ABOUT THE LAB

Welcome to the Xu lab. Our research focuses on microbiome and host interaction. We apply bioinformatics, microbiology, and animal model to understand how microbiome can be precisely engineered to modulate host phenotypes. Specifically, we are working on the following areas:

microbiome bioinformatics: Microbiome data have some idiosyncratic properties (eg sparse and compositional) and require careful treatment. We have been developing scalable and robust bioinformatic tools to mine multi-omic data and discover patterns and knowledge. We are part of the QIIME2 development team and involved in developing multiple tools including scikit-bio, deblur, and calour. These are successfully applied to microbiome studies.

genomics: We have developed algorithms to identify novel regulatory ncRNAs and predict their secondary structures. With the ever-increasing microbial genomes available from whole-genomic and metagenomic shotgun sequencing data, there is a bottleneck to understand the function potential (ncRNA, coding gene, CRPISPR, prophage, etc.) of these genomes. We are using deep learning techniques to develop high-quality, consistent annotations for comparative genomics.

zebrafish model: We are using zebrafish as a model to study microbiome & host interaction because of the advantages of zebrafish model, including low cost, scalability, genetic tractability, transparency for imaging, and system for complex social behavior analysis.

We are looking for prospective students and faculty to join us on this exciting research field.