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Eran Mukamel

Title(s)Professor, Cognitive Science
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    3/3 High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease
    NIH U01MH122592May 1, 2020 - Feb 28, 2025
    Role: Principal Investigator
    Single Neuron Analyzer for Multi-modal, Cross-dataset (Epi)genomic Cell Type Datasets
    NIH RF1MH120015Sep 18, 2019 - Aug 31, 2022
    Role: Principal Investigator
    Global cortical dynamics in sleep and general anesthesia
    NIH R00NS080911Jul 1, 2014 - Jun 30, 2018
    Role: Principal Investigator
    Global cortical dynamics in sleep and general anesthesia
    NIH K99NS080911Sep 1, 2012 - Aug 31, 2014
    Role: Principal Investigator

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    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. Cell-type specific impact of opioid use disorder and HIV on the human forebrain and cerebellum. bioRxiv. 2026 Mar 03. Green AA, Vashist TD, Jakhmola S, Chen X, Baidwan G, Buchanan J, Tiwari SK, Griffin E, Howell A, Lee Y, Moore DJ, Gianella S, Smith DM, Zhu Q, Walss-Bass C, Wang A, Mukamel EA, Gaulton KJ, Rana TM. PMID: 41867821; PMCID: PMC13001470.
      View in: PubMed   Mentions:
    2. Postnatal conversion of methylcytosine to hydroxymethylcytosine reconfigures the human neuronal epigenome. bioRxiv. 2026 Feb 19. Xu H, Chien JF, Kozlenkov A, Vadukapuram R, Li J, Wei Y, Dwork AJ, Liu C, Dracheva S, Mukamel EA. PMID: 41757014; PMCID: PMC12934748.
      View in: PubMed   Mentions:
    3. A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons. bioRxiv. 2026 Jan 29. Heffel MG, Xu H, Pastor-Alonso O, Li X, Baig MS, Irfan Ghoor R, Li R, Kern C, Kum J, Zhang Y, Paino J, Tsai MJ, Tai CY, Tucker G, Zhao Z, Hou A, von Behren Z, Bhade M, Li S, Sandoval K, Scholes J, Codrea F, Calimlim J, Liao EK, Leung G, Kim J, Eskin E, Flint J, Cotter JA, Pasaniuc B, Bintu B, Zhu Q, Mukamel EA, Ernst J, Paredes MF, Luo C. PMID: 41659519; PMCID: PMC12874046.
      View in: PubMed   Mentions:
    4. Spatial transcriptomics reveals brain-wide circadian disruption in an Alzheimer's disease model. bioRxiv. 2026 Jan 28. Gelber A, Romero H, Burrows D, Whittaker DS, Carlin D, Mukamel EA, Desplats P. PMID: 41659563; PMCID: PMC12874051.
      View in: PubMed   Mentions:
    5. A phenotypic brain organoid atlas and biobank for neurodevelopmental disorders. Cell Stem Cell. 2025 Dec 04; 32(12):1923-1940.e7. Wang L, Nakamura Y, Li J, Sievert D, Liu Y, Nguyen T, Jetti PS, Thai E, Zhou RY, Weng J, Meave N, Yadavilli M, Howarth R, Camey K, Banka N, Owusu-Hammond C, Barrows C, Kingsmore SF, Zaki MS, Mukamel E, Gleeson JG. PMID: 41187745; PMCID: PMC13003759.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Cell-type-specific enrichment of somatic aneuploidy in the mammalian brain. Neuron. 2025 Sep 03; 113(17):2814-2821.e2. Mukamel EA, Liu H, Behrens MM, Ecker JR. PMID: 40907475; PMCID: PMC12416756.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    7. Identification of conserved frontal neurophysiological markers of cognitive flexibility in humans and rats. Commun Biol. 2025 Aug 23; 8(1):1268. Der-Avakian A, Barnes SA, Lees T, Schroder HS, Kangas BD, Linton SR, Nickels S, Robble MA, Breiger M, Iturra-Mena AM, Lobien R, Perlo S, Cárdenas EF, Nowicki GP, Wu Z, Pan H, Dillon DG, Kesby JP, Bergman J, Carlezon WA, Risbrough VB, Mukamel E, Leutgeb S, Pizzagalli DA. PMID: 40849367; PMCID: PMC12375130.
      View in: PubMed   Mentions: 1  Translation:HumansAnimals
    8. False positives in study of memory-related gene expression. Nature. 2025 Jun; 642(8066):E1-E3. Mukamel EA, Yu Z. PMID: 40467748.
      View in: PubMed   Mentions: 1     Fields:    
    9. Author Correction: Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation. Nat Commun. 2024 Nov 06; 15(1):9588. Li J, Jaiswal MK, Chien JF, Kozlenkov A, Jung J, Zhou P, Gardashli M, Pregent LJ, Engelberg-Cook E, Dickson DW, Belzil VV, Mukamel EA, Dracheva S. PMID: 39505881; PMCID: PMC11541863.
      View in: PubMed   Mentions:    Fields:    
    10. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature. 2024 11; 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: 24     Fields:    Translation:HumansCells
    11. Single-cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2R47H Alzheimer's risk gene mutation. Mol Psychiatry. 2025 Feb; 30(2):461-477. Johnston KG, Berackey BT, Tran KM, Gelber A, Yu Z, MacGregor GR, Mukamel EA, Tan Z, Green KN, Xu X. PMID: 39103533; PMCID: PMC11746152.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    12. The single-cell opioid responses in the context of HIV (SCORCH) consortium. Mol Psychiatry. 2024 Dec; 29(12):3950-3961. Ament SA, Campbell RR, Lobo MK, Receveur JP, Agrawal K, Borjabad A, Byrareddy SN, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton KJ, Giglio M, Giorgi FM, Gok B, Guda C, Hadas E, Herb BR, Hu W, Huttner A, Ishmam MR, Jacobs MM, Kelschenbach J, Kim DW, Lee C, Liu S, Liu X, Madras BK, Mahurkar AA, Mash DC, Mukamel EA, Niu M, O'Connor RM, Pagan CM, Pang APS, Pillai P, Repunte-Canonigo V, Ruzicka WB, Stanley J, Tickle T, Tsai SA, Wang A, Wills L, Wilson AM, Wright SN, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng CS, Corley MJ, Fox HS, Gerstein M, Gummuluru S, Heiman M, Ho YC, Kellis M, Kenny PJ, Kluger Y, Milner TA, Moore DJ, Morgello S, Ndhlovu LC, Rana TM, Sanna PP, Satterlee JS, Sestan N, Spector SA, Spudich S, Tilgner HU, Volsky DJ, White OR, Williams DW, Zeng H. PMID: 38879719; PMCID: PMC11609103.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    13. 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: 21     Fields:    Translation:HumansCells
    14. Transcriptomic sex differences in postmortem brain samples from patients with psychiatric disorders. Sci Transl Med. 2024 05 29; 16(749):eadh9974. Xia Y, Xia C, Jiang Y, Chen Y, Zhou J, Dai R, Han C, Mao Z, PsychENCODE Consortium, Liu C, Chen C. PMID: 38781321; PMCID: PMC13016617.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    15. Single-cell genomics and regulatory networks for 388 human brains. Science. 2024 05 24; 384(6698):eadi5199. Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, PsychENCODE Consortium‡, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M, PsychENCODE Consortium. PMID: 38781369; PMCID: PMC11365579.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansCells
    16. A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science. 2024 05 24; 384(6698):eadh1938. Huuki-Myers LA, Spangler A, Eagles NJ, Montgomery KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, PsychENCODE Consortium†, Hyde TM, Kleinman JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, Collado-Torres L, Maynard KR, PsychENCODE Consortium. PMID: 38781370; PMCID: PMC11398705.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    17. Massively parallel characterization of regulatory elements in the developing human cortex. Science. 2024 05 24; 384(6698):eadh0559. Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, PsychENCODE Consortium‡, Pollen AA, Nowakowski TJ, Ahituv N, Pollard KS, PsychENCODE Consortium. PMID: 38781390; PMCID: PMC12085231.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    18. Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science. 2024 05 24; 384(6698):eadh0829. Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, PsychENCODE Consortium†, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ, PsychENCODE Consortium. PMID: 38781368; PMCID: PMC12147038.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    19. Single-cell multi-cohort dissection of the schizophrenia transcriptome. Science. 2024 05 24; 384(6698):eadg5136. Ruzicka WB, Mohammadi S, Fullard JF, Davila-Velderrain J, Subburaju S, Tso DR, Hourihan M, Jiang S, Lee HC, Bendl J, PsychENCODE Consortium§, Voloudakis G, Haroutunian V, Hoffman GE, Roussos P, Kellis M, PsychENCODE Consortium. PMID: 38781388; PMCID: PMC12772489.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    20. 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:
    21. Brain-wide correspondence of neuronal epigenomics and distant projections. Nature. 2023 12; 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: 24     Fields:    Translation:AnimalsCells
    22. Single cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2R47H Alzheimer's risk gene mutation. Res Sq. 2023 Dec 07. Johnston K, Berackey BB, Tran KM, Gelber A, Yu Z, MacGregor G, Mukamel EA, Tan Z, Green K, Xu X. PMID: 38106071; PMCID: PMC10723554.
      View in: PubMed   Mentions:
    23. Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation. Nat Commun. 2023 09 15; 14(1):5714. Li J, Jaiswal MK, Chien JF, Kozlenkov A, Jung J, Zhou P, Gardashli M, Pregent LJ, Engelberg-Cook E, Dickson DW, Belzil VV, Mukamel EA, Dracheva S. PMID: 37714849; PMCID: PMC10504300.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    24. 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: 26     Fields:    Translation:HumansAnimalsCells
    25. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. Cell Genom. 2023 Jul 12; 3(7):100342. Xie F, Armand EJ, Yao Z, Liu H, Bartlett A, Behrens MM, Li YE, Lucero JD, Luo C, Nery JR, Pinto-Duarte A, Poirion OB, Preissl S, Rivkin AC, Tasic B, Zeng H, Ren B, Ecker JR, Mukamel EA. PMID: 37492103; PMCID: PMC10363915.
      View in: PubMed   Mentions: 12     Fields:    
    26. Cellular and genetic drivers of RNA editing variation in the human brain. Nat Commun. 2022 05 30; 13(1):2997. Dredge WH, Li J, Fan X, Kozenkov A, Lalli M, Khalique S, Dracheva S, Mukamel EA, Breen MS. PMID: 35637184; PMCID: PMC9151768.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    27. 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: 18     Fields:    Translation:AnimalsCells
    28. 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:    
    29. 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: 95     Fields:    
    30. Multiple Comparisons and Inappropriate Statistical Testing Lead to Spurious Sex Differences in Gene Expression. Biol Psychiatry. 2022 01 01; 91(1):e1-e2. Mukamel EA. PMID: 34674833; PMCID: PMC10725829.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    31. 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: 197     Fields:    Translation:AnimalsCells
    32. 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: 169     Fields:    Translation:AnimalsCells
    33. 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: 402     Fields:    Translation:HumansAnimalsCells
    34. 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: 119     Fields:    Translation:HumansAnimalsCells
    35. 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: 44     Fields:    Translation:AnimalsCells
    36. 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: 230     Fields:    Translation:AnimalsCells
    37. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes. Neuron. 2021 01 06; 109(1):11-26. Armand EJ, Li J, Xie F, Luo C, Mukamel EA. PMID: 33412093; PMCID: PMC7808568.
      View in: PubMed   Mentions: 133     Fields:    Translation:HumansCells
    38. Evolution of regulatory signatures in primate cortical neurons at cell-type resolution. Proc Natl Acad Sci U S A. 2020 11 10; 117(45):28422-28432. Kozlenkov A, Vermunt MW, Apontes P, Li J, Hao K, Sherwood CC, Hof PR, Ely JJ, Wegner M, Mukamel EA, Creyghton MP, Koonin EV, Dracheva S. PMID: 33109720; PMCID: PMC7668098.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    39. Maternal immune activation impairs cognitive flexibility and alters transcription in frontal cortex. Neurobiol Dis. 2019 05; 125:211-218. Amodeo DA, Lai CY, Hassan O, Mukamel EA, Behrens MM, Powell SB. PMID: 30716470; PMCID: PMC6474674.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    40. Perspectives on defining cell types in the brain. Curr Opin Neurobiol. 2019 06; 56:61-68. Mukamel EA, Ngai J. PMID: 30530112; PMCID: PMC6551297.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    41. A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons. Sci Adv. 2018 09; 4(9):eaau6190. Kozlenkov A, Li J, Apontes P, Hurd YL, Byne WM, Koonin EV, Wegner M, Mukamel EA, Dracheva S. PMID: 30263963; PMCID: PMC6157969.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansCells
    42. A transient cortical state with sleep-like sensory responses precedes emergence from general anesthesia in humans. Elife. 2018 08 10; 7. Lewis LD, Piantoni G, Peterfreund RA, Eskandar EN, Harrell PG, Akeju O, Aglio LS, Cash SS, Brown EN, Mukamel EA, Purdon PL. PMID: 30095069; PMCID: PMC6086660.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    43. Environmental enrichment increases transcriptional and epigenetic differentiation between mouse dorsal and ventral dentate gyrus. Nat Commun. 2018 01 19; 9(1):298. Zhang TY, Keown CL, Wen X, Li J, Vousden DA, Anacker C, Bhattacharyya U, Ryan R, Diorio J, O'Toole N, Lerch JP, Mukamel EA, Meaney MJ. PMID: 29352183; PMCID: PMC5775256.
      View in: PubMed   Mentions: 66     Fields:    Translation:AnimalsCells
    44. 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: 311     Fields:    Translation:HumansAnimalsCells
    45. 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: 32     Fields:    Translation:AnimalsCells
    46. 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: 90     Fields:    Translation:AnimalsCells
    47. 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: 7     Fields:    
    48. Disruption of mGluR5 in parvalbumin-positive interneurons induces core features of neurodevelopmental disorders. Mol Psychiatry. 2015 Oct; 20(10):1161-72. Barnes SA, Pinto-Duarte A, Kappe A, Zembrzycki A, Metzler A, Mukamel EA, Lucero J, Wang X, Sejnowski TJ, Markou A, Behrens MM. PMID: 26260494; PMCID: PMC4583365.
      View in: PubMed   Mentions: 60     Fields:    Translation:AnimalsCells
    49. Turning over DNA methylation in the mind. Front Neurosci. 2015; 9:252. Lister R, Mukamel EA. PMID: 26283895; PMCID: PMC4519686.
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    50. 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: 461     Fields:    Translation:AnimalsCells
    51. 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: 407     Fields:    Translation:HumansCells
    52. A transition in brain state during propofol-induced unconsciousness. J Neurosci. 2014 Jan 15; 34(3):839-45. Mukamel EA, Pirondini E, Babadi B, Wong KF, Pierce ET, Harrell PG, Walsh JL, Salazar-Gomez AF, Cash SS, Eskandar EN, Weiner VS, Brown EN, Purdon PL. PMID: 24431442; PMCID: PMC3891963.
      View in: PubMed   Mentions: 66     Fields:    Translation:Humans
    53. 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: 1093     Fields:    Translation:HumansAnimalsCells
    54. Electroencephalogram signatures of loss and recovery of consciousness from propofol. Proc Natl Acad Sci U S A. 2013 Mar 19; 110(12):E1142-51. Purdon PL, Pierce ET, Mukamel EA, Prerau MJ, Walsh JL, Wong KF, Salazar-Gomez AF, Harrell PG, Sampson AL, Cimenser A, Ching S, Kopell NJ, Tavares-Stoeckel C, Habeeb K, Merhar R, Brown EN. PMID: 23487781; PMCID: PMC3607036.
      View in: PubMed   Mentions: 339     Fields:    Translation:HumansCTClinical Trials
    55. Rapid fragmentation of neuronal networks at the onset of propofol-induced unconsciousness. Proc Natl Acad Sci U S A. 2012 Dec 04; 109(49):E3377-86. Lewis LD, Weiner VS, Mukamel EA, Donoghue JA, Eskandar EN, Madsen JR, Anderson WS, Hochberg LR, Cash SS, Brown EN, Purdon PL. PMID: 23129622; PMCID: PMC3523833.
      View in: PubMed   Mentions: 204     Fields:    Translation:Humans
    56. Unified resolution bounds for conventional and stochastic localization fluorescence microscopy. Phys Rev Lett. 2012 Oct 19; 109(16):168102. Mukamel EA, Schnitzer MJ. PMID: 23215134; PMCID: PMC3521605.
      View in: PubMed   Mentions: 16     Fields:    
    57. Statistical deconvolution for superresolution fluorescence microscopy. Biophys J. 2012 May 16; 102(10):2391-400. Mukamel EA, Babcock H, Zhuang X. PMID: 22677393; PMCID: PMC3353000.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    58. Beamforming approach to phase-amplitude modulation analysis of multi-channel EEG. Annu Int Conf IEEE Eng Med Biol Soc. 2012; 2012:6731-4. Sampson AL, Babadi B, Prerau MJ, Mukamel EA, Brown EN, Purdon PL. PMID: 23367474; PMCID: PMC3753031.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    59. Robust time-varying multivariate coherence estimation: application to electroencephalogram recordings during general anesthesia. Annu Int Conf IEEE Eng Med Biol Soc. 2011; 2011:4725-8. Wong KF, Mukamel EA, Salazar AF, Pierce ET, Harrell PG, Walsh JL, Sampson A, Brown EN, Purdon PL. PMID: 22255393; PMCID: PMC3293406.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    60. Phase-based measures of cross-frequency coupling in brain electrical dynamics under general anesthesia. Annu Int Conf IEEE Eng Med Biol Soc. 2011; 2011:1981-4. Mukamel EA, Wong KF, Prerau MJ, Brown EN, Purdon PL. PMID: 22254722; PMCID: PMC3282123.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    61. Bayesian analysis of trinomial data in behavioral experiments and its application to human studies of general anesthesia. Annu Int Conf IEEE Eng Med Biol Soc. 2011; 2011:4705-8. Wong KF, Smith AC, Pierce ET, Harrell PG, Walsh JL, Salazar AF, Tavares CL, Cimenser A, Prerau MJ, Mukamel EA, Sampson A, Purdon PL, Brown EN. PMID: 22255388; PMCID: PMC3282046.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    62. Automated analysis of cellular signals from large-scale calcium imaging data. Neuron. 2009 Sep 24; 63(6):747-60. Mukamel EA, Nimmerjahn A, Schnitzer MJ. PMID: 19778505; PMCID: PMC3282191.
      View in: PubMed   Mentions: 375     Fields:    Translation:HumansAnimalsCells
    63. Motor behavior activates Bergmann glial networks. Neuron. 2009 May 14; 62(3):400-12. Nimmerjahn A, Mukamel EA, Schnitzer MJ. PMID: 19447095; PMCID: PMC2820366.
      View in: PubMed   Mentions: 164     Fields:    Translation:AnimalsCells
    64. Advances in light microscopy for neuroscience. Annu Rev Neurosci. 2009; 32:435-506. Wilt BA, Burns LD, Wei Ho ET, Ghosh KK, Mukamel EA, Schnitzer MJ. PMID: 19555292; PMCID: PMC2820375.
      View in: PubMed   Mentions: 113     Fields:    Translation:HumansAnimalsCells
    65. High-speed, miniaturized fluorescence microscopy in freely moving mice. Nat Methods. 2008 Nov; 5(11):935-8. Flusberg BA, Nimmerjahn A, Cocker ED, Mukamel EA, Barretto RP, Ko TH, Burns LD, Jung JC, Schnitzer MJ. PMID: 18836457; PMCID: PMC2828344.
      View in: PubMed   Mentions: 167     Fields:    Translation:Animals
    66. Lock-and-key mechanisms of cerebellar memory recall based on rebound currents. J Neurophysiol. 2008 Oct; 100(4):2328-47. Wetmore DZ, Mukamel EA, Schnitzer MJ. PMID: 17671105; PMCID: PMC2576199.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    67. Retinal coding of visual scenes -- repetitive and redundant too? Neuron. 2005 May 05; 46(3):357-9. Mukamel EA, Schnitzer MJ. PMID: 15882630.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    68. Direct measurement of the spatial Wigner function with area-integrated detection. Opt Lett. 2003 Aug 01; 28(15):1317-9. Mukamel E, Banaszek K, Walmsley IA, Dorrer C. PMID: 12906075.
      View in: PubMed   Mentions: 4     Fields:    
    69. Managing photons for quantum information processing. Philos Trans A Math Phys Eng Sci. 2003 Jul 15; 361(1808):1493-506. U'Ren AB, Mukamel E, Banaszek K, Walmsley IA. PMID: 12869324.
      View in: PubMed   Mentions:    Fields:    
    70. Phase diagram for unzipping DNA with long-range interactions. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Sep; 66(3 Pt 1):032901. Mukamel EA, Shakhnovich EI. PMID: 12366167.
      View in: PubMed   Mentions: 3     Fields:    
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