Publications | The Dong Lab

2025

Shea A, Sun S, Kennedy J, Zhang L, Vijg J, Dong X. SomaMutDB 2.0: A comprehensive database for exploring somatic mutations and their functional impact in normal human tissues. Nucleic Acids Res. 2025. Epub 20251126. PMID: 41296554.

Pitcher LE, Mukherjee B, Saathoff AM, Eduvas ZA, Bartz J, Zhang X, Giorgadze N, Pirtskhalava T, Habib AA, LeBrasseur NK, Tchkonia T, Kirkland JL, Dong X, Burma S, Robbins PD. Space radiation induces distinct senescent phenotypes: Implications for space travel. NPJ Aging. 2025;11(1):95. Epub 20251127. PMID: 41309663; PMCID: PMC12660773.

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. Commun Biol. 2025;8(1):1450. Epub 20251009. PMID: 41068321; PMCID: PMC12511636.

Ren P, Zheng C, Pang Y, Qiang Y, Sun S, Wang Q, Xu W, Lee M, Lu Z, Zhou M, He J, Liu N, Maslov AY, Dong X, Zhang C, Gao J, Vijg J. Single-cell analysis of the somatic mutational landscape in human chondrocytes during aging and in osteoarthritis. Nat Aging. 2025;5(12):2417-31. Epub 20251117. PMID: 41249560; PMCID: PMC12705439.

Zhang L, Lee M, Hao X, Ma X, Xia C, Zhao Y, Ehlert J, Chi Z, Jin B, Cutler R, Maslov AY, Barabási AL, Hoeijmakers JHJ, Edelmann W, Vijg J, Dong X. Divergent accumulation patterns of SNVs and INDELs reveal negative selection in noncancerous cells. Innovation (Camb). 2025;6(10):101008. Epub 20250625. PMID: 41113919; PMCID: PMC12529607.

Das S, Ma X, Hailemariam K, Sierra-Pagan JE, Larson TA, Choi YG, Le AQ, Leonard RJ, Cho A, Sadek HA, Zhang JJ, Garry MG, Dong X, Gong W, Garry DJ. The pioneer factor, ETV2, regulates networks to specify the embryonic endothelial lineage. Cardiovasc Res. 2025;121(12):1883-97. PMID: 40832854.

Zhang T, Nunes A, O'Kelly R, Angelini L, Masternak MM, Suh Y, Dong X, Niedernhofer LJ, Robbins PD. Identification of miR-106b-5p as a senolytic miRNA. EBioMedicine. 2025;117:105810. Epub 20250618. PMID: 40554391; PMCID: PMC12219373.

Zhang T, Nunes ADC, Lee J, Larocca D, Camussi G, Lim SK, Bascones VU, Angelini L, O'Kelly RD, Dong X, Niedernhofer LJ, Robbins PD. Identification of Senomorphic miRNAs in Embryonic Progenitor and Adult Stem Cell-Derived Extracellular Vesicles. Aging Cell. 2025;24(7):e70071. Epub 20250424. PMID: 40275616; PMCID: PMC12266766.

Mahmud S, Zheng C, Santiago FE, Zhang L, Robbins PD, Dong X. A machine learning approach identifies cellular senescence on transcriptome data of human cells in vitro. Geroscience. 2025;47(3):5287-301. Epub 20241230. PMID: 39738795; PMCID: PMC12181610.

2024

Fredrickson G, Florczak K, Barrow F, Mahmud S, Dietsche K, Wang H, Parthiban P, Hakeem A, Almutlaq R, Adeyi O, Herman A, Bartolomucci A, Staley C, Dong X, Jahansouz C, Williams J, Mashek DG, Ikramuddin S, and Revelo XS. TREM2 macrophages mediate the beneficial effects of bariatric surgery against MASH. Hepatology 2024. PMID: 39292863.

Santiago FE, Adige T, Mahmud S, Dong X, Niedernhofer LJ, Robbins PD, miR-96-5p expression is sufficient to induce and maintain the senescent cell fate in the absence of stress. PNAS 2024 Oct;121(40):e2321182121. doi: 10.1073/pnas.2321182121.

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, De Cecco M, 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. Aging Biology. 2023 Jun 27;1,1-6. doi: 10.59368/agingbio.20230005.

Shea A, Bartz J, Zhang L, Dong X. Predicting mutational function using machine learning. Mutation Research. 2023 Mar 23;791:108457. doi: 10.1016/j.mrrev.2023.108457. Review. PMID: 36965820.

Bartz J, Jung H, Wasiluk K, Zhang L, Dong X. Progress in discovering transcriptional noise in aging. International Journal of Molecular Sciences. 2023 Feb 12;24(4):3701. doi: 10.3390/ijms24043701. Review. PMID: 36835113 PMCID: PMC9966367..

2022

Ren P, Dong X, Vijg J. Age-related somatic mutation burden in human tissues. Front Aging. 2022;3:1018119. doi: 10.3389/fragi.2022.1018119. eCollection 2022. PubMed PMID:36213345; PubMed Central PMCID: PMC9534562.

Soto-Palma C, Niedernhofer LJ, Faulk CD, Dong X. Epigenetics, DNA damage, and aging. J ClinInvest. 2022 Aug 15;132(16). doi: 10.1172/JCI158446. PubMed PMID: 35968782; PubMed Central PMCID: PMC9374376.

Huang Z, Sun S, Lee M, Maslov AY, Shi M, Waldman S, Marsh A, Siddiqui T, Dong X, Peter Y, Sadoughi A, Shah C, Ye K, Spivack SD, Vijg J. Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking. Nat Genet. 2022 Apr;54(4):492-498. doi: 10.1038/s41588-022-01035-w. Epub 2022 Apr 11. PubMed PMID: 35410377.

Maslov AY, Makhortov S, Sun S, Heid J, Dong X, Lee M, Vijg J. Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing. Sci Adv. 2022 Apr 8;8(14):eabm3259. doi: 10.1126/sciadv.abm3259. Epub 2022 Apr 8. PubMed PMID: 35394831; PubMed Central PMCID: PMC8993124.

Sun S, Wang Y, Maslov AY, Dong X, Vijg J. SomaMutDB: a database of somatic mutations in normal human tissues. Nucleic Acids Res. 2022 Jan 7;50(D1):D1100-D1108. doi:10.1093/nar/gkab914. PubMed PMID: 34634815; PubMed Central PMCID: PMC8728264.

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. Epub 2021 Oct 27. PMID: 34705500.

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 May 21:e13357. doi: 10.1111/acel.13357. Epub ahead of print. PMID: 34018656.

Olcha M, Dong X, Feil H, Hao X, Lee M, Jindal S, Buyuk E, Vijg J. A workflow for simultaneous DNA copy number and methylome analysis of inner cell mass and trophectoderm cells from human blastocysts. Fertility and Sterility. 2021 Feb 12:S0015-0282(20)32675-3. doi: 10.1016/j.fertnstert.2020.11.007. PubMed PMID: 33589136. PMCID: PMC7701142.

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. Frontiers in Genetics. 2020 Nov 16;11:505441. doi: 10.3389/fgene.2020.505441. PubMed PMID: 33304377; PMCID: PMC7701142.

Vijg J, Dong X. Pathogenic mechanisms of somatic mutation and genome mosaicism in aging. Cell. 2020;182(1):12-23. Epub 2020/07/11. doi: 10.1016/j.cell.2020.06.024. PubMed PMID: 32649873; PMCID: PMC7354350.

Brazhnik K, Sun S, Alani O, Kinkhabwala M, Wolkoff AW, Maslov AY, Dong X, Vijg J. Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver. Science Advances. 2020;6(5):eaax2659. doi: 10.1126/sciadv.aax2659. PubMed PMID: 32064334; PMCID: PMC6994209.

View all PubMed publications
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.

Chen K, Luan X, Liu Q, Wang J, Chang X, Snijders AM, Mao JH, Secombe J, Dan Z, Chen JH, Wang Z, Dong X, Qiu C, Chang X, Zhang D, Celniker SE, Liu X. Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance. Cell Host Microbe. 2019 Apr 10;25(4):537-552.e8. doi: 10.1016/j.chom.2019.02.003. PubMed PMID: 30902578.

2018

Liu Z, Dong X, Li Y. A genome-wide study of allele-specific expression in colorectal cancer. Frontiers in Genetics.2018 Nov 27;9:570. doi: 10.3389/fgene.2018.00570. PubMed PMID: 30538721; PMCID: PMC6277598.

Quispe-Tintaya W, Lee M, Dong X, Weiser DA, Vijg J, Maslov AY. Bleomycin-induced genome structural variations in normal, non-tumor cells. Scientific Reports. 2018;8(1):16523. doi: 10.1038/s41598-018-34580-8. PubMed PMID: 30410071; PMCID: PMC6224559.

Maggi EC, Gravina S, Cheng H, Piperdi B, Yuan Z, Dong X, Libutti SK, Vijg J, Montagna C. Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model. Frontiers in Genetics. 2018;9(6):6. doi: 10.3389/fgene.2018.00006. PubMed PMID: 29410677; PMCID: PMC5787102.

Dong X, Shi M, Lee M, Toro R, Gravina S, Han W, Yasuda S, Wang T, Zhang Z, Vijg J, Suh Y, Spivack SD. Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung. Epigenetics. 2018;13(3):264-74. Epub 2018/02/22. doi: 10.1080/15592294.2018.1441650. PubMed PMID: 29465290.

Milholland B, Dong X, Vijg J. The shortness of human life constitutes its limit. arXiv. 2018. arXiv:1803.04024

Vijg J, Gravina S, Dong X. Chapter 9 - Intratissue DNA Methylation Heterogeneity in Aging A2 - Moskalev, Alexey. In: Vaiserman AM, editor. Epigenetics of Aging and Longevity. Boston: Academic Press; 2018. p. 201-9.

2017

Yu B, Dong X, Gravina S, Kartal O, Schimmel T, Cohen J, Tortoriello D, Zody R, Hawkins RD, Vijg J. Genome-wide, Single-Cell DNA Methylomics Reveals Increased Non-CpG Methylation during Human Oocyte Maturation. Stem Cell Reports. 2017;9(1):397-407. Epub 2017/06/27. doi: 10.1016/j.stemcr.2017.05.026. PubMed PMID: 28648898; PMCID: PMC5511109.

Wiley CD, Flynn JM, Morrissey C, Lebofsky R, Shuga J, Dong X, Unger MA, Vijg J, Melov S, Campisi J. Analysis of individual cells identifies cell-to-cell variability following induction of cellular senescence. Aging Cell. 2017;16(5):1043-50. Epub 2017/07/13. doi: 10.1111/acel.12632. PubMed PMID: 28699239; PMCID: PMC5595671.

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.

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.

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.

Dong X, Vijg J. Ageing: Biomarkers get physical. Nature Biomedical Engineering. 2017;1(7):s41551-017-0102.

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.

Milholland B, Dong X, Vijg J. "Best-Guess" MRAD Provides Robust Evidence for a Limit to Human Lifespan: Reply to de Grey (Rejuvenation Res. 2017;20:261-262). Rejuvenation Research. 2017;20(5):437-40. Epub 2017/10/07. doi: 10.1089/rej.2017.2008. PubMed PMID: 28982266.

2016

Liu Z, Gui T, Wang Z, Li H, Fu Y, Dong X, Li Y. cisASE: a likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data. Bioinformatics. 2016;32(21):3291-7. Epub 2016/07/15. doi: 10.1093/bioinformatics/btw416. PubMed PMID: 27412088.

Gravina S, Dong X, Yu B, Vijg J. Single-cell genome-wide bisulfite sequencing uncovers extensive heterogeneity in the mouse liver methylome. Genome Biology. 2016;17(1):150. Epub 2016/07/07. doi: 10.1186/s13059-016-1011-3. PubMed PMID: 27380908; PMCID: PMC4934005.

Dong X, Milholland B, Vijg J. Evidence for a limit to human lifespan. Nature. 2016;538(7624):257-9. doi: 10.1038/nature19793. PubMed PMID: 27706136.

2015

Johnson SC, Dong X, Vijg J, Suh Y. Genetic evidence for common pathways in human age-related diseases. Aging Cell. 2015;14(5):809-17. Epub 2015/06/17. doi: 10.1111/acel.12362. PubMed PMID: 26077337; PMCID: PMC4568968.

Gui T, Dong X, Li R, Li Y, Wang Z. Identification of hepatocellular carcinoma-related genes with a machine learning and network analysis. Journal of Computational Biology. 2015;22(1):63-71. Epub 2014/09/24. doi: 10.1089/cmb.2014.0122. PubMed PMID: 25247452.

2014

Liu Z, Zheng G, Dong X, Wang Z, Ying B, Zhong Y, Li Y. Investigating co-evolution of functionally associated phosphosites in human. Molecular Genetics and Genomics. 2014;289(6):1217-23. Epub 2014/07/10. doi: 10.1007/s00438-014-0881-x. PubMed PMID: 25005854.

Liu Z, Yang J, Xu H, Li C, Wang Z, Li Y, Dong X, Li Y. Comparing computational methods for identification of allele-specific expression based on next generation sequencing data. Genetic Epidemiology. 2014;38(7):591-8. Epub 2014/09/04. doi: 10.1002/gepi.21846. PubMed PMID: 25183311.

Li R, Dong X, Ma C, Liu L. Computational identification of surrogate genes for prostate cancer phases using machine learning and molecular network analysis. Theoretical Biology and Medical Modelling. 2014;11:37. Epub 2014/08/26. doi: 10.1186/1742-4682-11-37. PubMed PMID: 25151146; PMCID: PMC4159107.

Li C, Dong X, Fan H, Wang C, Ding G, Li Y. The 3DGD: a database of genome 3D structure. Bioinformatics.2014;30(11):1640-2. Epub 2014/02/15. doi: 10.1093/bioinformatics/btu081. PubMed PMID: 24526713.

2013

Xu T, Holzapfel C, Dong X, Bader E, Yu Z, Prehn C, Perstorfer K, Jaremek M, Roemisch-Margl W, Rathmann W, Li Y, Wichmann HE, Wallaschofski H, Ladwig KH, Theis F, Suhre K, Adamski J, Illig T, Peters A, Wang-Sattler R. Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study. BMC Medicine. 2013;11:60. Epub 2013/03/19. doi: 10.1186/1741-7015-11-60. PubMed PMID: 23497222; PMCID: PMC3653729.

Ma C, Dong X, Li R, Liu L. A computational study identifies HIV progression-related genes using mRMR and shortest path tracing. PloS One. 2013;8(11):e78057. Epub 2013/11/19. doi: 10.1371/journal.pone.0078057. PubMed PMID: 24244287; PMCID: PMC3823927.

Li H, Gan W, Lu L, Dong X, Han X, Hu C, Yang Z, Sun L, Bao W, Li P, He M, Sun L, Wang Y, Zhu J, Ning Q, Tang Y, Zhang R, Wen J, Wang D, Zhu X, Guo K, Zuo X, Guo X, Yang H, Zhou X, Consortium D, Consortium A-TD, Zhang X, Qi L, Loos RJ, Hu FB, Wu T, Liu Y, Liu L, Yang Z, Hu R, Jia W, Ji L, Li Y, Lin X. A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans. Diabetes. 2013;62(1):291-8. Epub 2012/09/11. doi: 10.2337/db12-0454. PubMed PMID: 22961080; PMCID: PMC3526061.

Dong X, Zhong T, Xu T, Xia Y, Li B, Li C, Yuan L, Ding G, Li Y. Evaluating coverage of exons by HapMap SNPs. Genomics. 2013;101(1):20-3. Epub 2012/09/25. doi: 10.1016/j.ygeno.2012.09.003. PubMed PMID: 23000193.

Dai Y, Li S, Dong X, Sun H, Li C, Liu Z, Ying B, Ding G, Li Y. The de novo sequence origin of two long non-coding genes from an inter-genic region. BMC Genomics. 2013;14 Suppl 8:S6. Epub 2014/02/26. doi: 10.1186/1471-2164-14-S8-S6. PubMed PMID: 24564579; PMCID: PMC4042238.

2012

Dong X, Chinese translation of a chapter in Understanding Bioinformatics, Chinese Edition, Zvelebil M and Baum JO, Science Press; 2012, ISBN: 9787030328328

2011

Huang T, Zhang J, Xie L, Dong X, Zhang L, Cai YD, Li YX. Crosstissue coexpression network of aging. Omics.2011;15(10):665-71. Epub 2011/07/15. doi: 10.1089/omi.2011.0034. PubMed PMID: 21751870.

2010

Wang Z, Dong X, Ding G, Li Y. Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes. Genetics, Selection, Evolution. 2010;42:24. Epub 2010/06/30. doi: 10.1186/1297-9686-42-24. PubMed PMID: 20584267; PMCID: PMC2902415.

Huang T, Wang P, Ye ZQ, Xu H, He Z, Feng KY, Hu L, Cui W, Wang K, Dong X, Xie L, Kong X, Cai YD, Li Y. Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties. PloS One.2010;5(7):e11900. Epub 2010/08/07. doi: 10.1371/journal.pone.0011900. PubMed PMID: 20689580; PMCID: PMC2912763.

Dong X, Li C, Chen Y, Ding G, Li Y. Human transcriptional interactome of chromatin contribute to gene co-expression. BMC Genomics. 2010;11:704. Epub 2010/12/16. doi: 10.1186/1471-2164-11-704. PubMed PMID: 21156067; PMCID: PMC3053592.