Xiao Dong, Ph.D.

Associate.

 

Email: xiao.dong at einstein.yu.edu

 

 

Education and Training

 

Postdoctoral    Albert Einstein College of Medicine, USA, 2013 - present

 

Ph.D.               University of Chinese Academy of Sciences, China 2013

 

Honors B.S.    Zhejiang University, China 2008

 

 

Honors and Awards

 

2018   NIH K99 Career Development Award

 

 

Research interests

 

Dr. Dong develops computational methodologies to discover DNA mutation and epigenetic variations from a single cell, and tests computationally the hypothesis that accumulation of (epi) mutation in normal somatic cells is a cause of aging. He also studies genetics and epigenetics of human aging and age-related diseases, as well as the epidemiology of human lifespan.

 

 

Publications

 

Preprint Original Research

 

  1. Dong X, Zhang L, Brazhnik K, Lee M, Hao X, Maslov AY, Zhang Z, Wang T, Vijg J. Spontaneous retrotranspositions in normal tissues are rare and associated with cell-type-specific differentiation. bioRxiv. 2019. doi: https://doi.org/10.1101/536896.

  2. 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. bioRxiv. 2019. doi: https://doi.org/10.1101/535807.

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

 

Peer-Reviewed Original Research

 

  1. 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. Proceedings of the National Academy of Sciences. 2019; 116 (18), 9014-901. (*Co-first author)

  2. Liu Z, Dong X#, Li Y. A genome-wide study of allele-specific expression in colorectal cancer. Front Genet. 2018 Nov 27;9:570. doi: 10.3389/fgene.2018.00570. PubMed PMID: 30538721; PMCID: PMC6277598. (#Co-corresponding author)

  3. 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.

  4. 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. Front Genet. 2018;9(6):6. doi: 10.3389/fgene.2018.00006. PubMed PMID: 29410677; PMCID: PMC5787102.

  5. 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.

  6. 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. (*Co-first author)

  7. 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.

  8. 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)

  9. 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.

  10. 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. (#Co-corresponding author)

  11. 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. (*Co-first author)

  12. 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.

  13. 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. (*Co-first author)

  14. 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. (*Co-first author)

  15. 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.

  16. 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. (#Co-corresponding author)

  17. 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. (*Co-first author)

  18. 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. (*Co-first author)

  19. 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.

  20. 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. (*Co-first author)

  21. 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. (*Co-first author)

  22. 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.

  23. 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.

  24. 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.

  25. 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.

  26. 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.

  27. 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.

 

Chapters, Books, Opinions and Reviews:

 

  1. 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.

  2. 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.

  3. 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.

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

  5. Dong X, Milholland B, Vijg J. Dong et al. reply to "Contesting the evidence for limited human lifespan". Nature. 2017;546(7660):E7. doi: 10.1038/nature22785. PubMed PMID: 28658231.

  6. Dong X, Milholland B, Vijg J. Dong et al. reply to "Many possible maximum lifespan trajectories". Nature. 2017;546(7660):E9-E10. doi: 10.1038/nature22787. PubMed PMID: 28658240.

  7. Dong X, Milholland B, Vijg J. Dong et al. reply to "Is there evidence for a limit to human lifespan?". Nature. 2017;546(7660):E12. doi: 10.1038/nature22789. PubMed PMID: 28658233.

  8. Dong X, Milholland B, Vijg J. Dong et al. reply to "Questionable evidence for a limit to human lifespan". Nature. 2017;546(7660):E14-E5. doi: 10.1038/nature22791. PubMed PMID: 28658219.

  9. Dong X, Milholland B, Vijg J. Dong et al. reply to "Maximum human lifespan may increase to 125 years". Nature. 2017;546(7660):E21. doi: 10.1038/nature22793. PubMed PMID: 28658215.

  10. 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.

 

 

Software developed

 

 

 

Database developed

 

  • 3DGD: a database of genome 3D structure. Li C, et al., Bioinformatics 2014. http://3dgd.biosino.org (Website no longer available)

 

Copyright © 2019 Vijg Lab.