Chaohui Li

Ph.D. Student
UC San Diego
chl221@ucsd.edu

About Me

I am a Ph.D. student in Computer Science advised by Prof. Vineet Bafna at the University of California San Diego, where I also earned a Master’s degree in Computer Science. I received a Bachelor’s degree in Computer Science from City University of Hong Kong, where I was advised by Prof. Shuai Cheng Li.

Research Interests

My research interests are in bioinformatics and computational biology, particularly applied algorithms on cancer genomics and complex structural variants. I am broadly interested in designing optimization and machine learning methods that can efficiently and effectively make core scientific insights into biology and medicine.

News

[September 2026] Completed a 3-month internship at Meta as a Research Intern working on reinforcement learning models for feed recommendations.
[July 2026] Our paper on “detecting and reconstructing BFB cycles from long-read sequencing data” was published in Bioinformatics.
[May 2026] Our latest paper on BFB has been accepted for presentation at ISMB 2026.
[December 2025] Our paper on “reconstructing the 3D structure of ecDNA from Hi-C data” was published in Nature Communications.
[June 2025] I earned a Master’s degree in Computer Science from UC San Diego.

Education

University of California San Diego

Ph.D. in Computer Science 2023–Present

M.S. in Computer Science 2023–2025

City University of Hong Kong

B.S. in Computer Science 2017–2021

Work Experience

Meta Platforms, Inc.

Research Intern June–September 2026

Department of Computer Science
City University of Hong Kong

Research Assistant 2021–2023

Selected Publications

Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect

Chaohui Li, Siavash Raeisi Dehkordi, Daniel Muliaditan, Ramanuj DasGupta, Jens Luebeck, Kaiyuan Zhu, and Vineet Bafna

ISMB & Bioinformatics, 2026

Paper Code BibTeX
Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D

Biswanath Chowdhury*, Kaiyuan Zhu*, Chaohui Li*, ..., and Vineet Bafna

Nature Communications, 2025

Paper Code BibTeX (* joint first authorship, same below)
Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram

Chaohui Li*, Lingxi Chen*, Guangze Pan, Wenqian Zhang, and Shuai Cheng Li

Nature Communications, 2023

Paper Code BibTeX
Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics

Lingxi Chen*, Yuhao Qing*, Ruikang Li*, Chaohui Li*, Hechen Li, Xikang Feng, and Shuai Cheng Li

Briefings in Bioinformatics, 2021

Paper Project Page BibTeX

Selected Awards

Conference Fellowship, 34th Conference on Intelligent Systems for Molecular Biology (ISMB), 2026
CityU Mainland Student Scholarship (Full Tuition), City University of Hong Kong, 2017-2021
Silver Award, the 12th “Challenge Cup” National Business Plan Competition for College Students, 2020
CityU Scholarship, City University of Hong Kong, 2020

Teaching

Teaching Assistant, CSE8A: Introduction to Programming and Computational Problem-Solving I - UC San Diego (July 2025)
Student Teaching Assistant, CS2310: Computer Programming - City University of Hong Kong (January − May 2019 & 2020)

Services

Reviewed for journals: BMC Genomics and BMC Bioinformatics

Miscellaneous

I like jogging, hiking, and singing. I am also a football fan of Real Madrid CF.