Dake Zhang, Ph.D. in Genetics, Associate Professor of Biomedical Engineering Advanced Innovation Center, Beihang University, Member of Youth Innovation Promotion Association, Chinese Academy of Sciences. 

Professional experience

2022/01-, Associate Professor, School of Engineering Medicine, Beihang University

2020/04-, Associate Professor, Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University

2012/01-2020/03            Associate Professor (Project), Beijing Institute of Genomics, Chinese Academy of Sciences.

2014/12-2015/12 Visiting Scholar, Department of Molecular and Human Genetics, Baylor College of Medicine

2009/07-2012/01            Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences.

2023/3-Pres, Associate Editor, BMC Medicine, Oncology Section

2022/10-Pres, Associate Editor, Heliyon, Cell Press, Genetic Section

2021/01-Pres, Section Editor, Medicine in Novel Technology and Devices

2021/08-2023/08, Young Editor, The Innovation

2021/01-2022/12, Early Career Editor, Journal of Clinical and Translational Hepatology

2020/02-Pres, Review Editor, Frontiers of Oncology / Frontiers in Bioinformatics / Frontiers in Drug Discovery

Education

2004/09-2009/06 Ph.D. Genetics, Beijing Institute of Genomics, Chinese Academy of Sciences.

Publications

 

1.       Fan H, Song L, Fan J, Ma J, Li X, Zhang J, Hu J, Wu Z, Zhang D$, Wang L$. Decoding meningioma heterogeneity and neoplastic cell-macrophage interaction through single-cell transcriptome profiling across pathological grades. J Transl Med. 2023 Oct 25;21(1):751.

2.       Zhang F, Zhang X, Zhang H, Lin D, Fan H, Guo S, An F, Zhao Y, Li J$, Schrodi SJ$, Zhang D$. Pan-precancer and cancer DNA methylation profiles revealed significant tissue specificity of interrupted biological processes in tumorigenesis. Epigenetics. 2023 Dec 31;18(1):2231222.

3.       Li X, Fan H, Song X, Song B, Liu W, Dong R, Zhang H, Guo S, Liang H, Schrodi SJ, Fu X, Kaushal S, Ren Y$, Zhang D$. DNA methylome and transcriptome profiling reveal key electrophysiology and immune dysregulation in hypertrophic cardiomyopathy. Epigenetics. 2023;18(1):2195307.

4.       Zhang H, Dong P, Fan H, Liang H, Zhang K, Zhao Y, Guo S, Schrodi SJ, Fan Y$, Zhang D$. Gene body hypomethylation of pyroptosis-related genes NLRP7, NLRP2, and NLRP3 facilitate non-invasive surveillance of hepatocellular carcinoma. Functional & Integrative Genomics. 2023 Jun;23(2):198.

5.       Luo M, Zhang D, Tian C, Sun B, Huang T, Zhang H, Shi Y, Gao YZ, Luo R, Zhu JK. The Innovation Life: An international journal of life sciences. The Innovation Life. 2023 May 28;1(1):100001-.

6.       Guo S, Zhang D, Wang H, An Q, Yu G, Han J, Jiang C, Huang J. Editorial: Computational and systematic analysis of multi-omics data for drug discovery and development. Front Med (Lausanne). 2023 Feb 21;10:1146896.

7.       Jin F, Liu M, Zhang D^$, Wang X^$. Translational perspective on bone-derived cytokines in inter-organ communications. The Innovation 2023;4.

8.       Zhang M, Zhang H, Cheng X, Wang X, Xu H, Gao X, Wu R, Zhang D^$, Xia Y^$ and Niu J^$. Liver biopsy of chronic hepatitis B patients indicates HBV integration profile may complicate the endpoint and effect of entecavir treatment. Antiviral Research 2022, 204, p.105363.

9.       Wen L, Li G, Huang T, Geng W, Pei H, Yang J, Zhu M, Zhang P, Hou R, Tian G, Su W, Chen J, Zhang D, Zhu P, Zhang W, Zhang X, Zhang N, Zhao Y, Cao X, Peng G, Ren X, Jiang N, Tian C, Chen Z-J. Single-cell technologies: From research to application. The Innovation 2022, 3(6): 100342.

10.     Hong Y*, Zhang D*, Zhou X*, Chen A*, Abliz A*, Ba J, Wang L, Hu Q, Gong K, Guan X, Liu M, Zheng X, Lai S, Qu H, Zhao F, Hao S, Wu Z, Cai H, Hu S, Ma Y, Zhang J, Ke Y, Wang Q-F, Chen W, Zeng C. Common Postzygotic Mutational Signatures in Healthy Adult Tissues Related to Embryonic Hypoxia. Genomics, Proteomics & Bioinformatics 2022, 20(1): 177-191.

11.     Wu, D., Liu, Y., Chen, W., Shao, J., Zhuoma, P., Zhao, D., Yu, Y., Liu, T., Yu, R., Gan, Y. and Yuzheng, B. How placenta promotes the successful reproduction in high-altitude populations: a transcriptome comparison between adaptation and acclimatization. Molecular Biology and Evolution 2022, 39(6), p.msac120.

12.     Deng L, Xu J, Chen W, Guo S, Steiner RD, Chen Q, Cheng Z, Xu Y, Yao B, Li X, Wang X, Deng K, Schrodi SJ, Zhang D^$, Xin H^$. Remediation of ABCG5-Linked Macrothrombocytopenia With Ezetimibe Therapy. Front Genet 2021, 12: 769699.

13.     Xie, S., Leung, A.W.S., Zheng, Z., Zhang, D., Xiao, C., Luo, R., Luo, M. and Zhang, S. Applications and potentials of nanopore sequencing in the (epi) genome and (epi) transcriptome era. The Innovation 2021, 2(4), p.100153.

14.     Zhang D^$, Guo S, Schrodi SJ^$. Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties. International Journal of Molecular Sciences. 2021; 22(18)

15.     Zhang D^$, Zhang K, Protzer U, Zeng C. HBV Integration Induces Complex Interactions between Host and Viral Genomic Functions at the Insertion Site. J Clin Transl Hepatol 2021, 9(3): 399-408.

16.     Wang L, Guan X, Hu Q, Wu Z, Chen W, Song L, Wang K, Tian K, Cao C, Zhang D, Ma J, Tong X, Zhang B, Zhang J, Zeng C. TGFB3 downregulation causing chordomagenesis and its tumor suppression role maintained by Smad7. Carcinogenesis 2021, 42(7): 913-923.

17.     Zhang H, Dong P, Guo S, Tao C, Chen W, Zhao W, Wang J, Cheung R, Villanueva A, Fan J, Ding H, Schrodi S. J, Zhang D^$ and Zeng C^$. Hypomethylation in HBV integration regions aids non-invasive surveillance to hepatocellular carcinoma by low-pass genome-wide bisulfite sequencing. BMC Med.2020;18(1):200.

18.     Chen W*, Zhang K*, Dong P*, Fanning G, Tao C, Zhang H, Guo S, Wang Z, Hong Y, Yang X, Lai S, Ding H, Zhao H, Zeng C^$, Protzer U^$, Zhang D^$. Noninvasive chimeric DNA profiling identifies tumor-originated HBV integrants contributing to viral antigen expression in liver cancer. Hepatol Int.2020;14(3):326-337.

19.     Fan J, Li J, Guo S, Tao C, Zhang H, Wang W, Zhang Y, Zhang D^$, Ding S^$ and Zeng C^$.Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma.Clin Epigenetics.2020;12(1):56.

20.     Ma J*, Hong Y*, Chen W, Li D, Tian K, Wang K, Yang Y, Zhang Y, Chen Y, Song L, Chen L, Zhang L, Du J, Zhang J, Wu Z^$, Zhang D^$ and Wang L^$. High Copy-Number Variation Burdens in Cranial Meningiomas From Patients With Diverse Clinical Phenotypes Characterized by Hot Genomic Structure Changes. Front Oncol.2020;10.1382.

21.     Zhao F*, Zhang D*, Zhou Q, Zhao F, He M, Yang Z, Su Y, Zhai Y, Yan J, Zhang G, Xue A, Tang J, Han X, Shi Y, Zhu Y, Liu T, Zhuang W, Huang L, Hong Y, Wu D, Li Y, Lu Q, Chen W, Jiao S, Wang Q, Srinivasalu N, Wen Y, Zeng C, Qu J^$ and Zhou X^$. Scleral HIF-1alpha is a prominent regulatory candidate for genetic and environmental interactions in human myopia pathogenesis. EBioMedicine. 2020;57.102878.

22.     Zhao F*, Zhang D*, Ge C, Zhang L, Reinach P. S, Tian X, Tao C, Zhao Z, Zhao C, Fu W, Zeng C and Chen W. Metagenomic Profiling of Ocular Surface Microbiome Changes in Meibomian Gland Dysfunction. Invest Ophthalmol Vis Sci.2020;61(8):22.

23.     Liu S*, Hong Y *, Cui K, Guan J, Han L, Chen W, Xu Z, Gong K, Ou Y, Zeng C, Li S, Zhang D^$, Hu D^$. Four-Generation Pedigree of Monozygotic Female Twins to Reveal Genetic Factors in Twinning Process by Whole-Genome Sequencing. Twin Res Hum Genet 2018, 1-8.

24.     Zhang H*, Zhao F*, Hutchinson D*, Sun W, Ajami N, Lai S, Wong M, Petrosino JF, Fang J, Jiang J, Chen W, Reinach P, Qu J, Zeng C, Zhang D^$, and Zhou X^$. Conjunctival Microbiome Changes Associated With Soft Contact Lens and Orthokeratology Lens Wearing Conjunctival Microbiome in Contact Lens Wearers. Invest Ophthalmol Vis Sci, 2017, 58(1): 128-136.

25.     Li F*, Zhang D*^,$, Li Y, Jiang D, Luo S, Du N, Chen W, Deng L, Zeng C^$. Whole genome characterization of hepatitis B virus quasispecies with massively parallel pyrosequencing. Clin Microbiol Infect. Epub 2014 Oct 29.

26.     Zhang D*, Du N*, Ma S*, Hu Q, Lu G, Chen W, Zeng C^$ In vitro Transcriptome Analysis of Two Chinese Isolates of Streptococcus suis Serotype 2. Genomics, Proteomics & Bioinformatics. 2014 pii: S1672-0229(14)00134-X.

27.     Lin Z*, Gong K*, Pang B, Zeng C, Zhang D^$. Birt-hogg-dubé syndrome with clear cell renal cell carcinoma in a Chinese family. Internal medicine (Tokyo, Japan) 2014, 53 (24), 2825.

28.     Xu Z, Wu G, Li F, Bai J, Xing W, Zhang D^$, Zeng C^$. Positive selection signals of hepatitis B virus and their association with disease stages and viral genotypes. Infect Genet Evol 2013, 19C:176-187.

29.     Zhang D*, Dong P*, Zhang K, Deng L, Bach C, Chen W, Li F, Protzer U, Ding H, Zeng C. Whole genome HBV deletion profiles and the accumulation of preS deletion mutant during antiviral treatment. BMC Microbiology 2012, 12:307.

30.     Zhang D*, Ma S*, Zhang X*, Zhao H, Ding H, Zeng C. Prevalent HBV point mutations and mutation combinations at BCP/preC region and their association with liver disease progression. BMC Infect Dis 2010, 10:271.

31.     Deng L, Tang X, Chen W, Lin J, Lai Z, Liu Z, Zhang D^$: Scanning for genomic regions subject to selective sweeps using SNP-MaP strategy. Genomics Proteomics Bioinformatics 2010, 8(4):256-261.

32.     Zhang D*, Chen J, Deng L, et al. Evolutionary selection associated with the multi-function of overlapping genes in the hepatitis B virus. Infect Genet Evol. Jan 2010;10(1):84-88.

33.     Deng L, Tang X, Chen W, Lin J, Lai Z, Liu Z, Zhang D^$. Scanning for Genomic Regions Subject to Selective Sweeps Using SNP-MaP Strategy. Genomics Proteomics Bioinformatics. 2010 Dec; 8(4): 256-261.

34.     Li, Y, Xia, Y, Han, M, Chen, G, Zhang, D, Thasler, W.E, Protzer, U, and Ning, Q. 2017. IFN-alpha-mediated Base Excision Repair Pathway Correlates with Antiviral Response Against Hepatitis B Virus Infection. Scientific Reports. 7, 12715.

35.     Hu J, Xu Y, Li C, Hao J, Peng S, Chu X, Zhang D, Xu D, Meng S$. A cross-talk between Hepatitis B virus and host mRNAs confers viral adaptation to liver. Scientific Reports. 2015 Jul 17;5:10572.

36.     Xia H, Hu C, Zhang D, S Tang S, Zhang Z, Kou Z, Fan Z, Bente D, Zeng C, Li T. Metagenomic Profile of the Viral Communities in Rhipicephalus spp. Ticks from Yunnan, China. PloS One 2015 10 (3), e0121609.

37.     Tang X, Deng L, Zhang D, Lin J, Wei Y, Zhou Q, Li X, Li G, Liang S. Gene2DGE: A Perl Package for Gene Model Renewal with Digital Gene Expression Data. Genomics Proteomics Bioinformatics 2012, 10(1):51-54.

38.     Tang H, Yao Y, Zhang D, Meng X, Wang L, Yu H, Ma L, Xu P. A Novel NADH-dependent and FAD-containing Hydroxylase Is Crucial for Nicotine Degradation by Pseudomonas putida. J Biol Chem 2011, 286(45):39179-39187.

39.     Deng L, Zhang D, Richards E, et al. Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes. J Genet Genomics. Dec 2009;36 (12):703-709.

40.     Tang H, Wang S, Ma L, Meng X, Deng Z, Zhang D, Ma C, Xu P. A novel gene, encoding 6-hydroxy-3-succinoylpyridine hydroxylase, involved in nicotine degradation by Pseudomonas putida strain S16. Appl Environ Microbiol 2008, 74(5):1567-1574.