I am Yarong Wu, an associate professor and principal investigator at the School of Life Sciences, Tianjin University. My research focuses on the evolution and genomic epidemiology of pathogenic microorganisms. I am particularly interested in three fundamental questions: where pathogens come from, how they evolve, and where they are heading. To address these, I have developed an integrated framework that combines multi-scale variant detection, population genetic analysis, and inference of adaptive evolution, linking evolutionary theory with practical applications in genomic epidemiology.

My work has been published as first or corresponding author (including co-authored roles) in journals such as Nature Genetics, Nature Communications, The Lancet Microbe, and PNAS. In recent years, I have led or contributed to multiple research projects, including the National Natural Science Foundation of China. I have co-authored two academic books, hold one invention patent and two software copyrights, and serve as a reviewer for journals including Nature Communications and Communications Biology.

In my research, I work at the interface between “invisible microbes” and “visible data.” I analyze large-scale genomic datasets using bioinformatics approaches and interpret them through the lens of evolutionary theory, aiming to connect fine-scale genetic variation with broader evolutionary patterns. 

I welcome students with backgrounds in bioinformatics, biology/microbiology, public health, computer science, mathematics, or related fields to join my group. As the lab is currently growing, you will not only participate in ongoing research but also help shape its future direction. If you are curious about pathogen evolution and enjoy exploring questions through data and computation, this could be an excellent place to start.

Researcher ID: https://www.researchgate.net/profile/Yarong-Wu

ORCID: http://orcid.org/0000-0003-4900-315X

Representative Work in Pathogen Evolution and Genomic Epidemiology

1. Structural Variation in Bacterial Pangenomes and Conceptual Advances

Beyond SNPs, large-scale genomic rearrangements represent more complex and less-characterized forms of variation. This work systematically characterizes the patterns and evolutionary drivers of genome rearrangements in Yersinia pestis at the population level, establishing a robust analytical framework for studying highly rearranged microbial genomes. The study demonstrates that rearrangements are shaped by strong stepwise positive selection, providing new insights into pangenome evolution. Identified rearrangement hotspots and affected operons offer candidate targets for dissecting virulence mechanisms, vaccine design, and diagnostic development based on structural variants (Nature Genetics, 2025).

2. Core Genome Variation and Mechanisms of Mutation Hotspots
Although mutations arise stochastically, they often cluster in genomic “hotspots” that influence key phenotypes such as virulence, transmission, and antimicrobial resistance. By integrating over 3,000 global Y. pestis genomes, this study systematically identifies 45 mutation hotspots and shows that regions with similar population distributions are also closely connected in protein interaction networks, suggesting higher-order interactions. After accounting for sequence composition and homologous recombination, the results indicate that positive selection alone does not fully explain hotspot formation; instead, regional variation in mutation rates may reflect a “bet-hedging” evolutionary strategy. This work advances understanding of how mutations arise and become fixed in bacterial genomes (Nature Communications, 2025), and was highlighted by Nature Reviews Microbiology (Genome Watch).

3. Genomic Epidemiology for Pathogen Tracing and Public Health Applications
Integrating historical, archaeological, ecological, and genomic data, this work reconstructs the origins and transmission dynamics of the second plague pandemic, showing that its persistence in Western Europe was closely associated with repeated introductions from Central Asia or Eastern Europe (PNAS, 2021). The study was accompanied by a PNAS commentary describing it as a “paradigm shift” in understanding plague history and has been widely cited by Science, Nature Reviews Microbiology, and Trends in Microbiology. Building on this foundation, the research extends to modern public health challenges, developing genomic frameworks for outbreak surveillance and source tracing. These approaches have been applied to investigations of Mycoplasma pneumoniae outbreaks, regional plague dynamics, and the spread of drug-resistant Klebsiella pneumoniae, with results published in The Lancet Microbe (2025), Emerging Infectious Diseases (2024), Emerging Microbes & Infections (2022), and Communications Biology (2023, 2025).