Chaohui Li

About Me

I am a Ph.D. student in Computer Science advised by Prof. Vineet Bafna at 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 fortunately 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

• [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 have been accepted by ISMB 2026 and will be presented at the conference.
• [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.

Selected Publications

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.