker AB. PMID: 15466219; PMCID: PMC523354.
      View in: PubMed   Mentions: 58     Fields:    Translation:Animals
    256. The central role of PhEIN2 in ethylene responses throughout plant development in petunia. Plant Physiol. 2004 Oct; 136(2):2900-12. Shibuya K, Barry KG, Ciardi JA, Loucas HM, Underwood BA, Nourizadeh S, Ecker JR, Klee HJ, Clark DG. PMID: 15466231; PMCID: PMC523352.
      View in: PubMed   Mentions: 38     Fields:    Translation:AnimalsCells
    257. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2004 Aug; 2(8):E234. Mitchell RS, Beitzel BF, Schroder AR, Shinn P, Chen H, Berry CC, Ecker JR, Bushman FD. PMID: 15314653; PMCID: PMC509299.
      View in: PubMed   Mentions: 405     Fields:    Translation:HumansCells
    258. 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. Mockler TC, Yu X, Shalitin D, Parikh D, Michael TP, Liou J, Huang J, Smith Z, Alonso JM, Ecker JR, Chory J, Lin C. PMID: 15310842; PMCID: PMC515126.
      View in: PubMed   Mentions: 81     Fields:    Translation:Animals
    259. Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. Dev Cell. 2004 Aug; 7(2):193-204. Li H, Johnson P, Stepanova A, Alonso JM, Ecker JR. PMID: 15296716.
      View in: PubMed   Mentions: 129     Fields:    Translation:AnimalsCells
    260. 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. Chen JG, Pandey S, Huang J, Alonso JM, Ecker JR, Assmann SM, Jones AM. PMID: 15181210; PMCID: PMC514125.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    261. 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. Pfund C, Tans-Kersten J, Dunning FM, Alonso JM, Ecker JR, Allen C, Bent AF. PMID: 15195952.
      View in: PubMed   Mentions: 44     Fields:    Translation:AnimalsCells
    262. Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics. 2004 Jun; 167(2):907-17. Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker JR, Berry CC, Chory J. PMID: 15238539; PMCID: PMC1470895.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
    263. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol. 2004 Jun; 135(2):1008-19. Tyler L, Thomas SG, Hu J, Dill A, Alonso JM, Ecker JR, Sun TP. PMID: 15173565; PMCID: PMC514135.
      View in: PubMed   Mentions: 227     Fields:    Translation:Animals
    264. 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. Page ML, Hamel PP, Gabilly ST, Zegzouti H, Perea JV, Alonso JM, Ecker JR, Theg SM, Christensen SK, Merchant S. PMID: 15159384.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
    265. Regulation of ethylene gas biosynthesis by the Arabidopsis ETO1 protein. Nature. 2004 Apr 29; 428(6986):945-50. Wang KL, Yoshida H, Lurin C, Ecker JR. PMID: 15118728.
      View in: PubMed   Mentions: 141     Fields:    Translation:AnimalsCells
    266. 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. Novillo F, Alonso JM, Ecker JR, Salinas J. PMID: 15004278; PMCID: PMC374356.
      View in: PubMed   Mentions: 198     Fields:    Translation:Animals
    267. Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling. Plant Cell. 2004 Mar; 16(3):658-71. To JP, Haberer G, Ferreira FJ, Deruère J, Mason MG, Schaller GE, Alonso JM, Ecker JR, Kieber JJ. PMID: 14973166; PMCID: PMC385279.
      View in: PubMed   Mentions: 294     Fields:    
    268. The ethylene signaling pathway: new insights. Curr Opin Plant Biol. 2004 Feb; 7(1):40-9. Guo H, Ecker JR. PMID: 14732440.
      View in: PubMed   Mentions: 300     Fields:    Translation:AnimalsCells
    269. Plant genomics: the third wave. Annu Rev Genomics Hum Genet. 2004; 5:443-77. Borevitz JO, Ecker JR. PMID: 15485356.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    270. 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. Guo H, Ecker JR. PMID: 14675532.
      View in: PubMed   Mentions: 332     Fields:    Translation:AnimalsCells
    271. 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. Catala R, Santos E, Alonso JM, Ecker JR, Martinez-Zapater JM, Salinas J. PMID: 14630965; PMCID: PMC282833.
      View in: PubMed   Mentions: 57     Fields:    Translation:Animals
    272. A growth regulatory loop that provides homeostasis to phytochrome a signaling. Plant Cell. 2003 Dec; 15(12):2966-78. Lariguet P, Boccalandro HE, Alonso JM, Ecker JR, Chory J, Casal JJ, Fankhauser C. PMID: 14615593; PMCID: PMC282841.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    273. Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science. 2003 Nov 07; 302(5647):1049-53. Michael TP, Salomé PA, Yu HJ, Spencer TR, Sharp EL, McPeek MA, Alonso JM, Ecker JR, McClung CR. PMID: 14605371.
      View in: PubMed   Mentions: 170     Fields:    Translation:Animals
    274. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 2003 Oct 31; 302(5646):842-6. 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 JR. PMID: 14593172.
      View in: PubMed   Mentions: 333     Fields:    Translation:AnimalsCells
    275. Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. Plant Cell. 2003 Sep; 15(9):1962-80. Monte E, Alonso JM, Ecker JR, Zhang Y, Li X, Young J, Austin-Phillips S, Quail PH. PMID: 12953104; PMCID: PMC181324.
      View in: PubMed   Mentions: 84     Fields:    Translation:AnimalsCells
    276. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science. 2003 Aug 01; 301(5633):653-7. 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 JR. PMID: 12893945.
      View in: PubMed   Mentions: 2388     Fields:    Translation:AnimalsCells
    277. 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.
      View in: PubMed   Mentions: 56     Fields:    Translation:AnimalsCells
    278. 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.
      View in: PubMed   Mentions: 164     Fields:    Translation:AnimalsCells
    279. 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.
      View in: PubMed   Mentions: 346     Fields:    Translation:AnimalsCells
    280. 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.
      View in: PubMed   Mentions: 199     Fields:    Translation:AnimalsCells
    281. 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.
      View in: PubMed   Mentions: 150     Fields:    Translation:Animals
    282. 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.
      View in: PubMed   Mentions: 230     Fields:    Translation:AnimalsCells
    283. 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.
      View in: PubMed   Mentions: 241     Fields:    Translation:Animals
    284. 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.
      View in: PubMed   Mentions: 230     Fields:    Translation:AnimalsCells
    285. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsPHPublic Health
    286. 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.
      View in: PubMed   Mentions: 118     Fields:    Translation:AnimalsCells
    287. 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.
      View in: PubMed   Mentions: 81     Fields:    Translation:AnimalsCells
    288. 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.
      View in: PubMed   Mentions: 732     Fields:    Translation:HumansCells
    289. 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.
      View in: PubMed   Mentions: 63     Fields:    Translation:AnimalsCells
    290. 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.
      View in: PubMed   Mentions: 35     Fields:    Translation:Animals
    291. Ethylene biosynthesis and signaling networks. Plant Cell. 2002; 14 Suppl:S131-51. Wang KL, Li H, Ecker JR. PMID: 12045274; PMCID: PMC151252.
      View in: PubMed   Mentions: 549     Fields:    Translation:AnimalsCells
    292. 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.
      View in: PubMed   Mentions: 169     Fields:    Translation:AnimalsCells
    293. 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.
      View in: PubMed   Mentions: 72     Fields:    Translation:AnimalsCells
    294. 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.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    295. 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.
      View in: PubMed   Mentions: 73     Fields:    Translation:Animals
    296. Ethylene signaling: from mutants to molecules. Curr Opin Plant Biol. 2000 Oct; 3(5):353-60. Stepanova AN, Ecker JR. PMID: 11019801.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    297. 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.
      View in: PubMed   Mentions: 23     Fields:    Translation:Animals
    298. 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.
      View in: PubMed   Mentions: 137     Fields:    Translation:AnimalsCells
    299. Regulation of differential growth in the apical hook of Arabidopsis. Development. 1999 Aug; 126(16):3661-8. Raz V, Ecker JR. PMID: 10409511.
      View in: PubMed   Mentions: 67     Fields:    Translation:Animals
    300. 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.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    301. 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.
      View in: PubMed   Mentions: 500     Fields:    Translation:AnimalsCells
    302. 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.
      View in: PubMed   Mentions: 121     Fields:    Translation:HumansAnimalsCells
    303. 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.
      View in: PubMed   Mentions: 485     Fields:    Translation:AnimalsCells
    304. 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.
      View in: PubMed   Mentions: 64     Fields:    Translation:HumansAnimalsCells
    305. Ethylene gas: perception, signaling and response. Curr Opin Plant Biol. 1998 Oct; 1(5):393-8. Solano R, Ecker JR. PMID: 10066624.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    306. 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.
      View in: PubMed   Mentions: 197     Fields:    Translation:AnimalsCells
    307. Genome sequencing. Genes blossom from a weed. Nature. 1998 Jan 29; 391(6666):438-9. Ecker JR. PMID: 9461207.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    308. [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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    309. The ethylene gas signal transduction pathway: a molecular perspective. Annu Rev Genet. 1998; 32:227-54. Johnson PR, Ecker JR. PMID: 9928480.
      View in: PubMed   Mentions: 159     Fields:    Translation:AnimalsCells
    310. BRI-ghtening the pathway to steroid hormone signaling events in plants. Cell. 1997 Sep 05; 90(5):825-7. Ecker JR. PMID: 9298893.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    311. 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.
      View in: PubMed   Mentions: 357     Fields:    Translation:AnimalsCells
    312. 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.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    313. 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.
      View in: PubMed   Mentions: 165     Fields:    Translation:AnimalsCells
    314. 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.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    315. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    316. The ethylene signal transduction pathway in plants. Science. 1995 May 05; 268(5211):667-75. Ecker JR. PMID: 7732375.
      View in: PubMed   Mentions: 184     Fields:    Translation:AnimalsCells
    317. 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.
      View in: PubMed   Mentions: 199     Fields:    Translation:AnimalsCells
    318. 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.
      View in: PubMed   Mentions: 408     Fields:    Translation:AnimalsCells
    319. Ethylene gas: it's not just for ripening any more! Trends Genet. 1993 Oct; 9(10):356-62. Kieber JJ, Ecker JR. PMID: 8273151.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    320. 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.
      View in: PubMed   Mentions: 664     Fields:    Translation:AnimalsCells
    321. 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.
      View in: PubMed   Mentions: 85     Fields:    Translation:AnimalsCells
    322. 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.
      View in: PubMed   Mentions: 101     Fields:    Translation:AnimalsCells
    323. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    324. 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.
      View in: PubMed   Mentions: 84     Fields:    Translation:HumansCells
    325. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    326. 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.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    327. 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.
      View in: PubMed   Mentions: 444     Fields:    Translation:Animals
    328. 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.
      View in: PubMed   Mentions: 116     Fields:    
    329. 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.
      View in: PubMed   Mentions: 70     Fields:    
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