bigdataage
Yong Peng's CV
1. About Me
Full Name: Yong Peng (彭勇)
Gender: Man
Marital status: Married
Place of Birth: Yibin of Sichuan Province, P. R. China.
Citizenship: China
Email: yongp@outlook.com
GitHub: https://github.com/CTLife
ORCID: https://orcid.org/0000-0003-3405-8836
2. Research Interests
The epitranscriptome and epigenome play crucial roles for precisely regulating the spatiotemporal specificity of gene expression. My research mainly focuses on the crosstalk between epitranscriptome and epigenome in aging and age-related diseases as well as its application in traditional Chinese medicine (TCM):
(1) Develop and use a combination of experimental and computational multi-omics methods to discover the mechanisms of epitranscriptome-epigenome crosstalk, such as crosstalk among RNA m6A/Ψ/m5C, DNA 5mC/5hmC and histone modifications, as well as their functions in aging and age-related diseases.
(2) Discover Chinese herbal medicines or medicinal natural products how to delay aging and increase longevity through epigenetic mechanisms and correct epitranscriptome-epigenome crosstalk disorders in aging and age-related diseases.
(3) Large-scale plant multi-omics data analysis for medicinal natural products discovery and biosynthesis to facilitate rapid discovery of unknown metabolic pathways/enzymes for the production of new bioactive compounds.
(4) Develop novel methods of liquid biopsy based on integration of cell-free multi-omics signals to provide molecular basis for the concept of evidence-based medicine and the characteristics of precision medicine in TCM.
3. Experience
2025.07~now, Associate Professor, Innovative Institute of Chinese Medicine and Pharmacy, Institute of Herbgenomics @ Chengdu University of Traditional Chinese Medicine , Chengdu, China.
2025.02~2025.04, Assistant Researcher, Cancer Research Center @ Fudan University , Shanghai, China.
2020.01~2025.01, Postdoctoral Researcher, Chuan He Group @ Department of Chemistry, and Mengjie Chen Group @ Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
2019.02~2019.11, Jie Qiao Group @ Peking University Third Hospital, Beijing, China.
4. Education
Ph. D., 2013.09~2019.01, Integrative Life Sciences, Peking-Tsinghua Center for Life Sciences and AAIS @ Peking University, Beijing, China. (2013.07-2013.12 Rotation; 2014.01-2017.04 Aibin He Lab; 2017.05-2019.01 Jie Qiao Lab)
M. Sc., 2010.09~2013.06, Physics, School of Physical Science and Technology @ Inner Mongolia University, Hohhot, China.
B. Sc., 2006.09~2010.06, Biotechnology, School of Life Sciences @ Heilongjiang University, Haerbin, China.
PhD. Dissertation (Chinese): Epigenetic Outcomes of Assisted Reproduction in the Offspring. @ Jie Qiao Group .
M. Sc. thesis (Chinese):Predicting subnuclear location of proteins and subcellular location of ncRNAs based on multi-information fusion and multi-label ensemble classifier. @ Qianzhong Li Group .
B. Sc. thesis (Chinese): Optimize the nitrogen sources of a red pigment-producing strain for generating more pigments. @ Tao Jin Group .
5. Peer Reviewed Publications and Submitted Manuscripts
(#) First authorship; (*) Senior authorship
Selected publications:
[8] Andrew Shafik#*, Yong Peng#, Zijie Zhang, Chen Chang, Pingluan Wang, Junghwa Lim, Hongjun Song, Chuan He, Mengjie Chen* & Peng Jin*. 2025. Multi-region m6A epitranscriptome profiling of the human brain reveals both spatial and temporal signatures and an association with disease-risk genes. Nature Neuroscience. PMID: 41366183
[7] Xiao Jiang#, Chu Xu#, Enzhuo Yang#, Danhua Xu#, Yong Peng#, Zhuo Liu, Qinxin Shao, Xue Han, Qiuxiao Chen, Weizhi He, Shuang He, Yanhui Xu, Chuan He, Xinxin Huang* & Lulu Hu*. 2025. Deciphering the RNA Landscapes on Mammalian Cell Surfaces. Protein & Cell. PMID: 40973153
[6] Yong Peng#, Jason Karpus#, Jyoti D. Patel, Everett E. Vokes, Marina Chiara Garassino, Zhou Zhang, Wei Zhang, Mengjie Chen, Chuan He*, Christine M. Bestvina*. 2025. Epigenomic exploration of disease status of EGFR-mutated non-small cell lung cancer using plasma cell-free DNA hydroxymethylomes. Cancer Communications, 45(1):51-55. PMID: 39527101
[5] Yong Peng#, Hanzhe Meng#, Ruiqi Ge#, Shun Liu#, Mengjie Chen, Chuan He* & Lulu Hu*. 2022. Detection of m6A RNA modifications at single-nucleotide resolution using m6A-selective allyl chemical labeling and sequencing. STAR Protocols, 3(4), 101677. PMID: 36112507
[4] Lulu Hu#, Shun Liu#, Yong Peng#, Ruiqi Ge#, Rui Su#, Chamara Senevirathne, Bryan T. Harada, Qing Dai, Jiangbo Wei, Lisheng Zhang, Ziyang Hao, Liangzhi Luo, Huanyu Wang, Yuru Wang, Minkui Luo, Mengjie Chen*, Jianjun Chen* & Chuan He*. 2022. m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nature Biotechnology. PMID: 35288668
[3] Siming Kong#, Yong Peng#, Wei Chen#, Xinyi Ma,Yuan Wei, Yangyu Zhao, Rong Li, Jie Qiao*, Liying Yan*. 2020. Epigenetic Consequences of Hormonal Interactions between Opposite-sex Twin Fetuses. Clinical and Translational Medicine, 10(8): e234. PMID: 33377650
[2] Wei Chen#, Yong Peng#, Xinyi Ma#, Siming Kong, Shuangyan Tan,Yuan Wei,Yangyu Zhao, Wenxin Zhang, Yang Wang*, Liying Yan*, Jie Qiao*. 2020. Integrated Multi-omics Reveal Epigenomic Disturbance of Assisted Reproductive Technologies in Human Offspring. eBioMedicine, 61, 103076. PMID:33099088
[1] Shanshan Ai#, Yong Peng#, Chen Li, Fei Gu, Xianhong Yu, Yanzhu Yue, Qing Ma, Jinghai Chen, Zhiqiang Lin, Pingzhu Zhou, Huafeng Xie, Terence W Prendiville, Wen Zheng,Yuli Liu, Stuart H Orkin, Da-Zhi Wang, Jia Yu,William T Pu*, Aibin He*. 2017. EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent. eLife, 6:e24570. PMID:28394251
Other publications:
[13]. Alex Wardale, Yong Peng, Ruiqi Ge, Tor Erik Jørgensen, Steinar Daae Johansen, Chuan He & Igor Babiak. 2025. Single-nucleotide resolution mapping of m6A of zebrafish mRNAs in early embryonic development links m6A modifications to the maternal-to-zygotic transition. Communications biology,under review. (Available on bioRXiv, doi: https://doi.org/10.1101/2025.11.19.688951 )
[12]. Daniel A. Kuppers, Sonali Arora, Cindy L. Wladyka, Ruiqi Ge, Shun Liu, Yong Peng, Rui Su, Anne Wilhite, Jianjun Chen, Chuan He, Andrew C. Hsieh & Patrick J. Paddison. 2025. N6-methyladenosine regulation of mRNA translation is essential for early human erythropoiesis. (Available on bioRXiv, doi: https://doi.org/10.1101/2025.11.10.687731 )
[11]. Jong Jin Jeong#, Trinath Das#, Shannon Delaney, John Froehlich, Xiu Chen, Linda Degenstein, Ahri Choe, Prasanth Kumar Punathil Kannan, Hyun Lee, Kith Pradhan, Srinivas Aluri, Yong Peng, Alana Beadell, Charith Wickrema, Jagadeesh Ramasamy, Sriram Sundarave, Chuan He, Amit Verma & Amittha Wickrema. 2025. Inhibition of TET2 phosphorylation activates fetal hemoglobin in sickle cell 1 disease. Nature Communications, under review.
[10]. Weizhi He#, Chu Xu#, Wen Chen#, Yuhang Wang, Yong Peng, Shujuan Chang, Wei Zhu，Jiuhong Kang* & Lulu Hu*. 2025. Uli-epic: profiling RNA modifications from ultra-low input samples. Genome biology, 26, 384. PMID:41219823
[9]. Yutao Zhao, Sun Hui-Lung, Wenlong Li, Chang Ye, Xiaoyang Dou, Yong Peng, Tong Wu, Pingluan Wang, Cheng-Wei Ju, Shun Liu, Yu-Hao Zhong, Qing Dai, Kinga Pajdzik & Chuan He. 2025. Pseudouridylation of 7SK by PUS7 regulates Pol II transcription elongation. Nature Communications, 16, 9595. PMID:41168165
[8]. Ruiqi Ge#, Chang Ye#, Yong Peng, Qing Dai, Yutao Zhao, Shun Liu, Pingluan Wang, Lulu Hu* & Chuan He*. 2022. m6A-SAC-seq for quantitative whole transcriptome m6A profiling. Nature Protocols, 18(2), 626-657. PMID:37349502
[7]. Hanshuang Li#,Chunshen Long#,Yan Hong, Lemuge Chao,Yong Peng, and Yongchun Zuo*. 2022. The Cumulative Formation of R-loop Interacts with Histone Modifications to Shape Cell Reprogramming. International Journal of Molecular Sciences, 23(3):1567. PMID:35163490
[6]. Zhiqiang Yan#, Jianting An#, Yong Peng, Siming Kong, Qiang Liu, Ming Yang, Qilong He, Shi Song, Yidong Chen, Wei Chen, Rong Li, Jie Qiao*, Liying Yan*. 2021. DevOmics: an integrated multi-omics database of human and mouse early embryo. Briefings in Bioinformatics, bbab208. PMID:34097004
[5]. Chengchuan Ma, Rong Niu, Tianxiao Huang, Li-Wa Shao, Yong Peng, Wanqiu Ding, Ye Wang, Guifang Jia, Chuan He, Chuan-Yun Li, Aibin He, and Ying Liu*. 2018. N6-methyldeoxyadenine is a transgenerational epigenetic signal for mitochondrial stress adaptation. Nature Cell Biology, 21(3):319-327. PMID:30510156
[4] Shanshan Ai#, Xianhong Yu#, Yumei Li#, Yong Peng, Chen Li, Yanzhu Yue, Ge Tao, Chuan-Yun Li, William T Pu*, and Aibin He*. 2017. Divergent Requirements for EZH1 in Heart Development Versus Regeneration. Circulation Research, 121(2):106-112. PMID:28512107
[3] Yong-Chun Zuo*, Yong Peng, Li Liu, Wei Chen, Lei Yang*, and Guo-Liang Fan*. 2014. Predicting peroxidase subcellular location by hybridizing different descriptors of Chou’ pseudo amino acid patterns. Analytical Biochemistry, 458:14-19. PMID:24802134
[2] Yongchun Zuo*, Pengfei Zhang, Li Liu, Tao Li, Yong Peng, Guangpeng Li, and Qianzhong Li*. 2014. Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome. Chromosome Research, 22(3):321-334. PMID:24728765
[1] Tao Li, Qian-Zhong Li*, Shuai Liu, Guo-Liang Fan, Yong-Chun Zuo, and Yong Peng. 2013. PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information. Bioinformatics, 29(6):678-685. PMID:23335013
6. Blog
English Blog: http://yongpeng.org
Chinese Blog: http://blog.sciencenet.cn/u/bigdataage
7. Skills
7 Levels from Newbie 1 to God Level 7:
1:Newbie(炼气期), 2:Basic(筑基期), 3:Familiar(金丹期), 4:Professional(元婴期), 5:Very Professional(化神期), 6:Top 10 Experts(炼虚), 7:God Level (Surpassing human's limit)(渡劫).
| Skill | Level | Skill | Level | Skill | Level | ||
|---|---|---|---|---|---|---|---|
| Python | 3 | Mojo | 1 | Snakemake/Containers/Anaconda | 2 | ||
| R | 4 | Julia | 1 | SQL and noSQL | 1 | ||
| Perl | 4 | Linux Bash Shell | 3 | Markup Languages | 1 | ||
| C | 2 | C++ | 1 | Go | 2 | ||
| Statistics | 3 | Statistical Physics | 2 | Molecular Simulation | 1 | ||
| Complex Networks | 2 | Nonlinear Dynamics | 1 | Systems Biology | 2 | ||
| Machine Learning | 2 | Deep Neural Networks | 1 | Artificial Intelligence | 1 | ||
| Bioinformatics | 4 | Epigenetics | 3 | Population and Quantitative Genetics | 2 | ||
| Biology | 3 | English | 3 | TCM | 2 |