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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 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

Selected Publications

  1. Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D
    Biswanath Chowdhury*, Kaiyuan Zhu*, Chaohui Li*, ..., and Vineet Bafna
    bioRxiv, 2025
    Paper Code (* joint first authorship, same below)

  2. 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

  3. 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

Selected Awards

Teaching

Miscellaneous

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