Biography

Hello! I am a Ph.D. student at the Department of Integrative Physiology, University of Colorado Boulder, advised by Prof. Matthew R. Olm at the Integrative Microbiome Research Laboratory. My research interests are microbiome, public health, and bioinformatics. Previously, I completed my Master’s degree at Shanghai Jiao Tong University School of Medicine Shanghai Jiao Tong University School of Medicine, and my Bachelor’s degree at Anhui Medical University. Feel free to drop me an email to chat!

News

• [2024.03] Our work Metagenomic insights into correlation of microbiota and antibiotic resistance genes in the worker-pig-soil interface: A One Health surveillance on Chongming Island, China has been submitted to Environment International!
• [2023.10] Our work Correlation of microbiota and antibiotic resistance genes in the swine manure-soil interface in Chongming Island was accepted by Chinese Journal of Microecology!
• [2023.9] I spent a lovely summer interning with Prof. Zehang Richard Li at UCSC.
• [2023.5] Our survey One Health: a holistic approach for food safety in livestock was accepted by Science in One Health.
• [2022.6] Our survey Antibiotic-resistant microbes, antibiotic resistance genes and One Health was accepted by Microbiology China.
• [2022.6] I completed the courses Machine Learning & Neural Networks and Deep Learning by Andrew Ng, as well as Oxford Machine Learning Summer School for ML Health track.

Projects

Label combination in cause-of-death analysis

We focus on cause-of-death analysis where post-training label combination is important if we want to yield appropriately ambiguous results without sacrificing essential information. Existing label combination methods are designed exclusively for classification tasks, so we need to extend them to tasks with a different loss like cause-of-death analysis. Our key design is to formulate the label combination problem as a new optimization problem with a proposed regularizer to control the combination degree.

Microbiota and antibiotic resistance genes at human-pig-soil interface

Mapping microbial connectivity of people, animals and their environment. [LeftFig-HighRes] [RightFig-HighRes]

We propose a unique design and epidemiological environment to sample workers, pigs, and soil from 5 farms. Our analytical pipeline includes genome assembly programs, taxonomic classifiers, read mappers, and pathway reconstruction tools. This hybrid assembly approach has lower error rates, produces more contiguous assemblies, generates metagenomic assembled genomes, and allows for the reconstruction of near-complete genomes.

A survey of antibiotic resistance from a One Health perspective

Transmission of antibiotic resistance genes at the human-animal-environment interfaces. [LeftFig-HighRes] [RightFig-HighRes]

One Health is a holistic approach to understand the complex relationships among humans, animals, and environments. This paper depicts the main pathogen spectrum of livestock and animal products, summarizes the flow of antibiotic-resistant bacteria and genes between humans and livestock along the food-chain production. With One Health framework, we advocate that multi-disciplinary efforts should be enhanced to solve this global concern on antimicrobial resistance.