Dr. Yanyi Chu leads an interdisciplinary research group at the intersection of artificial intelligence and life sciences, driving the advancement of biomedical research through innovative computational methods. Her lab focuses on developing deep learning frameworks to decode, predict, and rationally design functional RNA elements for next generation therapeutics, building precise immune interaction prediction and optimization platforms, and utilizing graph neural networks and multimodal deep learning to analyze complex biomolecular networks. Her research aspires to make substantial contributions to the pharmaceutical industry, with publications in Nat Mach Intell and Brief Bioinform.

Programmable RNA Regulation

Computational Immunotherapy

Biomolecular Interaction Prediction

2017.09 - 2022.06 Ph.D. in Bioinformatics and Computational Biology

Shanghai Jiao Tong University, China

Supervisors: Dong-Qing Wei and Yi Xiong

Dissertation: AI methods for biomolecular association prediction and neoantigen design

2021.01 - 2022.04 Visiting Ph.D. Researcher in Cheminformatics

University of Calgary, Canada

Supervisor: Dennis Russell Salahub

2013.09 - 2017.06 B.S. in Pharmaceutics

Shenyang Pharmaceutical University, China

Supervisor：Yihui Deng

2026.01 - Present Principal Investigator

Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, China

2024.10 - 2026.01 Postdoctoral Researcher

Arc Institute, Palo Alto, CA, USA

Mentor: Hani Goodarzi

2022.10 - 2024.10 Postdoctoral Researcher

Stanford University and Princeton University, USA

Mentors: Le Cong and Mengdi Wang

1. Yanyi Chu#, Di Yin#, Dan Yu, Guangxue Xu, Junze Zhang, Xiaotong Wang, Yue Shen, Yupeng Li, Ning Zhao, Yi Zhu, Jason Zhang, Hani Goodarzi, Mengdi Wang*, and Le Cong*. (2026). Programmable RNA translation through deep-learning-driven IRES discovery and de novo generation. Nature Machine Intelligence.

2. Yanyi Chu#, Dan Yu#, Yupeng Li, Kaixuan Huang, Yue Shen, Le Cong, Jason Zhang, and Mengdi Wang*. (2024). A 5' UTR language model for decoding untranslated regions of mRNA and function predictions. Nature Machine Intelligence.

3. Yanyi Chu#, Yan Zhang#, Qiankun Wang, Lingfeng Zhang, Xuhong Wang, Yanjing Wang, Dennis Russell Salahub, Qin Xu, Jianmin Wang, Xue Jiang, Yi Xiong*, and Dong-Qing Wei*. (2022). A transformer-based model to predict peptide-HLA class I binding and optimize mutated peptides for vaccine design. Nature Machine Intelligence, 4, 300-311.

4. Yanyi Chu, Xuhong Wang, Qiuying Dai, Yanjing Wang, Qiankun Wang, Shaoliang Peng, Xiaoyong Wei, Jingfei Qiu, Dennis Russell Salahub, Yi Xiong*, and Dong-Qing Wei*. (2021). MDA-GCNFTG: Identifying miRNA-disease associations based on graph convolutional networks via graph sampling through feature and topology graph. Briefings in Bioinformatics, 22(6), bbab165.

5. Yanyi Chu, Xiaoqi Shan, Tianhang Chen, Mingming Jiang, Yanjing Wang, Qiankun Wang, Dennis Russell Salahub, Yi Xiong*, and Dong-Qing Wei*. (2021). DTI-MLCD: Predicting drug-target interactions using multi-label learning with community detection method. Briefings in Bioinformatics, 22(3), bbaa205.

6. Yanyi Chu, Aman Chandra Kaushik, Xiangeng Wang, Wei Wang, Yufang Zhang, Xiaoqi Shan, Dennis Russell Salahub, Yi Xiong*, and Dong-Qing Wei*. (2021). DTI-CDF: A cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. Briefings in Bioinformatics, 22(1), 451-462.

#Co-first authors; *Corresponding authors

• Start-up Funding, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 2026

• Director's Fund, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 2026

• Shanghai Pujiang Talent Program, Principal Investigator, 2026

• Industry Research Support, Benyuan Zhishu

• Industry Research Support, Zipcode Bio

Current Students

谢宗余  硕士研究生  071010-生物化学与分子生物学  

葛玉礼  硕士研究生  0710J3-生物信息学

• 2022 Outstanding Graduate Development Scholarship, Shanghai Jiao Tong University

• 2022 Outstanding Graduate, Shanghai

• 2021 National Scholarship, Ministry of Education of China

• 2020 National Scholarship, Ministry of Education of China

• 2017 Outstanding Graduate, Shenyang Pharmaceutical University

• 2016 Outstanding University Student, Shenyang

• 2015 Top Ten Outstanding University Students, Shenyang Pharmaceutical University