2025
Shea, A., Sun, S., Kennedy, J., Zhang, L., Vijg, J., & Dong, X.. SomaMutDB 2.0: a database of somatic mutations in normal human tissues. Nucleic Acids Res, Accepted.
Bartz, J., Ma, X., Zhang, L., Dong, X., Human Cell Aging Transcriptome Atlas (HCATA): A single-cell atlas of age-associated transcriptomic alterations across human tissues. Communications Biology, Accepted.
Zhang, L., Lee, M., Hao, X., Ma, X., Xia, C., Zhao, Y., Ehlert, J., Chi, Z., Jin, B., Maslov, A. Y., Barabási, A-L., Hoeijmakers, J. A. J., Edelmann, W., Vijg, J., & Dong, X., Divergent accumulation patterns of SNVs and INDELs reveal negative selection in noncancerous cells. The Innovation, Accepted. Online access before formal publication.
2024
Mahmud S, Zheng C, Santiago FE, Robbins PD, Zhang L, Dong X. Evaluating
performance of machine learning methods to discover in vitro cellular senescence from
bulk RNA sequencing data. Geroscience. 2024 Dec 30. doi: 10.1007/s11357-024-01485-6. Online ahead of print. PMID: 39738795.
Zhang L, Lee M, Maslov AY, Montagna C, Vijg J, Dong X. Analyzing somatic mutations
by single-cell whole-genome sequencing. Nature Protocols. 2023 Nov 23. doi: 10.1038/s41596-023-00914-8. PMID: 37996541.
Mahmud S, Pitcher LE, Torbenson E, Robbins PD, Zhang L, Dong X. Developing transcriptomic signatures as a biomarker of cellular senescence. Ageing Research Reviews. 2024 Aug;99:102403. doi:10.1016/j.arr.2024.102403. Epub 2024 Jul 2. PMID:38964507.
2023
Zhang L, Lee M, Maslov AY, Montagna C, Vijg J, Dong X. Analyzing somatic mutations by single-cell whole-genome sequencing. Nature Protocols. 2023 Nov 23. doi: 10.1038/s41596-023-00914-8. PMID: 37996541.
Zhang L, Cecco MD, Lee M, Hao X, Maslov AY, Dong X#, Sedivy JM#, Vijg J#. Single-cell whole-genome sequencing discovers accumulation of somatic mutations during cellular senescence. Under revision. (Co-corresponding author)
Zhang L#, Lee M, Maslov AY, Vijg J, Dong X#. Single-cell whole-genome sequencing for discovering somatic mutations. Under revision. (#Co-corresponding author)
Shea A, Bartz J, Zhang L, Dong X. Predicting mutational function using machine learning. Under revision.
Bartz J, Jung H, Wasiluk K, Zhang L, Dong X#. Progress in Discovering Transcriptional Noise in Aging. Int. J. Mol. Sci. 2023, 23.
View all PubMed Publications
2021
Zhang L#, Dong X, Tian X, Lee M, Ablaeva J, Firsanov D, Lee SG, Maslov AY, Gladyshev VN, Seluanov A, Gorbunova V, Vijg J. Maintenance of genome sequence integrity in long-and short-lived rodent species. Sci. Adv. 2021 Oct 29;7(44): eabj3284. doi: 10.1126/sciadv.abj3284. PubMed PMID: 34705500. (#Co-corresponding author)
Zhang Q, Tombline G, Ablaeva J, Zhang L, Zhou X, Smith Z, Zhao Y, Xiaoli AM, Wang Z, Lin JR, Jabalameli MR, Mitra J, Nguyen N, Vijg J, Seluanov A, Gladyshev VN, Gorbunova V, Zhang ZD. Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation. Cell Rep. 2021 Nov 9;37(6):109965.
Dong X, Sun S, Zhang L*, Kim S, Tu Z, Montagna C, Maslov AY., Suh Y, Wang T, Campisi J, Vijg J. Age-related telomere attrition causes aberrant gene expression in sub-telomeric regions. Aging Cell. 2021 Jun;20(6):e13357. (*Co-first author)
2020
Dong X, Zhang L, Hao X, Wang T, Vijg J. SCCNV: A software tool for identifying copy number variation from single-cell whole-genome sequencing. Front Genet. 2020 Nov 16. 11:505441. doi: 10.3389/fgene.2020.505441. PubMed PMID: 33304377.
2019
Zhang L, Dong X, Lee M, Maslov AY, Wang T, Vijg J. Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan. Proc Natl Acad Sci U S A. 2019 Apr 16. pii: 201902510. doi: 10.1073/pnas. PubMed PMID: 30992375.
2018
Zhang L, Vijg J. Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging. Annual Review of Genetics. 2018;52:397-419. Epub 2018/09/14. doi: 10.1146/annurev-genet-120417-031501. PubMed PMID: 30212236; PMCID: PMC6414224.
2017
Vijg J, Dong X, Zhang L. A high-fidelity method for genomic sequencing of single somatic cells reveals a very high mutational burden. Experimental Biology and Medicine. 2017;242(13):1318-24. Epub 2017/07/25. doi: 10.1177/1535370217717696. PubMed PMID: 28737476; PMCID: PMC5529006.
Vijg J, Dong X, Milholland B, Zhang L. Genome instability: a conserved mechanism of ageing? Essays in Biochemistry. 2017;61(3):305-15. Epub 2017/05/28. doi: 10.1042/EBC20160082. PubMed PMID: 28550046; PMCID: PMC5988260.
Milholland B, Dong X, Zhang L*, Hao X, Suh Y, Vijg J. Differences between germline and somatic mutation rates in humans and mice. Nature Communications. 2017;8:15183. Epub 2017/05/10. doi: 10.1038/ncomms15183. PubMed PMID: 28485371; PMCID: PMC5436103. (*Co-first author)
Dong X, Zhang L, Milholland B, Lee M, Maslov A, Wang T, Vijg J. Single-Cell Multiple Displacement Amplification (SCMDA). Protocol Exchange. 2017. doi: 10.1038/protex.2017.061
Dong X, Zhang L*, Milholland B, Lee M, Maslov AY, Wang T, Vijg J. Accurate identification of single-nucleotide variants in whole-genome-amplified single cells. Nature Methods. 2017;14(5):491-3. Epub 2017/03/21. doi: 10.1038/nmeth.4227. PubMed PMID: 28319112; PMCID: PMC5408311. (*Co-first author)
Nie X, Yang B, Zhang L, Gu Y, Yang S, Jiang W, Yang C. PTS regulation domain-containing transcriptional activator CelR and sigma factor sigma(54) control cellobiose utilization in Clostridium acetobutylicum. Molecular Microbiology. 2016;100(2):289-302. Epub 2015/12/23. doi: 10.1111/mmi.13316. PubMed PMID: 26691835.
Zhang L, Nie X, Ravcheev DA, Rodionov DA, Sheng J, Gu Y, Yang S, Jiang W, Yang C. Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum. Journal of Bacteriology. 2014;196(22):3949-63. Epub 2014/09/04. doi: 10.1128/jb.02037-14. PubMed PMID: 25182496; PMCID: PMC4248821.
Liu L, Zhang L*, Tang W, Gu Y, Hua Q, Yang S, Jiang W, Yang C. Phosphoketolase pathway for xylose catabolism in Clostridium acetobutylicum revealed by 13C metabolic flux analysis. Journal of Bacteriology. 2012;194(19):5413-22. Epub 2012/08/07. doi: 10.1128/jb.00713-12. PubMed PMID: 22865845; PMCID: PMC3457242. (*Co-first author)
Zhang L, Leyn SA, Gu Y, Jiang W, Rodionov DA, Yang C. Ribulokinase and transcriptional regulation of arabinose metabolism in Clostridium acetobutylicum. Journal of Bacteriology. 2012;194(5):1055-64. Epub 2011/12/24. doi: 10.1128/jb.06241-11. PubMed PMID: 22194461; PMCID: PMC3294803.
Gu Y, Li J, Zhang L, Chen J, Niu L, Yang Y, Yang S, Jiang W. Improvement of xylose utilization in Clostridium acetobutylicum via expression of the talA gene encoding transaldolase from Escherichia coli. Journal of Biotechnology. 2009;143(4):284-7. Epub 2009/08/22. doi: 10.1016/j.jbiotec.2009.08.009. PubMed PMID: 19695296.