Papers

[Google Scholar]

1. Learning maximally spanning representations improves protein function annotation

   Jiaqi Luo, and Yunan Luo

   RECOMB, 2025 (accepted)
2. Rewiring protein sequence and structure generative models to enhance protein stability prediction

   Ziang Li, and Yunan Luo

   RECOMB, 2025 (accepted)
3. BioDolphin as a comprehensive database of lipid–protein binding interactions

   Li-Yen Yang, Kaike Ping, Yunan Luo, and Andrew C McShan

   Communications Chemistry, 2024

   Website
4. Machine learning-guided co-optimization of fitness and diversity facilitates combinatorial library design in enzyme engineering

   Kerr Ding, Michael Chin, Yunlong Zhao, Wei Huang, Binh Khanh Mai, Huanan Wang, Peng Liu, Yang Yang, and Yunan Luo

   Nature Communications, 2024
5. Opportunities and challenges of graph neural networks in electrical engineering

   Eli Chien, Mufei Li, Anthony Aportela, Kerr Ding, Shuyi Jia, Supriyo Maji, Zhongyuan Zhao, Javier Duarte, Victor Fung, Cong Hao, Yunan Luo, Olgica Milenkovic, David Pan, Santiago Segarra, and Pan Li

   Nature Reviews Electrical Engineering, 2024

   PDF
6. 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, Yunan Luo, and Jian Peng

   ICML, 2024 (Spotlight)

   arXiv HTML
7. Leveraging conformal prediction to annotate enzyme function space with limited false positives

   Kerr Ding, Jiaqi Luo, and Yunan Luo

   PLOS Computational Biology, 2024
8. Contrastive Fitness Learning: Reprogramming Protein Language Models for Low-N Learning of Protein Fitness Landscape

   Junming Zhao, Chao Zhang, and Yunan Luo

   RECOMB, 2024

   bioRxiv
9. Calibrated geometric deep learning improves kinase-drug binding predictions

   Yunan Luo, Yang Liu, and Jian Peng

   Nature Machine Intelligence, 2023

   PDF
10. LinkerNet: Fragment Poses and Linker Co-Design with 3D Equivariant Diffusion

    Jiaqi Guan, Xingang Peng, PeiQi Jiang, Yunan Luo, Jian Peng, and Jianzhu Ma

    NeurIPS, 2023 (Spotlight)
11. Supervised biological network alignment with graph neural networks

    Kerr Ding, Sheng Wang, and Yunan Luo

    ISMB, 2023
12. Metabolic activity organizes olfactory representations

    Wesley W Qian, Jennifer N Wei, Benjamin Sanchez-Lengeling, Brian K Lee, Yunan Luo, Marnix Vlot, Koen Dechering, Jian Peng, Richard C Gerkin, and Alexander B Wiltschko

    eLife, 2023
13. Enzyme function prediction using contrastive learning

    Tianhao Yu, Haiyang Cui, Jianan Li, Yunan Luo, Guangde Jiang, and Huimin Zhao

    Science, 2023
14. Sensing the shape of functional proteins with topology

    Yunan Luo

    Nature Computational Science, 2023 (News & Views)

    PDF
15. Interpretable Geometric Deep Learning via Learnable Randomness Injection

    Siqi Miao, Yunan Luo, Mia Liu, and Pan Li

    ICLR, 2023
16. Contrastive learning of protein representations with graph neural networks for structural and functional annotations

    Jiaqi Luo, and Yunan Luo

    PSB, 2023
17. Next Decade’s AI-Based Drug Development Features Tight Integration of Data and Computation

    Yunan Luo, Jian Peng, and Jianzhu Ma

    Health Data Science, 2022 (Perspective)
18. scPretrain: multi-task self-supervised learning for cell-type classification

    Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, and Sheng Wang

    Bioinformatics, 2022
19. ECNet is an evolutionary context-integrated deep learning framework for protein engineering

    Yunan Luo*, Guangde Jiang*, Tianhao Yu, Yang Liu, Lam Vo, Hantian Ding, Yufeng Su, Wesley Wei Qian, Huimin Zhao, and Jian Peng

    Nature Communications, 2021
20. Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

    Xianggen Liu, Yunan Luo, Pengyong Li, Sen Song, and Jian Peng

    PLoS computational biology, 2021
21. Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients

    Jianzhu Ma, Samson H. Fong, Yunan Luo, Christopher J. Bakkenist, John Paul Shen, Soufiane Mourragui, Lodewyk F. A. Wessels, Marc Hafner, Roded Sharan, Jian Peng, and Trey Ideker

    Nature Cancer, 2021
22. Crowdsourced mapping of unexplored target space of kinase inhibitors

    Anna Cichońska, and Others (including Yunan Luo in the challenge-winning team)

    Nature Communications, 2021
23. An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19

    Yiyue Ge, Tingzhong Tian, Suling Huang, Fangping Wan, Jingxin Li, Shuya Li, Xiaoting Wang, Hui Yang, Lixiang Hong, Nian Wu, Enming Yuan, Yunan Luo, Lili Cheng, Chengliang Hu, Yipin Lei, Hantao Shu, Xiaolong Feng, Ziyuan Jiang, Yunfu Wu, Ying Chi, Xiling Guo, Lunbiao Cui, Liang Xiao, Zeng Li, Chunhao Yang, Zehong Miao, Ligong Chen, Haitao Li, Hainian Zeng, Dan Zhao, Fengcai Zhu, Xiaokun Shen, and Jianyang Zeng

    Signal Transduction and Targeted Therapy, 2021
24. Evolutionary context-integrated deep sequence modeling for protein engineering

    Yunan Luo, Lam Vo, Hantian Ding, Yufeng Su, Yang Liu, Wesley Wei Qian, Huimin Zhao, and Jian Peng

    RECOMB, 2020
25. Characterization of SARS-CoV-2 viral diversity within and across hosts

    Palash Sashittal*, Yunan Luo*, Jian Peng, and Mohammed El-Kebir

    bioRxiv:2020.05.07.083410, 2020
26. 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, Sibo Wang, and Yizhi Huang

    Remote Sensing, 2020
27. When causal inference meets deep learning

    Yunan Luo, Jian Peng, and Jianzhu Ma

    Nature Machine Intelligence, 2020 (News & Views)

    PDF
28. Deriving high-spatiotemporal-resolution leaf area index for agroecosystems in the U.S. Corn Belt using Planet Labs CubeSat and STAIR fusion data

    Hyungsuk Kimm, Kaiyu Guan, Chongya Jiang, Bin Peng, Laura F. Gentry, Scott C. Wilkin, Sibo Wang, Yaping Cai, Carl J. Bernacchi, Jian Peng, and Yunan Luo

    Remote Sensing of Environment, 2020
29. Integrating Deep Neural Networks and Symbolic Inference for Organic Reactivity Prediction

    Wesley Wei Qian, Nathan T. Russell, Claire L. W. Simons, Yunan Luo, Martin D. Burke, and Jian Peng

    chemRxiv:11659563, 2020
30. Sequence Modeling of Temporal Credit Assignment for Episodic Reinforcement Learning

    Yang Liu, Yunan Luo, Yuanyi Zhong, X. Chen, Qiang Liu, and Jian Peng

    arXiv:1905.13420, 2019
31. 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, Yunan Luo, and Sibo Wang

    arXiv:1911.03607, 2019
32. Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction

    Yufeng Su*, Yunan Luo*, Xiaoming Zhao, Yang Liu, and Jian Peng

    PLoS computational biology, 2019 (Presented at GLBIO’19)
33. Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning

    Yunan Luo*, Jianzhu Ma*, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, and Jian Peng

    RECOMB, 2019
34. Metagenomic binning through low-density hashing

    Yunan Luo*, Yun William Yu*, Jianyang Zeng, Bonnie Berger, and Jian Peng

    Bioinformatics, 2018
35. STAIR: A generic and fully-automated method to fuse multiple sources of optical satellite data to generate a high-resolution, daily and cloud-/gap-free surface reflectance product

    Yunan Luo, Kaiyu Guan, and Jian Peng

    Remote Sensing of Environment, 2018
36. Deciphering Signaling Specificity with Deep Neural Networks

    Yunan Luo*, Jianzhu Ma*, Yang Liu, Qing Ye, Trey Ideker, and Jian Peng

    RECOMB, 2018
37. Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action

    Yunan Luo, Sheng Wang, Jinfeng Xiao, and Jian Peng

    PSB, 2018
38. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

    Yunan Luo*, Xinbin Zhao*, Jingtian Zhou*, Jinglin Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng, Ligong Chen, and Jianyang Zeng

    Nature communications, 2017 (Extended version of the RECOMB’17 paper)
39. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

    Yunan Luo*, Xinbin Zhao*, Jingtian Zhou*, Jinglin Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng, Ligong Chen, and Jianyang Zeng

    RECOMB, 2017
40. Low-density locality-sensitive hashing boosts metagenomic binning

    Yunan Luo, Jianyang Zeng, Bonnie Berger, and Jian Peng

    RECOMB, 2016