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Publications
Scholarly Journals--Published
- BIBLIOGRAPHY, LLU 1. Chen Z, Song LJ, Chen W, and Wang C. Single-cell profiling of H3K27me3-H3K4me1 reveals bivalent regulation of abnormal neuronal development caused by prenatal e-cigarette vaporing. Communications Biology, 2025, 8:1326 2. Chen X, Fang LT, Chen Z, …Xiao C, Wang C. A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data. Precis Clin Med. 2025 Jun;8(2). PubMed PMID: 40584741; PubMed Central PMCID: PMC12204187. 3. Walayat A, …Chen Z, …Wang C, Xiao D. Maternal e-cigarette exposure alters DNA methylome, site-specific CpG and CH methylation, and transcriptomic signatures in the neonatal brain. Sci Rep. 2024 Oct 16;14(1):24263. PubMed PMID: 39414906; PubMed Central PMCID: PMC11484909. 4. Mirshahidi S, Yuan IJ, Chen Z…Wang C, Yuan X. Tumor Cell Stemness and Stromal Cell Features Contribute to Oral Cancer Outcome Disparity in Black Americans. Cancers (Basel). 2024 Jul 31;16(15. PubMed PMID: 39123459; PubMed Central PMCID: PMC11311411. 5. Wang S, Wu J, Chen Z,…Song Y. DNA methylation reprogramming mediates transgenerational diabetogenic effect induced by early-life p,p'-DDE exposure. Chemosphere. 2024 Feb: 349: 140907. PubMed PMID: 38092165. 6. Sanchez-Hernandez ES, …Chen Z, Kremsky I, Wang C, Casiano CA. Glucocorticoid Receptor Regulates and Interacts with LEDGF/p75 to Promote Docetaxel Resistance in Prostate Cancer Cells. Cells. 2023 Aug 11;12(16). PubMed PMID: 37626856; PubMed Central PMCID: PMC10453226. 7. Oyefeso FA, Goldberg G, Opoku NYPS, Vazquez M, Bertucci A, Chen Z, Wang C, Muotri AR, Pecaut MJ. Effects of acute low-moderate dose ionizing radiation to human brain organoids. PLoS One. 2023;18(5):e0282958. PubMed PMID: 37256873; PubMed Central PMCID: PMC10231836. 8. Liu T, Chen Z, Chen W, Evans R, Xu J, Reeves ME, de Vera ME, Wang C. Dysregulated miRNAs modulate tumor microenvironment associated signaling networks in pancreatic ductal adenocarcinoma. Precis Clin Med. 2023 Mar;6(1). PubMed PMID: 37007745; PubMed Central PMCID: PMC10052370. 9. Talsania K, Shen TW, Chen X, Jaeger E, Li Z, Chen Z, …Wang C, Xiao W, Zhao Y. Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies. Genome Biol. 2022 Dec 13;23(1):255. PubMed PMID: 36514120; PubMed Central PMCID: PMC9746098. 10. Xiao C, Chen Z, …Wang C, Xiao W. Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples. Genome Biol. 2022 Nov 9;23(1):237. PubMed PMID: 36352452; PubMed Central PMCID: PMC9648002. 11. Chen Z, Chen W, Li Y, Moos M Jr, Xiao D, Wang C. Single-nucleus chromatin accessibility and RNA sequencing reveal impaired brain development in prenatally e-cigarette exposed neonatal rats. iScience. 2022 Aug 19;25(8):104686. PubMed PMID: 35874099; PubMed Central PMCID: PMC9304611. 12. Chen Z, Wang C, Blood A, Bragg S, Mata-Greenwood E. Renal functional, transcriptome, and methylome adaptations in pregnant Sprague Dawley and Brown Norway rats. PLoS One. 2022;17(6):e0269792. PubMed PMID: 35709218; PubMed Central PMCID: PMC9202892. 13. Yang Z, Chen Z, …Wang C, Li J. Rural environment reduces allergic inflammation by modulating the gut microbiota. Gut Microbes. 2022 Jan-Dec;14(1):2125733. PubMed PMID: 36193874; PubMed Central PMCID: PMC9542937. 14. Foox J, …Chen Z, …Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol. 2021 Dec 6;22(1):332. PubMed Central PMCID: PMC8650396. 15. Zhao Y, …Chen Z, …Xiao W. Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study. Sci Data. 2021 Nov 9;8(1):296. PubMed PMID: 34753956; PubMed Central PMCID: PMC8578599. 16. Gatto NM, …Chen Z, Paul J, Fraser G, Wang C, Lee GJ. Vegetarian Dietary Patterns and Cognitive Function among Older Adults: The Adventist Health Study-2. J Nutr Gerontol Geriatr. 2021 Oct-Dec;40(4):197-214. PubMed PMID: 34412570. 17. Fang LT, Zhu B, …Chen Z, …Wang C, Xiao W. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nat Biotechnol. 2021 Sep;39(9):1151-1160. PubMed PMID: 34504347; PubMed Central PMCID: PMC8532138. 18. Xiao W, Ren L, Chen Z,… Shi L. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nat Biotechnol. 2021 Sep;39(9):1141-1150. PubMed PMID: 34504346; PubMed Central PMCID: PMC8506910. 19. Liu T, Chen Z, Chen W, Chen X, Hosseini M, Yang Z, Li J, Ho D, Turay D, Gheorghe CP, Jones W, Wang C. A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples. iScience. 2021 Aug 20;24(8):102892. PubMed PMID: 34308277; PubMed Central PMCID: PMC8294598. 20. Chen Z, Stanbouly S, Nishiyama NC, Chen X, Delp MD, Qiu H, Mao XW, Wang C. Spaceflight decelerates the epigenetic clock orchestrated with a global alteration in DNA methylome and transcriptome in the mouse retina. Precis Clin Med. 2021 Jun;4(2):93-108. PubMed PMID: 34179686; PubMed Central PMCID: PMC8220224. 21. Liu T, Gatto NM, Chen Z, Qiu H, Lee G, Duerksen-Hughes P, Fraser G, Wang C. Vegetarian diets, circulating miRNA expression and healthspan in subjects living in the Blue Zone. Precis Clin Med. 2020 Dec;3(4):245-259. PubMed PMID: 33391847; PubMed Central PMCID: PMC7757436 22. Paul JL, Dashtipour K, Chen Z, Wang C. DNA methylome study of human cerebellar tissues identified genes and pathways possibly involved in essential tremor. Precis Clin Med. 2019 Dec;2(4):221-234. PubMed PMID: 31886034; PubMed Central PMCID: PMC6927097 OTHER PUBLICATIONS 23. Chen Z, Gallie DR. Ethylene Regulates Energy-Dependent Non-Photochemical Quenching in Arabidopsis through Repression of the Xanthophyll Cycle. PLoS One. 2015;10(12):e0144209. 24. Chen Z, Jolley B, Caldwell C, Gallie DR. Eukaryotic translation initiation factor eIFiso4G is required to regulate violaxanthin De-epoxidase expression in Arabidopsis. J Biol Chem. 2014, 16;289(20):13926-36. 25. Botanga CJ, Bethke G, Chen Z, Gallie DR, Fiehn O, Glazebrook J. Metabolite profiling of Arabidopsis inoculated with Alternaria brassicicola reveals that ascorbate reduces disease severity. Mol Plant Microbe Interact. 2012, 25(12):1628-38. 26. Chen Z, Gallie DR. Violaxanthin de-epoxidase is rate-limiting for non-photochemical quenching under subsaturating light or during chilling in Arabidopsis. Plant Physiol Biochem. 2012, 58:66-82. 27. Chen Z, Gallie DR. Induction of monozygotic twinning by ascorbic acid in tobacco. PLoS One. 2012;7(6):e39147. 28. Chen Z, Gallie DR. Dehydroascorbate reductase affects non-photochemical quenching and photosynthetic performance. J Biol Chem. 2008, 283(31):21347-61. 29. Chen Z, Gallie DR. Dehydroascorbate reductase affects leaf growth, development, and function. Plant Physiol. 2006,142(2):775-87. 30. Chen Z, Gallie DR. Increasing tolerance to ozone by elevating foliar ascorbic acid confers greater protection against ozone than increasing avoidance. Plant Physiol. 2005, 38(3):1673-89. 31. Chen Z, Gallie DR. The ascorbic acid redox state controls guard cell signaling and stomatal movement. Plant Cell. 2004 May;16(5):1143-62. 32. Chen Z, Ling J, Gallie DR. RNase activity requires formation of disulfide bonds and is regulated by the redox state. Plant Mol Biol. 2004 May;55(1):83-96. doi: 10.1007/s11103-004-0438-1. 33. Chen Z, Young TE, Ling J, Chang SC, Gallie DR. Increasing vitamin C content of plants through enhanced ascorbate recycling. Proc Natl Acad Sci. 2003 Mar 18;100(6):3525-30. (09/2024) (link)