bigdataage.github.io
Yong Peng's CV
1. About Me
Full Name: Yong Peng
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 (My source codes for bioinformatics)
2. Research Interests
Epitranscriptomics, epigenomics, and bioinformatics.
Epitranscriptomic and epigenomic regulatory mechanisms of development and disease by using computational and experimental multi-omics technologies.
3. Experience
2020.01~now, Postdoctoral Researcher, Chuan He Group @ Department of Chemistry, and Mengjie Chen Group @ Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
2019.02~2019.12, Jie Qiao Group @ Key Laboratory of Assisted Reproduction-Ministry of Education, 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., 2010.09~2013.07, Physics, School of Physical Science and Technology @ Inner Mongolia University, Hohhot, China.
B. Sc., 2006.09~2010.07, 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 Manuscript
(^) First authorship; (*) Senior authorship
Selected publications:
[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*. 2024. Epigenomic basis exploration and noninvasive diagnosis for disease states of EGFR-mutated non-small cell lung cancer using plasma cell-free DNA hydroxymethylomes. (Submitted to Cancer Communications, Under Review)
[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.
[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:
[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.
[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, 2:Basic, 3:Familiar, 4:Professional, 5:Very Professional,
6:Top 10 Experts, 7:God Level (Surpassing human's limit).
| Skill | Level | Skill | Level | Skill | Level | ||
|---|---|---|---|---|---|---|---|
| Go | 2 | Python | 3 | Perl | 4 | ||
| R | 4 | Julia | 1 | Javascript | 1 | ||
| Linux Bash Shell | 2 | SQL and NoSQL | 1 | Markup Languages | 1 | ||
| Statistics | 3 | Statistical Physics | 2 | ||||
| Complex Networks | 2 | Nonlinear Dynamics | 2 | ||||
| Machine Learning | 2 | Deep Neural Networks | 1 | ||||
| Bioinformatics | 4 | Systems Biology | 1 | ||||
| Biology | 3 | English | 3 |