Yunan Luo

PhD Candidate
Department of Computer Science
University of Illinois Urbana-Champaign
Email: yunan [at] illinois.edu

I am currently a PhD candidate in the Department of Computer Science at the University of Illinois Urbana-Champaign, advised by Prof. Jian Peng. Before coming to CS@Illinois, I received my bachelor’s degree in Computer Science from Yao Class at Tsinghua University in 2016. During my college, I had been working in the Machine Learning and Computational Biology Group, advised by Prof. Jianyang Zeng. I recently received a CompGen Fellowship (2018-2020) and a Baidu Scholarship (2019-2021).

I am broadly interested in computational biology and machine learning, with a focus on developing AI and data science methods to reveals core scientific insights into biology and medicine. Recent interests include deep learning, transfer learning, sequence and graph representation learning, network and system biology, functional genomics, cancer genomics, drug repositioning and discovery, and AI-guided biological design and discovery.

📢 I will be joining Georgia Institute of Technology as an Assistant Professor in the School of Computational Science and Engineering (CSE) in January 2022!

CV | Google Scholar

Selected Honors and Awards

  • Baidu Scholarship, 2019-2021
  • Yunni and Maxine Pao Memorial Fellowship, UIUC, 2020
  • C.L. and Jane Liu Award (annually awarded to one junior CS Ph.D. showing exceptional research promise), UIUC, 2019
  • Winner of the IDG-DREAM Drug-Kinase Binding Prediction Challenge, 2019
  • CompGen Fellow (Ă—2), UIUC, 2018-2020
  • GLBIO Travel Fellowship, ISCB, 2019
  • PSB Travel Fellowship, ISCB, 2018
  • RECOMB Travel Fellowship (Ă—4), ISCB, 2016-2019
  • Computer Science Excellence Fellowship, UIUC, 2016-2017
  • Best Undergraduate Thesis Award, Tsinghua University, 2016
  • Member of Tsinghua Xuetang Talents Program, Tsinghua University, 2012-2016

Papers

(*=equal contribution)

  1. 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
  2. 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
  3. 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
  4. Crowdsourced mapping of unexplored target space of kinase inhibitors
    Anna Cichońska, and Others (including Yunan Luo in the challenge-winning team)
    Nature Communications, 2021
  5. 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
  6. 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
  7. 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
  8. 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
  9. When causal inference meets deep learning
    Yunan Luo, Jian Peng, and Jianzhu Ma
    Nature Machine Intelligence, 2020 (News & Views)
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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)
  15. 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
  16. Metagenomic binning through low-density hashing
    Yunan Luo*, Yun William Yu*, Jianyang Zeng, Bonnie Berger, and Jian Peng
    Bioinformatics, 2018
  17. 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
  18. Deciphering Signaling Specificity with Deep Neural Networks.
    Yunan Luo*, Jianzhu Ma*, Yang Liu, Qing Ye, Trey Ideker, and Jian Peng
    RECOMB, 2018
  19. Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action.
    Yunan Luo, Sheng Wang, Jinfeng Xiao, and Jian Peng
    PSB, 2018
  20. 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)
  21. 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
  22. Low-density locality-sensitive hashing boosts metagenomic binning
    Yunan Luo, Jianyang Zeng, Bonnie Berger, and Jian Peng
    RECOMB, 2016