Publications

(#equal contribution, *corresponding)

You can also find my articles on my Google Scholar profile.

1. Clc-db: an open-source online database of chiral ligands and catalysts
   Gufeng Yu#, Kaiwen Yu#, Xi Wang#, Chenxi Zhang, Yicong Luo, Xiaohong Huo*, Yang Yang*
   Journal of Cheminformatics, 2025, 17(1): 1-12.
   [Paper]

2. AtropDiff: Data-Scarce Atropisomer Generation via Multi-Task Pretrained Classifier-Guided Diffusion
   Letian Chen, Xi Wang, Gufeng Yu, Caihua Shan*, Yang Yang*
   ICLR 2025 DeLTa Workshop

3. YieldFCP: Enhancing Reaction Yield Prediction via Fine-grained Cross-modal Pre-training
   Runhan Shi, Gufeng Yu, Letian Chen, Yang Yang*
   Artificial Intelligence Chemistry, 2025, 3(1): 100085.
   [Paper]

4. ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions
   Yifei Gao, Runhan Shi, Gufeng Yu, Yuyang Huang, Yang Yang*
   Methods, 2025, 235: 45-52.
   [Paper]

5. Machine Learning for Reaction Performance Prediction in Allylic Substitution Enhanced by Automatic Extraction of a Substrate-Aware Descriptor
   Gufeng Yu#, Xi Wang#, Yicong Luo, Guanlin Li, Rui Ding, Runhan Shi, Xiaohong Huo*, Yang Yang*
   Journal of Chemical Information and Modeling, 2025, 65(1): 312-325.
   [Paper]

6. Prediction of chemical reaction yields with large-scale multi-view pre-training
   Runhan Shi, Gufeng Yu, Xiaohong Huo, Yang Yang*
   Journal of Cheminformatics, 2024, 16(1): 1-16.
   [Paper]

7. Enhancing Cancer Gene Prediction through Aligned Fusion of Multiple PPI Networks Using Graph Transformer Models
   Zebei Han, Gufeng Yu, Yang Yang*
   2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
   [Paper]

8. MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images
   Yuyang Huang#, Gufeng Yu#, Yang Yang*
   PLOS Computational Biology, 2023, 19(11): e1011623.
   [Paper]