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Single-cell DNA methylation and 3D genome architecture in the human brain. Science. 2023 Oct 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.
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1 Fields:
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HumansCells
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A comparative atlas of single-cell chromatin accessibility in the human brain. Science. 2023 Oct 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.
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3 Fields:
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HumansAnimalsCells
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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.
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2
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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.
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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.
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5 Fields:
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AnimalsCells
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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.
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1 Fields:
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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.
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27
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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.
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47 Fields:
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HumansAnimalsCells
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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.
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61 Fields:
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AnimalsCells
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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.
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137 Fields:
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HumansAnimalsCells
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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.
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56 Fields:
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AnimalsCells
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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.
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116 Fields:
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AnimalsCells
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Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nat Methods. 2021 03; 18(3):283-292.
Zhu C, Zhang Y, Li YE, Lucero J, Behrens MM, Ren B. PMID: 33589836; PMCID: PMC7954905.
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77 Fields:
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HumansAnimalsCells
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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.
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25 Fields:
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AnimalsCells
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An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat Struct Mol Biol. 2019 11; 26(11):1063-1070.
Zhu C, Yu M, Huang H, Juric I, Abnousi A, Hu R, Lucero J, Behrens MM, Hu M, Ren B. PMID: 31695190; PMCID: PMC7231560.
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112 Fields:
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HumansAnimalsCells
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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.
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56 Fields:
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HumansAnimalsCells
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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.
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210 Fields:
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HumansAnimalsCells
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Adolescent GBR12909 exposure induces oxidative stress, disrupts parvalbumin-positive interneurons, and leads to hyperactivity and impulsivity in adult mice. Neuroscience. 2017 03 14; 345:166-175.
Khan A, de Jong LA, Kamenski ME, Higa KK, Lucero JD, Young JW, Behrens MM, Powell SB. PMID: 27890827; PMCID: PMC5316310.
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PubMed Mentions:
3 Fields:
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AnimalsCells
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Early Adolescent Emergence of Reversal Learning Impairments in Isolation-Reared Rats. Dev Neurosci. 2015; 37(3):253-62.
Powell SB, Khan A, Young JW, Scott CN, Buell MR, Caldwell S, Tsan E, de Jong LA, Acheson DT, Lucero J, Geyer MA, Behrens MM. PMID: 26022788; PMCID: PMC4644772.
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13 Fields:
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Animals
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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.
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950 Fields:
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HumansAnimalsCells
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IL-6 mediated degeneration of forebrain GABAergic interneurons and cognitive impairment in aged mice through activation of neuronal NADPH oxidase. PLoS One. 2009; 4(5):e5518.
Dugan LL, Ali SS, Shekhtman G, Roberts AJ, Lucero J, Quick KL, Behrens MM. PMID: 19436757; PMCID: PMC2678193.
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PubMed Mentions:
80 Fields:
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AnimalsCells
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Prolonged alpha-tocopherol deficiency decreases oxidative stress and unmasks alpha-tocopherol-dependent regulation of mitochondrial function in the brain. J Biol Chem. 2008 Mar 14; 283(11):6915-24.
Cuddihy SL, Ali SS, Musiek ES, Lucero J, Kopp SJ, Morrow JD, Dugan LL. PMID: 18180306.
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17 Fields:
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AnimalsCells
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Ketamine-induced loss of phenotype of fast-spiking interneurons is mediated by NADPH-oxidase. Science. 2007 Dec 07; 318(5856):1645-7.
Behrens MM, Ali SS, Dao DN, Lucero J, Shekhtman G, Quick KL, Dugan LL. PMID: 18063801.
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286 Fields:
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AnimalsCells
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Gender differences in free radical homeostasis during aging: shorter-lived female C57BL6 mice have increased oxidative stress. Aging Cell. 2006 Dec; 5(6):565-74.
Ali SS, Xiong C, Lucero J, Behrens MM, Dugan LL, Quick KL. PMID: 17129217.
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48 Fields:
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AnimalsCells
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Transgenic mice with a reduced core body temperature have an increased life span. Science. 2006 Nov 03; 314(5800):825-8.
Conti B, Sanchez-Alavez M, Winsky-Sommerer R, Morale MC, Lucero J, Brownell S, Fabre V, Huitron-Resendiz S, Henriksen S, Zorrilla EP, de Lecea L, Bartfai T. PMID: 17082459.
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181 Fields:
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AnimalsCells
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Uncoupling protein 2 protects dopaminergic neurons from acute 1,2,3,6-methyl-phenyl-tetrahydropyridine toxicity. J Neurochem. 2005 Apr; 93(2):493-501.
Conti B, Sugama S, Lucero J, Winsky-Sommerer R, Wirz SA, Maher P, Andrews Z, Barr AM, Morale MC, Paneda C, Pemberton J, Gaidarova S, Behrens MM, Beal F, Sanna PP, Horvath T, Bartfai T. PMID: 15816872.
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44 Fields:
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AnimalsCells
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Focal cerebral ischemia preferentially affects neurons distant from their neighboring microvessels. J Cereb Blood Flow Metab. 2005 Feb; 25(2):257-66.
Mabuchi T, Lucero J, Feng A, Koziol JA, del Zoppo GJ. PMID: 15678127.
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26 Fields:
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AnimalsCells
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Activation systems for latent matrix metalloproteinase-2 are upregulated immediately after focal cerebral ischemia. J Cereb Blood Flow Metab. 2003 Dec; 23(12):1408-19.
Chang DI, Hosomi N, Lucero J, Heo JH, Abumiya T, Mazar AP, del Zoppo GJ. PMID: 14663336.
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53 Fields:
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AnimalsCells
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Neurons of the superior nucleus of the medial habenula and ependymal cells express IL-18 in rat CNS. Brain Res. 2002 Dec 20; 958(1):1-9.
Sugama S, Cho BP, Baker H, Joh TH, Lucero J, Conti B. PMID: 12468024.
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30 Fields:
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AnimalsCells