We present a method for inferring spatial gene expression from histology images using feature-level fusion of pathology foundation models.
📖 _Journal of Open Source Software_ · 2026 — Open-source toolkit for integrating spatial transcriptomics data from Xenium, CosMx and MERFISH into a standardised SpatialData …
📖 _Nature Communications_ · 2025 — A mathematical framework for mining higher-order triadic interactions in complex networks, showing how signed triadic relationships shape network …
PySlyde is a lightweight, open-source Python toolkit for preprocessing whole-slide images in digital pathology, enabling reproducible and scalable analysis pipelines.
📖 _Nature Cancer (under review)_ · 2025 — A spatio-molecular atlas characterising response trajectories in triple-negative breast cancer using spatial transcriptomics and …
Network ontology transcript annotation analysis reveals cross-cellular communication mechanisms underlying sex determination in Cannabis sativa.
📖 _Scientific Reports_ · 2024 — A formal connection between deep learning dynamics and Ricci flow on Riemannian manifolds, giving a geometric framework for neural network training.
📖 _Nature Communications_ · 2024 — Using Ricci flow to chart cellular differentiation trajectories and reveal the geometric structure of gene expression landscapes during …
We use multilayer network exploration to define the molecular landscape of premature aging diseases, revealing shared and distinct molecular mechanisms across progeroid syndromes.
We present a comprehensive framework for Random Walk with Restart on multilayer networks, extending its application from node prioritisation to supervised link prediction and …