个人简介 About me

三级教授，硕/博导，曾获国家高层次引进人才青年项目(2017-2020)和优秀青年科学基金(2021-2023)。主要研究方向为遗传学、生物信息学、进化系统生物学。2006年本科毕业于中山大学生物技术与应用专业（第二专业：计算机科学）。2011年于中山大学取得生化与分子生物学博士学位。2010至2016年于美国密歇根大学生态与进化生物学系任访问学者与博士后。2016年受聘为中山医学院教授。迄今已发表SCI论文41篇，包括作为（共同）通讯作者18篇，作为（共同）第一作者9篇，累计引用>3000，H指数19。  其中2016年至今作为通讯作者已在Nature Ecology & Evolution，Lancet Microbe，Molecular Biology & Evolution，Nature Comminications等多本国际一流杂志发表论文。

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.

研究方向 Research Interests

生命是进化的产物。进化因此与人类健康息息相关。我从突变对疾病与进化的调控，病原微生物进化，以及人类体细胞进化三个角度开展与医学相关的基础研究，试图揭示相关的进化规律及其对人类健康的潜在重大影响。我研究的切入点包括（但不限于）以下具体问题：

  • 突变对疾病与进化的调控
    • 遗传突变受基因表达调控并塑造进化轨迹（Nature Communications. 2023. 独立通讯; Nature Ecology and Evolution. 2021. 共同通讯）
    • 表型突变的功能及其对进化的影响（Molecular Biology and Evolution. 2021. 最后通讯；Nature Communications. 2025. 最后通讯）
  • 病原微生物进化
    • 抗生素耐药基因的进化（Lancet Microbe. 2024. 最后通讯；Molecular Biology and Evolution. 2022. 共同通讯）
    • 病毒基因组进化及其与宿主的相互作用（Nature Ecology and Evolution. 2020. 最后通讯；iScience. 2023. 最后通讯）
  • 人类体细胞进化
    • 生理/病理过程中的体细胞演化特征（Hepatology. 2024. 共同通讯;Journal of Genetics and Genomics. 2023. 最后通讯）
    • 通过细胞谱系树的测定与比对，精细分析体细胞进化模式（iScience. 2020. 最后通讯；Molecular Biology and Evolution. 2023. 独立通讯；Advanced Science. 2025. 独立通讯）

关于研究课题的更多信息请参阅我们已发表的文章（见下方）。另外，我在知乎也有少量创作介绍我感兴趣的研究。
 

Life is created by evolution. Human health is therefore intrinsically linked to evolution. My research explores medically relevant evolutionary questions from three perspectives: (i) the role of mutations in diseases and evolution, (2) pathogen evolution, and (3) somatic evolution in humans. Through these avenues, I aim to uncover evolutionary principles with potential significant implications for human health. Among the specific questions we are studying are:

  • Role of mutations in diseases and evolution
    • Mechanisms by which gene expression modulates mutational effects and influences evolution (Nature Communications 2023; Nature Ecology & Evolution 2021)
    • Functional roles of phenotypic mutations and their regulatory effects on evolution (Molecular Biology and Evolution 2021; Nature Communications 2025)
  • ​​Pathogen Evolution​​
    • Evolutionary dynamics and reversibility of antibiotic resistance genes (Lancet Microbe 2024; Molecular Biology and Evolution 2022)
    • Viral genome evolution, particularly synonymous codon usage bias and host-pathogen interactions (Nature Ecology & Evolution 2020; iScience 2023)
  • ​​Human Somatic Cell Evolution​​
    • Somatic evolution during physiological and pathological processes (e.g., carcinogenesis, aging) (Hepatology 2024; Journal of Genetics and Genomics 2023)
    • Reconstruction and comparison of high density cell lineage tree  (iScience 2020; Molecular Biology and Evolution 2023; Advanced Science 2025)

Please refer to publications listed below for more details on the researches in our lab

学术成果

代表学术论著

（完整论著列表请见 https://orcid.org/0000-0002-7807-9455）
Selected Publications：(Full list of pulications can be found on https://orcid.org/0000-0002-7807-9455)

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

  1. 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”)
  2. 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 as Frontispiece)
  3. 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)
  4. Xinkai Wu#, Mengze Xu#, Jian-Rong Yang*, Jian Lu*; Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster; Nature Communications; 2024; 15:8329 (16 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. Ning Mo, Xiaoyu Zhang, Wenjun Shi, Gongwang Yu, Xiaoshu Chen*, Jian-Rong Yang* ;Bidirectional genetic control of phenotypic heterogeneity and its implication for cancer drug resistance ; Molecular Biology and Evolution; 2021; 38(5); 1874-1887 
  10. 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")
  11. 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)
  12. Jianzhi Zhang*, Jian-Rong Yang; Determinants of the rate of protein sequence evolution; Nature Reviews Genetics; 2015; 16(7): 409-420

科研项目 Fundings

  1. 国自然优秀青年科学基金项目“进化基因组学”（主持；2022-2024）
  2. 国自然面上项目 “细胞发育谱系树比对算法的设计与应用”（主持；2019-2022）
  3. 国自然重点项目 “质粒介导多粘菌素耐药新机制MCR-1传播、进化和抑制剂研究”（第一参与人；2019-2023）

获奖荣誉

实验室成员所获荣誉/项目 Honors/grants won by group members

  1. 郭梓妍（2022级硕士生）中山大学2025年优秀硕士学位论文
  2. 吴卓幸（2017级硕博连读生） 2021年博士研究生国家奖学金；中山大学2022年优秀博士学位论文（在毕业典礼上作为学生代表发言）；中山大学中山医学院2021年生物信息学研究生论坛一等奖
  3. 陈家璧（2020级硕博连读生） 2021年硕士研究生国家奖学金；中山大学中山医学院2021年生物信息学研究生论坛二等奖，2020年广东光大升学深造奖学金；2025年SMBE Young Investigtor Attendance Award
  4. 桂倩（2018级硕士研究生） 中山大学2021年优秀硕士学位论文
  5. 吴鹏（2019级硕博连读生） 2020年硕士研究生国家奖学金
  6. 陈锋（2018博士后-2021特聘副研究员-2024副教授） 国自然青年科学基金（2020），面上项目（2022）资助

学术任职 Professional Service

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; 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.