Wenjun Zhao
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Publications


Publication list

Authors are listed alphabetically, unless not.

Preprints

  1. W Zhao, E Fertig, G Stein-O'Brien
    CycleGRN: Inferring Gene Regulatory Networks from Cyclic Flow Dynamics in Single-Cell RNA-seq (preprint)

  2. W Zhao, A Plaza-Rodriguez, P Luanpaisanon, EX Wang, L Gyllingberg, R Singh, E Fertig, G Stein-O'Brien
    Inferring the regulation dynamics of oscillatory networks from scRNA-seq data (preprint)

  3. W Zhao, DJ Sutherland, K Dao Duc.
    Fast and Interpretable Quantification of Biological Shape Heterogeneity via Stratified Wasserstein Kernel (preprint)

  4. AD Lipnick, EG Tabak, G Trigila, Y Wang, X Ye, and W Zhao.
    The Monge Optimal Transport Barycenter Problem (preprint)

  5. EG Tabak, G Trigila, and W Zhao.
    The Hierarchical Barycenter: Conditional Probability Simulation with Structured and Unobserved Covariates (preprint)

Published/Accepted

  1. S Yu, A Kushner, E Teasell, W Zhao, S Srebnik, and K Dao Duc.
    Advance Coarse Grained Model for Fast Simulation of Nascent Polypeptide Chain within the Ribosome (preprint) (publication)
    Biophysical Journal (2025).

  2. W Zhao, S Maffa, and B Sandstede.
    Data-driven Continuation of Patterns and their Bifurcations (poster) (preprint) (publication)
    SIAM Journal on Applied Dynamical Systems (2025).

  3. W Zhao, E Larschan, B Sandstede, and R Singh.
    Optimal Transport Reveals Dynamic Gene Regulatory Networks via Gene Velocity Estimation (preprint)(publication)
    PLOS Computational Biology (2025)

  4. W Zhao and EG Tabak.
    Adaptive Kernel Conditional Density Estimation (preprint)(publication)
    Information and Inference: A Journal of the IMA (2025).

  5. EG Tabak, G Trigila, and W Zhao.
    The Conditional Barycenter Problem, its Data-Driven Formulation and its Solution through Normalizing Flows (preprint)(publication)
    Communications in Mathematical Sciences (2024).

  6. H Zhang and W Zhao.
    A Memory-efficient Neural ODE Framework Based on High-level Adjoint Differentiation (preprint) (publication)
    IEEE Transactions on Artificial Intelligence (2022).

  7. EG Tabak, G Trigila, and W Zhao.
    Distributional Barycenter Problem through Data-Driven Flows (preprint) (publication)
    Pattern Recognition (2022).

  8. W Zhao.
    Sample-based Optimal Transport in Statistical Data analysis.
    PhD thesis

  9. EG Tabak, G Trigila, and W Zhao.
    Conditional Density Estimation and Simulation through Optimal Transport (preprint)(publication)
    Machine Learning (2020).

  10. EG Tabak, G Trigila, and W Zhao.
    Data Driven Conditional Optimal Transport (poster) (preprint) (publication)
    33rd Conference on Neural Information Processing Systems (NeurIPS) OTML Workshop (2019). (Extended version in Machine Learning (2021))