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
Selected Publications：(Full list of pulications can be found on https://orcid.org/0000-0002-7807-9455)
(*: Corresponding author; #: Authors with equal contribution)
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 (
highlight) - 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
- 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 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
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).
