The PKU-EMBL Lab investigates how microbial communities evolve, function, and can be translated into useful biological systems. We focus especially on extreme environments, where unconventional ecological pressures often reveal overlooked diversity, unusual metabolisms, and new biosynthetic potential.
Our long-term goal is to connect microbial discovery, mechanistic understanding, and engineering application. We combine environmental microbiology with artificial intelligence to identify novel taxa, interpret complex multi-omics data, and accelerate the path from sequence to function.
Extreme-environment microbial resource mining
We study hypersaline, acidic, and alkaline ecosystems to discover uncultivated or poorly characterized microorganisms and biosynthetic gene clusters with potential ecological and biotechnological relevance.
AI for microbiome and multi-omics science
We develop algorithms, software, and data-analysis workflows for metagenomics, metatranscriptomics, and integrative multi-omics, with growing interest in large language models and scientific agents for biological discovery.
Cultivation and functional validation
We pair computational predictions with cultivation, metabolomics, and genetic approaches to validate microbial functions and move beyond descriptive cataloging.
Research infrastructure and community resources
We build databases, pipelines, visualization tools, and reusable software that support reproducible microbiome research at scale.
Our work sits at the interface of field sampling, wet-lab experimentation, bioinformatics, and high-performance computing. This integrated approach allows us to address questions that are difficult to solve from a single disciplinary perspective alone.
Research led by Prof. Ke Yu has produced more than 90 SCI publications with over 5,000 citations, including papers in Nature Communications, Microbiome, Environmental Science & Technology, and Water Research. Representative studies from the broader research program have been recognized for advancing metatranscriptomics, multi-omics analysis, and genome-resolved microbiome research.
PKU EMBL