个人简介 About me

三级教授，硕/博导。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)获得者。主要研究方向为遗传学、基因组学、进化生物学、系统生物学、生物信息学。2006年本科毕业于中山大学生物技术与应用专业，并完成了计算机科学第二专业的学习。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作为访问学者与博士后完成研究工作。2016年作为中山大学人才引进，受聘为博彩公司排名 教授。迄今已发表SCI论文27篇，包括作为（共同）通讯作者7篇，作为（共同）第一作者9篇，累计引用>2500，H指数17（据Google Scholar）。  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

为什么人会生病？疾病最根本的特征之一是生命系统稳健性（Robustness）的失调。这里的失调既可能是由外部干扰（例如病原感染或环境变化）引起，也可能是由内部失衡（例如遗传病或发育异常）导致的。我们从时间（进化）和空间（基因组）两个维度研究生命稳健性的调控机制，通过高通量的实验和生物信息学方法，揭示相关生物学规律及其对人类健康的潜在重大影响。我们研究的切入点包括（但不限于）以下具体问题：

  • 细胞发育谱系的稳定性与可塑性，细胞类型的发育轨迹与进化路径
  • 癌细胞基因型和表型的异质性，以及癌症基因组的演化规律
  • 分子水平的不精确性（如DNA突变、RNA折叠、表达噪音，蛋白翻译错误等）如何影响人类健康
  • 病原微生物基因组的进化及其与环境、宿主的相互作用

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。
 

Why do we get sick? Dysregulation of biological robustness is one of the most fundamental characteristics of disease. This dysregulation can be caused by external perturbations (e.g., infections or environmental stress) or by loss of internal homostasis (e.g., genetic or developmental defects). Using high-throughput experimental and bioinformatic approaches, we investigate the mechanisms of robustness from the evolutionary and genomic perspectives, as well as their implications for general evolutionary principles and human health. Among the specific questions we are studying are:

  • The stability and plasticity of developmental cell lineage tree. The developmental trajectory and evolutionary origin of different cell types.
  • Genetic/phenotypic heterogeneity of cancer cells, and the evolution of cancer genome.
  • How does stochasticity at the molecular level (e.g. DNA mutation, RNA folding, expression noise, protein translation error) impact the expression of genetic information and human health.
  • The genomic evolution of pathogenic microbes and its interaction with environment and host.

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

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

  1. 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
  2. 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; 2023; (in press)
  3. 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
  4. 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
  5. 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 
  6. 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  ( F1000highlight)
  7. 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 
  8. 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. 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）；博彩公司排名-博彩公司评级 2021年生物信息学研究生论坛一等奖
  2. 陈家璧（2020级硕博连读生） 2021年硕士研究生国家奖学金；博彩公司排名-博彩公司评级 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
  3. 桂倩（2018级硕士研究生） 中山大学2021年优秀硕士学位论文
  4. 吴鹏（2019级硕博连读生） 2020年硕士研究生国家奖学金
  5. 陈锋（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)

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.