I am a Ph.D. candidate in Computer Science at the School of Computing and Data Science, The University of Hong Kong (HKU), where I am fortunate to be advised by Prof. Zhenqin (Michael) Wu.
I completed my M.S. in Biology at the School of Pharmaceutical Sciences and the School of Life Sciences from Tsinghua University, and I hold a B.S. in Biotechnology from Huazhong Agricultural University.
My research interests span AI4Science, bioinformatics, and computational biology, with particular focus on spatial biology, computational genomics, and the design of biological molecules including proteins and small molecules. I am passionate about deep learning algorithms, especially generative modeling approaches. Additionally, I bring hands-on experience in experimental biology from wet lab settings. I actively collaborate with clinical and industrial partners to develop innovative AI solutions for biological and medical applications.
News
Publications
# denotes equally contributed, * denotes corresponding author.
PLoS Biology 2019
RNA editing restricts hyperactive ciliary kinases
Ru Jia#, Dongdong Li#, Ming Li#, Yongping Chai, Yufan Liu, Zhongyun Xie, Wenxin Shao, Chao Xie, Liuju Li, Xiaoshuai Huang, Liangyi Chen, Wei Li and Guangshuo Ou*
bioRxiv 2025
Preprint
Modeling patient tissues at molecular resolution with Eva
Yufan Liu, Rishabh Sharma, Matthew Bieniosek, Amy Kang, Eric Wu, Peter Chou, Irene Li, Maha Rahim, Erica Bauer, Ran Ji, Wei Duan, Li Qian, Ruibang Luo, Padmanee Sharma, Renu Dhanasekaran, Christian M. Schürch, Gregory Charville, Aaron Mayer, James Zou, Alexandro E. Trevino*, Zhenqin Wu*
medRxiv 2025
Preprint
Residual Cardiovascular Risk Prediction in Statin-Treated Patients Using Machine Learning and Biomarker Analysis
Yufan Liu#, Yuhan Yang#, Tong Tong, Xiaoxiao Zhang, Zhang Jin, Mengwen Huang, Wenjie Liu, Zhenqin Wu, Ziyi Sun, Kuiwu Yao*
bioRxiv 2024
Preprint
Exploring Protein-DNA Binding Residue Prediction and Consistent Interpretability Analysis Using Deep Learning
Yufan Liu*
Education
The University of Hong Kong
Ph.D. candidate in Computer Science
Faculty: School of Computing and Data Science
Supervisor: Prof. Zhenqin (Michael) Wu
Tsinghua University
M.S. in Biology
Faculty: School of Pharmaceutical Sciences, School of Life Sciences
Supervisor: Prof. Boxue Tian and Prof. Guangshuo Ou
Thesis: Prediction of Protein-DNA Binding Sites Based on Deep Learning
Huazhong Agricultural University
B.S. in Biotechnology
Faculty: College of Life Science and Technology
Supervisor: Prof. Guangshuo Ou
Thesis: Functional Analysis of RNA Editing in C. elegans (completed at Tsinghua, Nov 2018 - May 2019)
Experience
Machine Learning Researcher — Guang'anmen Hospital, China Academy of Chinese Medical Sciences
Advisor: Prof. Kuiwu Yao
Machine learning methods for cardiovascular diseases
Machine Learning Intern — Tong Ren Hospital, Capital Medical University
Advisor: Prof. Lihui Huang
Machine learning methods for newborn deafness diagnosis
Undergraduate Research Intern — School of Life Sciences, Tsinghua University
Advisor: Prof. Xiao Liu
Bioinformatics analysis for Next-generation Sequencing (NGS) data
Undergraduate Research Intern — College of Informatics, Huazhong Agricultural University
Advisor: Prof. Jingbo Xia
Bioinformatics for bioarray data and biomedical NLP
Talks and Posters
2019-Suzhou-poster·RNA editing restricts hyperactive ciliary kinases
2019-Beijing-poster·Bioinformatics pipeline for RNA editing analysis
2025-HK-poster·SpaFormer: A multi-modal foundation model for spatial proteomics
Awards and Cerficates
Teaching
Fall 2025-Introduction to data science (CS2501A)-HKU, Hong Kong
Service
Conference reviewer - AAAI (25'), ICLR (25', DeLTa 25', 26'), ICML (24', 25'), NerIPS (24', 25'), AISTATS (25', 26'), ICCV (CVAMD 25')
Journal reviewer - Nature Communications