Publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

  1. Nature Methods
    scGPT: toward building a foundation model for single-cell multi-omics using generative AI
    H. Cui*, C. Wang*, H. Maan, K. Pang, F. Luo, N. Duan, and B. Wang
    Nature Methods. Pioneering single-cell foundation model with generative pretraining. , 2024
    DOI HTML
  2. Towards Multimodal Foundation Models in Molecular Cell Biology
    H. Cui, A. Tejada-Lapuerta, M. Brbić, J. Saez-Rodriguez, S. Cristea, H. Goodarzi, M. Lotfollahi, F.J. Theis, and B. Wang
    NatureForthcoming. Perspective on multimodal foundation models across the central dogma. , 2025
  3. bioRxiv
    LUMI-lab: a Foundation Model-Driven Autonomous Platform Enabling Discovery of New Ionizable Lipid Designs for mRNA Delivery
    H. Cui*, Y. Xu*, K. Pang, G. Li, F. Gong, B. Wang, and B. Li
    bioRxiv. Under review (Cell). Fully self-driving lab for active-learning experiments on lipid design. , 2025
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  4. bioRxiv
    scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics
    C.X. Wang*, H. Cui*, A.H. Zhang, R. Xie, H. Goodarzi, and B. Wang
    bioRxiv, 2025
  5. bioRxiv
    MethylGPT: a foundation model for the DNA methylome
    K. Ying*, J. Song*, H. Cui*, Y. Zhang, S. Li, X. Chen, H. Liu, A. Eames, D.L. McCartney, R.E. Marioni, and J.R. Poganik
    bioRxiv, 2024
  6. Nature Communications
    AGILE platform: a deep learning powered approach to accelerate LNP development for mRNA delivery
    Y. Xu*, S. Ma*, H. Cui*, J. Chen, S. Xu, F. Gong, A. Golubovic, M. Zhou, K.C. Wang, A. Varley, and R.X.Z. Lu
    Nature Communications, 2024
  7. Genome Biology
    DeepVelo: deep learning extends RNA velocity to multi-lineage systems with cell-specific kinetics
    H. Cui*, H. Maan*, M.C. Vladoiu, J. Zhang, M.D. Taylor, and B. Wang
    Genome Biology, 2024
  8. EMNLP 2022
    CodeExp: Explanatory Code Document Generation
    H. Cui, C. Wang, J. Huang, J.P. Inala, T. Mytkowicz, B. Wang, J. Gao, and N. Duan
    In Findings of the Association for Computational Linguistics: EMNLP 2022, Dec 2022
  9. bioRxiv
    scFormer: a universal representation learning approach for single-cell data using transformers
    H. Cui*, C. Wang*, H. Maan, N. Duan, and B. Wang
    bioRxiv, Dec 2022
  10. ICML 2022
    A Deep Learning Framework for Estimating Cell-specific Kinetic Rates of RNA Velocity
    H. Cui*, H. Maan*, M.D. Taylor, and B. Wang
    In The 2022 ICML Workshop on Computational Biology, Dec 2022
  11. Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease
    M.G. Sugiyama*, H. Cui*, D.Y.S. Redka, M. Karimzadeh, E. Rujas, H. Maan, S. Hayat, K. Cheung, R. Misra, J.B. McPhee, and R.D. Viirre
    Scientific Reports, Dec 2021
  12. arXiv
    Learning global and local consistent representations for unsupervised image retrieval via deep graph diffusion networks
    Z. Dou*, H. Cui*, L. Zhang, and B. Wang
    arXiv preprint arXiv:2001.01284, Dec 2020
  13. Nature Methods
    Transformers in single-cell omics: a review and new perspectives
    A. Szałata, K. Hrovatin, S. Becker, A. Tejada-Lapuerta, H. Cui, B. Wang, and F.J. Theis
    Nature Methods, Dec 2024
  14. Abstract A029: Evaluating and interpreting scGPT: A foundation model for single-cell biology in real-world cancer clinical trial data
    R. Tan, H. Cui, B. Wang, K. Perez, A.D. Costa, A. Jordan, T. Karacic, D. Elganainy, D.Y. Gui, S. Kim, and C. Yuan
    Cancer Research, Dec 2024
  15. Nature Biomedical Engineering
    Stretchable ultrasonic arrays for the three-dimensional mapping of the modulus of deep tissue
    H. Hu, Y. Ma, X. Gao, D. Song, M. Li, H. Huang, X. Qian, R. Wu, K. Shi, H. Ding, M. Lin, X. Chen, W. Zhao, B. Qi, S. Zhou, R. Chen, Y. Gu, Y. Chen, Y. Lei, C. Wang, C. Wang, Y. Tong, H. Cui, A. Abdal, Y. Zhu, X. Tian, Z. Chen, C. Lu, X. Yang, J. Mu, Z. Lou, M. Eghtedari, Q. Zhou, A. Oberai, and S. Xu
    Nature Biomedical Engineering, Dec 2023
  16. Abstract PO-018: Computational staining of tumor hypoxia from H&E images using convolutional neural networks
    M. Zaidi, H. Cui, B. Wang, T.D. McKee, and B.G. Wouters
    Clinical Cancer Research, Dec 2021
  17. DaSH 2022
    Execution-based Evaluation for Data Science Code Generation Models
    J. Huang, C. Wang, J. Zhang, C. Yan, H. Cui, J.P. Inala, C. Clement, N. Duan, and J. Gao
    In DaSH 2022, Dec 2022
  18. TALLIP
    Outline Extraction with Question-Specific Memory Cells
    J. Yang, H. Cui, S. Li, S. Gao, J. Guo, and Z. Lu
    ACM Transactions on Asian and Low-Resource Language Information Processing (TALLIP), Dec 2020
  19. Neurocomputing
    Finding decision jumps in text classification
    X. Liu, L. Mou, H. Cui, Z. Lu, and S. Song
    Neurocomputing, Dec 2020
  20. arXiv
    Jumper: Learning when to make classification decisions in reading
    X. Liu, L. Mou, H. Cui, Z. Lu, and S. Song
    arXiv preprint arXiv:1807.02314, Dec 2018
  21. Neurocomputing
    Training deep neural networks with discrete state transition
    G. Li, L. Deng, L. Tian, H. Cui, W. Han, J. Pei, and L. Shi
    Neurocomputing, Dec 2018
  22. ACL 2018
    Object-oriented Neural Programming (OONP) for Document Understanding
    Z. Lu, X. Liu, H. Cui, Y. Yan, and D. Zheng
    In Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), Jul 2018