About me

I am a professor in Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University.  My research interests can be broadly categorized under Genetics, Evolutionary Genomics, Systems Biology and Bioinformatics. I got my Bachelor's degree in 2006 from the School of Life Science, Sun Yat-sen University, with first major in Applied Biotechnology and second major in Computer Science. Then I got my Ph.D. from Sun Yat-sen University in 2011 under the supervision of Prof. Shi-Mei Zhuang, and did post-doctoral research with Prof. Jianzhi "George" Zhang in Department of Ecology and Evolution, University of Michigan. I joined Zhongshan School of Medicine as a professor in 2016. As a (co-)corresponding author, my work has been published on Cell，Nature Ecology & Evolution(*2)，Lancet Microbe，Nature Communications(*3)，Advanced Science，Hepatology，Molecular Biology & Evolution(*3), etc.

Research Interests

With the long-term goal of enhancing the predictability of evolution and its biomedical applications, we study the driving forces behind molecular evolution and their interactions by integrating computational and experimental approaches. Our research allows us to predict pathogen evolution, reveal the general rules of somatic evolution, and elucidate how mutational bias impacts evolution and human health. For more information about our research topics, please refer to our published articles below.

Publications

Selected Publications：(Full list of pulications can be found on https://orcid.org/0000-0002-7807-9455)

(*: Corresponding author; #: Authors with equal contribution)

  1. Linjin Fan*, Yulong Wang*, Yinghao Wang*, Zequn Wang, Xiaofeng Yang, Chudan Liang, Nan Liu, Jun Zheng, Weifang Kang, Pengfei Ye, Pei Sun, Wendi Shi, Xinyi Guo, Weijian Wu, Jian-Rong Yang*, Quan Liu*, Linna Liu*, Jun Qian*; Cell. 2026; (in press)
  2. Boyang Zheng#, Weijie Zhang#, Gongwang Yu#, Wenjun Shi, Shuyun Deng, Xiaoyi Zhang, Jingyu Chen, Ziwei Zhou, Yuyan Shan, Wanting Wu, Erping Long, Xiaoshu Chen*, Jian-Rong Yang*; Translational Fidelity and Longevity are Genetically Linked; Nature Communications; 2025; 16:7521 (13 pages) (Editors’ Highlights for “Genetics, genomics and epigenetics”)
  3. Xiaoyu Zhang#, Zizhang Li#, Jingyu Chen#, Wenjing Yang, Xingxing He, Peng Wu, Feng Chen, Ziwei Zhou, Chenze Ren, Yuyan Shan, Xiewen Wen, Vassily A. Lyubetsky, Leonid Yu. Rusin, Xiaoshu Chen Jian-Rong Yang*; Stereotyped Subclones Revealed by High Density Single-Cell Lineage Tracing Support Robust Development; Advanced Science; 2025; 12(30): 2406208 (19 pages) (Highlighted asFrontispiece)
  4. Ziyan Guo#, Siyuan Feng#, Lujie Liang#, Zhuoxing Wu#, Lulu Min, Ruizhi Wang, Jiachen Li, Lan-Lan Zhong, Hui Zhao, Xiaoshu Chen*, Guo-Bao Tian*, Jian-Rong Yang*; Reversibility of resistance in the absence of antibiotics and its relationship with the resistance gene's fitness cost – a genetic study with mcr-1; Lancet Microbe; 2024; 5(8):100846 (11 pages)
  5. Yasong Liu#, Jiaqi Xiao#, Jianye Cai#, Rong Li#, Xin Sui, Jiebin Zhang, Tongyu Lu, Haitian Chen, Guihua Chen, Haibo Li, Chenhao Jiang, Xuegang Zhao, Cuicui Xiao, Yunguo Lei, Jia Yao, Guo Lv, Jinliang Liang, Yingcai Zhang*, Jian-Rong Yang*, Jun Zheng*, Yang Yang*; Single-cell immune profiling of mouse liver aging reveals Cxcl2+ macrophages recruit neutrophils to aggravate liver injury; Hepatology; 2024; 79(3): 589-605
  6. Gongwang Yu#, Yao Liu#, Zizhang Li, Shuyun Deng, Zhuoxing Wu, Xiaoyu Zhang, Wenbo Chen, Junnan Yang, Xiaoshu Chen, Jian-Rong Yang*; Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect; Nature Communications; 2023; 14:5853 (18 pages)
  7. Feng Chen#, Zizhang Li#, Xiaoyu Zhang, Peng Wu, Wenjing Yang, Junnan Yang, Xiaoshu Chen, Jian-Rong Yang*; Phylogenetic comparative analysis of single-cell transcriptomes reveals constrained accumulation of gene expression heterogeneity during clonal expansion ; Molecular Biology and Evolution; 2023; 40(5): msad113 (20 pages)
  8. Zhuoxing Wu#, Xiujuan Cai#, Xin Zhang, Yao Liu, Guo-bao Tian, Jian-Rong Yang*, Xiaoshu Chen*; Expression level is a major modifier of the fitness landscape of a protein coding gene ; Nature Ecology and Evolution; 2022; 6(1): 103-115
  9. Feng Chen, Peng Wu, Shuyun Deng, Heng Zhang, Yutong Hou, Zheng Hu, Jianzhi Zhang*, Xiaoshu Chen*, Jian-Rong Yang* ; Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection ; Nature Ecology and Evolution; 2020; 4(3);  589-600  (F1000 highlighted “Very good")
  10. Meng Yuan#, Xujiang Yang#, Jinghua Lin#, Xiaolong Cao#, Feng Chen, Xiaoyu Zhang, Zizhang Li, Guifeng Zheng, Xueqin Wang, Xiaoshu Chen*, Jian-Rong Yang*; Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types; iScience; 2020; 23(7); 101273 (17 pages)
  11. Jianzhi Zhang*, Jian-Rong Yang; Determinants of the rate of protein sequence evolution; Nature Reviews Genetics; 2015; 16(7): 409-420

Research Projects and Fundings

  • National Natural Science Foundation of China (NSFC) International (Regional) Cooperation project: "Development of a database for cell type formation trajectories in evolution and development" (Principal Investigator; 2024 - 2026)
  • National Natural Science Foundation of China Excellent Young Scientists Fund Project: "Evolutionary Genomics" (Principal Investigator; 2022 - 2024)
  • National Natural Science Foundation of China General Project: "Design and Application of Cell Development Phylogenetic Tree Comparison Algorithms" (Principal Investigator; 2019 - 2022)
  • National Natural Science Foundation of China Key Project: "Research on the New Mechanism, Transmission, Evolution and Inhibitors of Plasmid-Mediated Polymyxin Resistance MCR-1" (First Participant; 2019 - 2023)

Honors and Grants Won by Group Members

  • Guo Ziyan (Master's Student, Class of 2022):
    Outstanding Master's Dissertation Award of Sun Yat-sen University in 2025.
  • Wu Zhuoxing (Master's and Doctoral Joint Program Student, Class of 2017):
    National Scholarship for Doctoral Students in 2021;
    Outstanding Doctoral Dissertation Award of Sun Yat-sen University in 2022 (delivered a speech as a student representative at the graduation ceremony);
    First Prize in the 2021 Bioinformatics Graduate Student Forum of the School of Medicine, Sun Yat-sen University.
  • Chen Jiabi (Master's and Doctoral Joint Program Student, Class of 2020):
    National Scholarship for Master's Students in 2021;
    Second Prize in the 2021 Bioinformatics Graduate Student Forum of the School of Medicine, Sun Yat-sen University;
    Guangdong Everbright Scholarship for Further Studies in 2020.
  • Gui Qian (Master's Student, Class of 2018):
    Outstanding Master's Dissertation Award of Sun Yat-sen University in 2021.
  • Wu Peng (Master's and Doctoral Joint Program Student, Class of 2019):
    National Scholarship for Master's Students in 2020.
  • Chen Feng (Associate Professor):
    National Natural Science Foundation of China Young Scientists Fund (2020);
    General Project funded by the National Natural Science Foundation of China (2022).
     

Professional Memberships/services

Society of Molecular Biology and Evolution
Atlas of Variant Effects (AVE) Alliance, Data Coordination and Dissemination (DCD) workstream
The Genetics Society of China
Chinese Society of Biotechnology
​International Society for Computational Biology - China (ISCB-China) (Council member)

Editorial Board member: Journal of Genetics and Genomics (2020-now); Frontiers in Ecology and Evolution (2020-now); Frontiers in Genetics (2020-now); iMeta (2024-now)

Ad hoc reviewer for Nature; Nature Ecology and Evolution; National Science Review; Nature Communications; Advanced Science; Molecular Biology and Evolution; Genome Biology; EMBO Reports; PLoS Genetics; PLoS Computational Biology; iScience; BMC Genomics;  Genome Biology and Evolution; Evolution;  BMC Evolutionary Biology;  Infection, Genetics and Evolution; iScience; Journal of Gene Medicine; Journal of Molecular Evolution; Journal of Theoretical Biology; PLoS ONE; Scientific Reports.