Synaptic dynamics and neuronal network connectivity are reflected in the distribution of times in Up states. - Khanh Dao Duc; Pierre Parutto; Xiaowei Chen; Jérôme Epsztein; Arthur Konnerth; David Holcman (Frontiers Comput. Neurosci., 2015)

The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels. - Jérémie Sibille; Khanh Dao Duc; David Holcman; Nathalie Rouach (PLoS Comput. Biol., 2015)

Oscillatory Survival Probability: Analytical and Numerical Study of a Non-Poissonian Exit Time. - Khanh Dao Duc; Zeev Schuss; David Holcman (Multiscale Model. Simul., 2016)

Using a Riemannian Elastic Metric for Statistical Analysis of Tumor Cell Shape Heterogeneity. - Wanxin Li; Ashok Prasad; Nina Miolane; Khanh Dao Duc (GSI (2), 2021)

MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX. - Arthur Ecoffet; Frédéric Poitevin; Khanh Dao Duc (Bioinform., 2021)

ICLR 2021 Challenge for Computational Geometry & Topology: Design and Results. - Nina Miolane; Matteo Caorsi; Umberto Lupo; Marius Guerard; Nicolas Guigui; Johan Mathe; Yann Cabanes; Wojciech Reise; Thomas Davies 001; António Leitão; Somesh Mohapatra; Saiteja Utpala; et al. (CoRR, 2021)

Defining an action of SO(d)-rotations on images generated by projections of d-dimensional objects: Applications to pose inference with Geometric VAEs. - Nicolas Legendre; Khanh Dao Duc; Nina Miolane (CoRR, 2022)

Testing geometric representation hypotheses from simulated place cell recordings. - Thibault Niederhauser; Adam Lester; Nina Miolane; Khanh Dao Duc; Manu S. Madhav (CoRR, 2022)

Quantifying Extrinsic Curvature in Neural Manifolds. - Francisco Acosta; Sophia Sanborn; Khanh Dao Duc; Manu S. Madhav; Nina Miolane (CVPR Workshops, 2023)

ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings. - Chenwei Zhang; Jordan Lovrod; Boyan Beronov; Khanh Dao Duc; Anne Condon (MLCB, 2023)

Visualizing DNA reaction trajectories with deep graph embedding approaches. - Chenwei Zhang; Khanh Dao Duc; Anne Condon (CoRR, 2023)

AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps. - Aryan Tajmir Riahi; Geoffrey Woollard; Frédéric Poitevin; Anne Condon; Khanh Dao Duc (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures. - Artem Kushner; Anton S. Petrov; Khanh Dao Duc (Nucleic Acids Res., 2023)

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets. - Wanxin Li; Jules Mirone; Ashok Prasad; Nina Miolane; Carine Legrand; Khanh Dao Duc (Frontiers Bioinform., 2023)

Synthetic High-resolution Cryo-EM Density Maps with Generative Adversarial Networks. - Chenwei Zhang; Anne Condon; Khanh Dao Duc (CoRR, 2024)

A comprehensive survey and benchmark of deep learning-based methods for atomic model building from cryo-electron microscopy density maps. - Chenwei Zhang; Anne Condon; Khanh Dao Duc (Briefings Bioinform., 2025)

CryoSAMU: Enhancing 3D Cryo-EM Density Maps of Protein Structures at Intermediate Resolution with Structure-Aware Multimodal U-Nets. - Chenwei Zhang; Anne Condon; Khanh Dao Duc (CoRR, 2025)