Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning. - Yunan Luo; Jianyang Zeng 001; Bonnie Berger; Jian Peng 001 (RECOMB, 2016)

A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information. - Yunan Luo; Xinbin Zhao; Jingtian Zhou; Jinling Yang; Yanqing Zhang 010; Wenhua Kuang; Jian Peng 001; Ligong Chen; Jianyang Zeng 001 (RECOMB, 2017)

Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action. - Yunan Luo; Sheng Wang 001; Jinfeng Xiao; Jian Peng 001 (PSB, 2018)

Deciphering Signaling Specificity with Deep Neural Networks. - Yunan Luo; Jianzhu Ma; Yang Liu 097; Qing Ye; Trey Ideker; Jian Peng 001 (RECOMB, 2018)

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. - Yunan Luo; Jianzhu Ma; Xiaoming Zhao 001; Yufeng Su; Yang Liu 097; Trey Ideker; Jian Peng 001 (RECOMB, 2019)

Metagenomic binning through low-density hashing. - Yunan Luo; Yun William Yu; Jianyang Zeng 001; Bonnie Berger; Jian Peng 001 (Bioinform., 2019)

Sequence Modeling of Temporal Credit Assignment for Episodic Reinforcement Learning. - Yang Liu 097; Yunan Luo; Yuanyi Zhong; Xi Chen; Qiang Liu 001; Jian Peng 001 (CoRR, 2019)

DeepMask: an algorithm for cloud and cloud shadow detection in optical satellite remote sensing images using deep residual network. - Ke Xu; Kaiyu Guan; Jian Peng 001; Yunan Luo; Sibo Wang 005 (CoRR, 2019)

Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction. - Yufeng Su; Yunan Luo; Xiaoming Zhao 001; Yang Liu 097; Jian Peng 001 (PLoS Comput. Biol., 2019)

Evolutionary Context-Integrated Deep Sequence Modeling for Protein Engineering. - Yunan Luo; Lam Vo; Hantian Ding; Yufeng Su; Yang Liu 097; Wesley Wei Qian; Huimin Zhao 007; Jian Peng 001 (RECOMB, 2020)

Pre-training of Graph Neural Network for Modeling Effects of Mutations on Protein-Protein Binding Affinity. - Xianggen Liu; Yunan Luo; Sen Song; Jian Peng 001 (CoRR, 2020)

When causal inference meets deep learning. - Yunan Luo; Jian Peng 001; Jianzhu Ma (Nat. Mach. Intell., 2020)

STAIR 2.0: A Generic and Automatic Algorithm to Fuse Modis, Landsat, and Sentinel-2 to Generate 10 m, Daily, and Cloud-/Gap-Free Surface Reflectance Product. - Yunan Luo; Kaiyu Guan; Jian Peng 001; Sibo Wang 005; Yizhi Huang (Remote. Sens., 2020)

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity. - Xianggen Liu; Yunan Luo; Pengyong Li; Sen Song; Jian Peng 001 (PLoS Comput. Biol., 2021)

scPretrain: multi-task self-supervised learning for cell-type classification. - Ruiyi Zhang; Yunan Luo; Jianzhu Ma; Ming Zhang 004; Sheng Wang 012 (Bioinform., 2022)

Interpretable Geometric Deep Learning via Learnable Randomness Injection. - Siqi Miao 001; Yunan Luo; Mia Liu; Pan Li 005 (ICLR, 2023)

LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion. - Jiaqi Guan; Xingang Peng; Peiqi Jiang; Yunan Luo; Jian Peng 001; Jianzhu Ma (NeurIPS, 2023)

Supervised biological network alignment with graph neural networks. - Kerr Ding; Sheng Wang 012; Yunan Luo (Bioinform., 2023)

Sensing the shape of functional proteins with topology. - Yunan Luo (Nat. Comput. Sci., 2023)

Calibrated geometric deep learning improves kinase-drug binding predictions. - Yunan Luo; Yang Liu 097; Jian Peng 001 (Nat. Mac. Intell., 2023)

FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames. - Ruidong Wu; Ruihan Guo; Rui Wang; Shitong Luo; Yue Xu; Jiahan Li; Jianzhu Ma; Qiang Liu 001; Yunan Luo; Jian Peng 001 (ICML, 2024)

Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape. - Junming Zhao; Chao Zhang; Yunan Luo (RECOMB, 2024)

Leveraging conformal prediction to annotate enzyme function space with limited false positives. - Kerr Ding; Jiaqi Luo; Yunan Luo (PLoS Comput. Biol., 2024)

Group Ligands Docking to Protein Pockets. - Jiaqi Guan; Jiahan Li; Xiangxin Zhou; Xingang Peng; Sheng Wang 001; Yunan Luo; Jian Peng 001; Jianzhu Ma (ICLR, 2025)

Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction. - Ziang Li; Yunan Luo (RECOMB, 2025)

Learning Maximally Spanning Representations Improves Protein Function Annotation. - Jiaqi Luo; Yunan Luo (RECOMB, 2025)