Nathan Zemke

Title(s)	, Cellular and Molecular Medicine
School	Vc-health Sciences-schools
Address	9500 Gilman Drive # La Jolla CA 92093
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Bibliographic

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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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:
Cell type-specific 3D-genome organization and transcription regulation in the brain. Sci Adv. 2025 Feb 28; 11(9):eadv2067. Liu S, Wang CY, Zheng P, Jia BB, Zemke NR, Ren P, Park HL, Ren B, Zhuang X. PMID: 40009678; PMCID: PMC11864200.

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Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor. bioRxiv. 2025 Jan 12. Grant ZL, Kuang S, Zhang S, Horrillo AJ, Rao KS, Kameswaran V, Joubran C, Lau PK, Dong K, Yang B, Bartosik WM, Zemke NR, Ren B, Kathiriya IS, Pollard KS, Bruneau BG. PMID: 39829922; PMCID: PMC11741296.

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Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina. bioRxiv. 2024 Dec 29. 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.

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Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues. Nat Struct Mol Biol. 2025 Mar; 32(3):479-490. Yu M, Zemke NR, Chen Z, Juric I, Hu R, Raviram R, Abnousi A, Fang R, Zhang Y, Gorkin DU, Li YE, Zhao Y, Lee L, Mishra S, Schmitt AD, Qiu Y, Dickel DE, Visel A, Pennacchio LA, Hu M, Ren B. PMID: 39681766; PMCID: PMC11919700.

View in: PubMed Mentions: Fields:
Mol Molecular Biology
Epigenetic and 3D genome reprogramming during the aging of human hippocampus. bioRxiv. 2024 Oct 17. Zemke NR, Lee S, Mamde S, Yang B, Berchtold N, Maximiliano Garduño B, Indralingam HS, Bartosik WM, Lau PK, Dong K, Yang A, Tani Y, Chen C, Zeng Q, Ajith V, Tong L, Seng C, Li D, Wang T, Xu X, Ren B. PMID: 39463924; PMCID: PMC11507755.

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Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler. Nucleic Acids Res. 2024 Sep 09; 52(16):9481-9500. Cantarella S, Vezzoli M, Carnevali D, Morselli M, Zemke NR, Montanini B, Daussy CF, Wodrich H, Teichmann M, Pellegrini M, Berk AJ, Dieci G, Ferrari R. PMID: 39011896; PMCID: PMC11381368.

View in: PubMed Mentions: Fields:
Bio Biochemistry
Translation:Humans Cells
Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters. Nucleic Acids Res. 2024 Jul 08; 52(12):6850-6865. Hsu E, Hutchison K, Liu Y, Nicolet CM, Schreiner S, Zemke NR, Farnham PJ. PMID: 38726870; PMCID: PMC11229363.

View in: PubMed Mentions: 1 Fields:
Bio Biochemistry
Translation:Humans Animals Cells
A fast, scalable and versatile tool for analysis of single-cell omics data. Nat Methods. 2024 Feb; 21(2):217-227. Zhang K, Zemke NR, Armand EJ, Ren B. PMID: 38191932; PMCID: PMC10864184.

View in: PubMed Mentions: 20 Fields:
Cli Clinical Laboratory Techniques
Translation:Cells
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:
Sci Science
Conserved and divergent gene regulatory programs of the mammalian neocortex. Nature. 2023 Dec; 624(7991):390-402. Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B. PMID: 38092918; PMCID: PMC10719095.

View in: PubMed Mentions: 9 Fields:
Sci Science
Translation:Humans Animals Cells
Cell-type-specific 3D-genome organization and transcription regulation in the brain. bioRxiv. 2023 Dec 05. Liu S, Zheng P, Wang CY, Jia BB, Zemke NR, Ren B, Zhuang X. PMID: 38105994; PMCID: PMC10723369.

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Adenovirus E1A binding to DCAF10 targets proteasomal degradation of RUVBL1/2 AAA+ ATPases required for quaternary assembly of multiprotein machines, innate immunity, and responses to metabolic stress. J Virol. 2023 12 21; 97(12):e0099323. Zemke NR, Hsu E, Barshop WD, Sha J, Wohlschlegel JA, Berk AJ. PMID: 37962355; PMCID: PMC10734532.

View in: PubMed Mentions: Fields:
Vir Virology
Translation:Humans Cells
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: 28 Fields:
Sci Science
Translation:Humans Animals Cells
SnapATAC2: a fast, scalable and versatile tool for analysis of single-cell omics data. bioRxiv. 2023 Sep 15. Zhang K, Zemke NR, Armand EJ, Ren B. PMID: 37745443; PMCID: PMC10515871.

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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.

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Promoter-specific changes in initiation, elongation, and homeostasis of histone H3 acetylation during CBP/p300 inhibition. Elife. 2021 03 11; 10. Hsu E, Zemke NR, Berk AJ. PMID: 33704060; PMCID: PMC8009678.

View in: PubMed Mentions: 19 Fields:
Bio Biology
Translation:Humans Cells
The dopamine receptor antagonist trifluoperazine prevents phenotype conversion and improves survival in mouse models of glioblastoma. Proc Natl Acad Sci U S A. 2020 05 19; 117(20):11085-11096. Bhat K, Saki M, Vlashi E, Cheng F, Duhachek-Muggy S, Alli C, Yu G, Medina P, He L, Damoiseaux R, Pellegrini M, Zemke NR, Nghiemphu PL, Cloughesy TF, Liau LM, Kornblum HI, Pajonk F. PMID: 32358191; PMCID: PMC7245100.

View in: PubMed Mentions: 20 Fields:
Sci Science
Translation:Animals
Dedifferentiation by adenovirus E1A due to inactivation of Hippo pathway effectors YAP and TAZ. Genes Dev. 2019 07 01; 33(13-14):828-843. Zemke NR, Gou D, Berk AJ. PMID: 31171701; PMCID: PMC6601516.

View in: PubMed Mentions: 18 Fields:
Mol Molecular Biology
Translation:Humans Animals Cells
Transcriptomic and ChIP-sequence interrogation of EGFR signaling in HER2+ breast cancer cells reveals a dynamic chromatin landscape and S100 genes as targets. BMC Med Genomics. 2019 02 08; 12(1):32. Nava M, Dutta P, Zemke NR, Farias-Eisner R, Vadgama JV, Wu Y. PMID: 30736768; PMCID: PMC6368760.

View in: PubMed Mentions: 4 Fields:
Gen Genetics
Translation:Humans Cells
Adenovirus E1A Activation Domain Regulates H3 Acetylation Affecting Varied Steps in Transcription at Different Viral Promoters. J Virol. 2018 09 15; 92(18). Hsu E, Pennella MA, Zemke NR, Eng C, Berk AJ. PMID: 29976669; PMCID: PMC6146688.

View in: PubMed Mentions: 11 Fields:
Vir Virology
Translation:Humans Cells
The Adenovirus E1A C Terminus Suppresses a Delayed Antiviral Response and Modulates RAS Signaling. Cell Host Microbe. 2017 Dec 13; 22(6):789-800.e5. Zemke NR, Berk AJ. PMID: 29241042; PMCID: PMC5736016.

View in: PubMed Mentions: 19 Fields:
Mic Microbiology
Translation:Humans Cells
Adenovirus small E1A employs the lysine acetylases p300/CBP and tumor suppressor Rb to repress select host genes and promote productive virus infection. Cell Host Microbe. 2014 Nov 12; 16(5):663-76. Ferrari R, Gou D, Jawdekar G, Johnson SA, Nava M, Su T, Yousef AF, Zemke NR, Pellegrini M, Kurdistani SK, Berk AJ. PMID: 25525796; PMCID: PMC4418520.

View in: PubMed Mentions: 68 Fields:
Mic Microbiology
Translation:Humans Cells
Caveolin isoform switching as a molecular, structural, and metabolic regulator of microglia. Mol Cell Neurosci. 2013 Sep; 56:283-97. Niesman IR, Zemke N, Fridolfsson HN, Haushalter KJ, Levy K, Grove A, Schnoor R, Finley JC, Patel PM, Roth DM, Head BP, Patel HH. PMID: 23851187; PMCID: PMC3791173.

View in: PubMed Mentions: 18 Fields:
Cel Cell Biology Mol Molecular Biology Neu Neurology
Translation:Animals Cells