Publications

Y Jia, B Gao, J Tan, J Zheng, X Hong, W Zhu, H Tan, Y Xiao, L Tan, H Cai, Y Huang, Z Deng, X Wu, Y Jin, Y Yuan, J Tian, W He, WY Ma, YQ Zhang, L Liu, C Yan, W Zhang, Y Lan. "Deep contrastive learning enables genome-wide virtual screening." Science, 2026.

Z Chen, Y Jia, Z Tian, WY Ma, Y Lan. "Manipulating 3D Molecules in a Fixed-Dimensional E(3)-Equivariant Latent Space." NeurIPS, 2025.

Z Yang, H Xie, Y Jia, X Kong, J Zheng, Z Zhang, Y Liu, L Liu, Y Lan. "CPSea: Large-scale cyclic peptide-protein complex dataset for machine learning in cyclic peptide design." NeurIPS, 2025.

W Zhu, C Li, X Tian, Y Wang, Y Jia, J Wang, B Gao, YQ Zhang, WY Ma, Y Lan. "Coder as Editor: Code-driven Interpretable Molecular Optimization." arXiv preprint arXiv:2510.14455, 2025.

Y Shi, Y Jia, W Zhang. "Molecular and neural basis of vomiting behavior in Drosophila melanogaster." Science Advances 11 (37), eadv1143, 2025.

W Zhu, J Wang, B Gao, Y Jia, H Tan, YQ Zhang, WY Ma, Y Lan. "AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation." arXiv preprint arXiv:2506.05768, 2025.

X Hong, B Gao, Y Jia, W Zhu, Q Chen, X Tian, Z Zhong, J Wang, Y Lan. "How Good is AlphaFold3 at Ranking Drug Binding Affinities?" ICML GenBio Workshop, 2025.

Y Huang, B Gao, Y Jia, H Ma, WY Ma, YQ Zhang, Y Lan. "Redefining the task of Bioactivity Prediction." ICLR, 2025.

H Tan, B Gao, J Li, Y Huang, W Zhu, J Wang, Y Jia, Y Mo, YQ Zhang, WY Ma, Y Lan. "Multi-Granular Contrastive Alignment and Fusion for Fragment-Enhanced Virtual Screening." ICML GenBio Workshop, 2025.

X Kong, Y Jia, W Huang, Y Liu. "Full-atom peptide design with geometric latent diffusion." NeurIPS, 2024.

X Peng, F Guo, R Guo, J Sun, J Guan, Y Jia, Y Xu, Y Huang, M Zhang, J Peng, X Wang, C Han, Z Wang, J Ma. "Atom-level generative foundation model for molecular interaction with pockets." bioRxiv, 2024.10.17.618827.

S Feng, J Zheng, Y Jia, Y Huang, F Zhou, WY Ma, Y Lan. "MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis." arXiv preprint arXiv:2406.17797, 2024.

Y Huang, B Gao, Y Jia, H Ma, WY Ma, YQ Zhang, Y Lan. "SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction." arXiv preprint arXiv:2406.08961, 2024.

Y Mo, X Hong, B Gao, Y Jia, Y Lan. "Multi-level interaction modeling for protein mutational effect prediction." arXiv preprint arXiv:2405.17802, 2024.

S Feng, M Li, Y Jia, W Ma, Y Lan. "Protein-ligand binding representation learning from fine-grained interactions." ICLR, 2024.

B Gao, Y Jia, Y Mo, Y Ni, W Ma, Z Ma, Y Lan. "ProFSA: Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment." ICLR, 2024.

B Gao, B Qiang, H Tan, Y Jia, M Ren, M Lu, J Liu, WY Ma, Y Lan. "Drugclip: Contrastive protein-molecule representation learning for virtual screening." NeurIPS, 2023.

P Jin, B Zhu, Y Jia, Y Zhang, W Wang, Y Shen, Y Zhong, Y Zheng, Y Wang, Y Tong, W Zhang, S Li. "Single-cell transcriptomics reveals the brain evolution of web-building spiders." Nature Ecology & Evolution 7 (12), 2125-2142, 2023.

Y Jia, S Li, X Guo, B Lei, J Hu, XH Xu, W Zhang. "Selfee, self-supervised features extraction of animal behaviors." eLife, 2022.

R Luo, Y Zhang, Y Jia, Y Zhang, Z Li, J Zhao, T Liu, W Zhang. "Molecular basis and homeostatic regulation of Zinc taste." Protein & cell 13 (6), 462-469, 2022.

Y Hu, Y Jia, T Deng, T Liu, W Zhang. "Molecular Mechanisms for Frequency Specificity in a Drosophila Hearing Organ." bioRxiv, 2021.07.11.451973.

P Wang, Y Jia, T Liu, YN Jan, W Zhang. "Visceral mechano-sensing neurons control Drosophila feeding by using Piezo as a sensor." Neuron 108 (4), 640-650. e4, 2020.

Z Zhang, T Li, Y Wu, Y Jia, C Tan, X Xu, G Wang, J Lv, W Zhang, Y He, J Pei, C Ma, G Li, H Xu, L Shi, H Peng, H Li. "Truly Concomitant and Independently Expressed Short‐and Long‐Term Plasticity in a Bi2O2Se‐Based Three‐Terminal Memristor." Advanced Materials 31 (3), 1805769, 2019.