About

I am a Ph.D. candidate in Biomedical Data Science at the University of Wisconsin-Madison, where I am part of the Kendziorski Lab. My current work focuses on bioinformatics and LLM agents: building agentic systems that can power bioinformatics workflows and help researchers reason over complex biological data.

I built CASSIA, a multi-agent tool for automated cell annotation, and AutoZyme, an agentic framework for optimizing bioinformatics software.

In my spare time, I love singing, playing the piano, playing basketball, and watching anime.

Education

2023 - now Ph.D. student, University of Wisconsin-Madison
2022-2023 M.S. in Data Science, University of Wisconsin-Madison
2017 - 2021 B.S. in Statistics, Xiamen University

News

Jun 2026
AutoZyme preprint is out on bioRxiv. (preprint)
Dec 2025
CASSIA was formally published in Nature Communications. (paper)

Publications

2026

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

bioRxiv E. Xie, L. Cheng, Y. Cai, J. Shireman, C. Kendziorski
2025

CASSIA: a multi-agent large language model for automated and interpretable cell annotation

Nature Communications E. Xie, L. Cheng, J. Shireman, Y. Cai, J. Liu, C. Mohanty, M. Dey, C. Kendziorski
2025

Gut-larynx axis and its contribution to laryngeal immunity

mSystems R. An, E. Xie, J. Binns, F. E. Rey, et al.
2025

Surrogate selection oversamples expanded T cell clonotypes

Annals of Applied Statistics P. Yu, Y. Lian, E. Xie, et al.
2024

Single-cell view into the role of microbiota shaping host immunity in the larynx

iScience R. An, Z. Ni, E. Xie, et al.
2024

Transcriptomic and proteomic spatial profiling of diffuse midline glioma

Scientific Reports M. D. S. Damodharan, E. Xie, et al.

Blog

The New Productivity Metric: Agent-Hours per Human-Hour

In the age of AI agents, competitive advantage comes from maximizing the surplus value of autonomous work.

Read More