Initially, Zhen Yang completed his PhD in Bioinformatics in 2011. He then worked for two year as Posdoc at the Institutes of Biomedical Sciences, Fudan University. In 2014, he joined the CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences. He then joined Fudan University in 2018. Now, he has taken up a Youth Associate Professor position. His broad research interests include Statistical Cancer Epigenomics, Network Biology and the application of bioinformatics to the analysis of complex multi-dimensional biological data. Specific areas of interest include systems biology of cancer and stem cells, microRNA and targets interaction, gene expression regulation, microbiome, as well as Epigenomics for early detection and risk prediction of cancer. He has published over 20 papers in peer-reviewed journals, including JAMA oncology, Nature Communications, Genome Biology, Nucleic Acids Research, EBioMedicine, Trends in Genetics, BMC Genomic. He is the recipient of numerous academic awards, such as the Fellow of Youth Innovation Promotion Association, CAS. He also got Research findings including the China Postdoctoral Science Foundation and Natural Science Foundation of China.
Fundings and Awards:
China Postdoctoral Science Foundation (ID: 2013M530178, 80,000 RMB)
National Natural Science Foundation of China Youth Fund Project (ID：31401120，2015-2018，240,000 RMB)
Member of the Youth Innovation Promotion Association of the Chinese Academy of Sciences (ID:2016252, 2016-2020, 800,000 RMB)
Sanofi - Outstanding Young Talent Award Fund of Shanghai Institutes for Life Sciences, Chinese Academy of Sciences (2017)
Major Research Program of the National Natural Science Foundation of China (ID: 91959106, 2020-2022, 800,000 RMB)
Program of Scientific Research Paradigm Reform and Subject Promotion by artificial intelligence, Shanghai Municipal Education Commission (ID: 24RGZNC02, 2024-2025, 200,000RMB)
Representative publications:
◎ Shaoying Zhu, Hui Yang Jun Liu, Qingsheng Fu, Wei Huang, Qi Chen, Andrew E. Teschendorff, Yungang He, Zhen Yang*, An improved reference library and method for accurate cell-type deconvolution of bulk-tissue miRNA data. Nature Communications (Accepted)
◎ Zhen Yang#*, Xiaocen Liu#, Hao Xu#, Andrew E Teschendorff, Lingjie Xu, Jingyi Li, Minjie Fu, Jun Liu, Hanyu Zhou, Yingying Wang, Licheng Zhang, Yungang He, Kun Lv*, Hui Yang*. Integrative analysis of genomic and epigenomic regulation reveals miRNA mediated tumor heterogeneity and immune evasion in lower grade glioma. Communications Biology. 2024 Jul 6;7(1):824.
◎ Zhen Yang*, Feng Xu, Andrew E. Teschendorff, Yi Zhao, Lei Yao, Jian Li, Yungang He. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Frontiers in Molecular Biosciences, 2022, 9: 1067406
◎ Feng Xu, Yifan Wang, Yunchao Ling, Chenfen Zhou, Haizhou Wang, Andrew E Teschendorff, Yi Zhao, Haitao Zhao, Yungang He*, Guoqing Zhang*, Zhen Yang*. dbDEMC 3.0: Functional exploration of differentially expressed miRNAs in cancers of human and model organisms. Genomics Proteomics Bioinformatics. 2022 May 25;S1672-0229(22)00068-7.
◎ Zhen Yang, Feng Xu, Aijuan Xue, Hong Lv, Yungang He*. Degree of Freedom of Gene Expression in Saccharomyces cerevisiae. Microbiology Spectrum. 2022 Apr 27;10(2):e0083821.
◎ Zhen Yang, Feng Xu, Hongdou Li, Yungang He*. Beyond samples: A metric revealing more connections of gut microbiota between individuals. Computational and Structural Biotechnology Journal. 2021 Jul 10;19:3930-3937.
◎ Zhen Yang*, Feng Xu, Haizhou Wang, Andrew E Teschendorff, Feng Xie, Yungang He*. Pan-cancer characterization of long non-coding RNA and DNA methylation mediated transcriptional dysregulation. EBioMedicine. 2021 Jun;68:103399.
◎ Xue Bai#, Xiaobo Yang#, Liangcai Wu#, Bangyou Zuo, Jianzhen Lin, Shanshan Wang, Jin Bian, Xinting Sang, Yungang He, Zhen Yang*, Haitao Zhao*. CMTTdb: the cancer molecular targeted therapy database. Annals of Translational Medicine, 2019 Nov;7(22):667.
◎ Zhenyu Bao#, Zhen Yang#, Zhou Huang, Yiran Zhou, Qinghua Cui*, Dong Dong*. LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Research. 2019 Jan 8;47(D1):D1034-D1037.
◎ Zhen Yang#, Liangcai Wu#, Anqiang Wang#, Wei Tang, Yi Zhao, Haitao Zhao*, Andrew E. Teschendorff*. dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers. Nucleic Acids Research. 2017 Jan 4;45(D1):D812-D818.
◎ Zhen Yang, Andrew Wong, Diana Kuh, Dirk S. Paul, Vardhman K. Rakyan, R. David Leslie, Shijie C. Zheng, Martin Widschwendter, Stephan Beck, Andrew E. Teschendorff*. Correlation of an epigenetic mitotic clock with cancer risk. Genome Biology. 2016 Oct 3;17(1):205.
◎ Zhen Yang, Allison Jones, Martin Widschwendter, Andrew E. Teschendorff*. An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer. Genome Biology. 2015 Jul 14;16:140.
◎ Andrew Teschendorff#, Zhen Yang#, Andrew Wong, Christodoulos P Pipinikas, Yinming Jiao, Allison Jones, Shahzia Anjum, Rebecca Hardy, Helga B Salvesen, Christina Thirlwell, Samuel M Janes, Diana Kuh, Martin Widschwendter*. Correlation of Smoking-Associated DNA Methylation Changes in Buccal Cells With DNA Methylation Changes in Epithelial Cancer. JAMA Oncology. 2015 Jul;1(4):476-85.
