Publications

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

2025

  1. Nature Commun
    Editor’s Highlight
    SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data
    Mingze Dong, David Su, Harriet Kluger, and 2 more authors
    Nature Communications (Featured Article, <5%), 2025
    HTML
  2. Preprint
    Predicting cellular responses to perturbation across diverse contexts with STATE
    Abhinav Adduri, Dhruv Gautam, Beatrice Bevilacqua, and 8 more authors
    bioRxiv, 2025
    HTML
  3. Nature Genetics
    Advancing biological understanding of cellular senescence with computational multiomics
    Sheng Li, Paula A. Agudelo Garcia, Constantin Aliferis, and 95 more authors
    Nature Genetics, 2025
    HTML
  4. NeurIPS
    Understanding and enhancing mask-based pretraining towards universal representations
    Mingze Dong, Leda Wang, and Yuval Kluger
    The Thirty-Ninth Annual Conference on Neural Information Processing Systems, 2025

2024

  1. Preprint
    Scaling deep identifiable models enables zero-shot characterization of single-cell biological states
    Mingze Dong, Kriti Agrawal, Rong Fan, and 3 more authors
    bioRxiv, 2024
    HTML
  2. Preprint
    Pertpy: an end-to-end framework for perturbation analysis
    Lukas Heumos, Yuge Ji, Lilly May, and 25 more authors
    bioRxiv, 2024
    HTML

2023

  1. Nature Methods
    Causal identification of single-cell experimental perturbation effects with CINEMA-OT
    Mingze Dong, Bao Wang, Jessica Wei, and 8 more authors
    Nature Methods, 2023
    HTML
  2. ICML
    Towards Understanding and Reducing Graph Structural Noise for GNNs
    Mingze Dong, and Yuval Kluger
    Proceedings of the 40th International Conference on Machine Learning, 2023
    HTML
  3. Nature
    Spatial epigenome–transcriptome co-profiling of mammalian tissues
    Di Zhang, Yanxiang Deng, Petra Kukanja, and 8 more authors
    Nature, 2023
    HTML

2022

  1. ICLR
    Spotlight
    GEASS: Neural causal feature selection for high-dimensional biological data
    Mingze Dong, and Yuval Kluger
    The Eleventh International Conference on Learning Representations (Spotlight), 2022
    HTML