<link>https://anthbapt.github.io/</link></image><item><title>Universal Multilayer Network Exploration by Random Walk with Restart</h1> <article> <h1>Universal Multilayer Network Exploration by Random Walk with Restart</h1> <p>Wed, 01 Jun 2022 00:00:00 +0000</p> </article> <article> <h1>MOSAIK: Multi-Origin Spatial Transcriptomics Analysis and Integration Kit</h1> <p>Thu, 01 Jan 2026 00:00:00 +0000</p> </article> <article> <h1>Mining higher-order triadic interactions</h1> <p>Mon, 01 Dec 2025 00:00:00 +0000</p> </article> <article> <h1>SMART: A Spatio-Molecular Atlas of Response Trajectories in Triple-Negative Breast Cancer</h1> <p>Wed, 01 Oct 2025 00:00:00 +0000</p> </article> <article> <h1>Deep Learning as Ricci Flow</h1> <p>Tue, 01 Oct 2024 00:00:00 +0000</p> </article> <article> <h1>Charting cellular differentiation trajectories with Ricci flow</h1> <p>Fri, 01 Mar 2024 00:00:00 +0000</p> </article> <article> <h1>Spatial gene expression inference from histology using feature-level fusion of pathology foundation models</h1> <p>Wed, 01 Apr 2026 00:00:00 +0000</p> </article> <article> <h1>PySlyde: A Lightweight, Open-Source Toolkit for Pathology Preprocessing</h1> <p>Sat, 01 Nov 2025 00:00:00 +0000</p> </article> <article> <h1>Unraveling Cross-Cellular Communication in Cannabis sativa Sex Determination: A Network Ontology Transcript Annotation Analysis</h1> <p>Thu, 01 May 2025 00:00:00 +0000</p> </article> <article> <h1>Cell-cell communications</h1> <p>Fri, 01 Nov 2024 00:00:00 +0000</p> <p>This project explores the use of random walk with restart (RWR) on tissue neighbourhood graphs to define cell–cell communication in the spatial transcriptomics context.</p> <p>Key contributions:</p> <ul> <li><strong>Synthetic data generator</strong>: Simulation of ligand-receptor signalling for benchmarking</li> <li><strong>Practical methods</strong>: Scalable RWR-based inference of communication patterns in spatial transcriptomics data</li> </ul> </article> <article> <h1>MOSAIK</h1> <p>Sun, 01 Sep 2024 00:00:00 +0000</p> <p>MOSAIK enables cross-platform integration of spatial transcriptomics data from Xenium (10x Genomics), CosMx (NanoString), and MERFISH (Vizgen) into a common SpatialData framework.</p> <p>The toolkit standardises coordinate systems, gene panels, and metadata to enable fair comparison and joint analysis across platforms.</p> </article> <article> <h1>Spatial Transcriptomics Analysis</h1> <p>Sun, 01 Sep 2024 00:00:00 +0000</p> <p>Course materials and tutorials covering:</p> <ul> <li>Introduction to spatial transcriptomics technologies (Xenium, CosMx, MERFISH)</li> <li>Data loading and quality control with SpatialData</li> <li>Cell type annotation with CellTypist</li> <li>Spatial statistics and neighbourhood analysis</li> <li>Visualisation and interpretation</li> </ul> <p><em>Materials coming soon.</em></p> </article> <article> <h1>METABRIC-MX</h1> <p>Sat, 01 Jun 2024 00:00:00 +0000</p> <p>METABRIC-MX (Multimodal eXplorer) is a platform for processing and analysing Xenium breast cancer spatial transcriptomics data from the METABRIC cohort. The pipeline handles:</p> <ul> <li><strong>Multi-modal registration</strong>: Aligning metallomics, immunofluorescence, H&E, and Xenium data into unified SpatialData/Zarr objects</li> <li><strong>Cell typing</strong>: Automated annotation using CellTypist with the Chen.pkl model trained on 600k+ cells</li> <li><strong>Batch correction</strong>: Harmony and scVI integration across tissue microarray cores</li> <li><strong>Spatial analysis</strong>: KNN smoothing, neighbourhood composition, and immune niche profiling</li> </ul> </article> <article> <h1>The molecular landscape of premature aging diseases defined by multilayer network exploration</h1> <p>Thu, 15 Feb 2024 00:00:00 +0000</p> </article> <article> <h1>Random Walk with Restart on multilayer networks: from node prioritisation to supervised link prediction and beyond</h1> <p>Thu, 01 Feb 2024 00:00:00 +0000</p> </article> <article> <h1>Geometry-Informed Data Representations</h1> <p>Mon, 01 Jan 2024 00:00:00 +0000</p> </article> <article> <h1>Experience</h1> <p>Tue, 24 Oct 2023 00:00:00 +0000</p> </article> <article> <h1>Zoo Guide to Network Embedding</h1> <p>Sun, 01 Jan 2023 00:00:00 +0000</p> </article> <article> <h1>Modèles multi-couches et méthodes d'exploration de réseaux biologiques</h1> <p>Sat, 01 Jan 2022 00:00:00 +0000</p> </article> <article> <h1>Microscopic origin of the scattering pre-peak in aqueous propylamine mixtures: X-Ray and Neutron experiments versus simulations</h1> <p>Mon, 01 Apr 2019 00:00:00 +0000</p> </article> <article> <h1>Modeling micro-heterogeneity in mixtures: the role of many body correlations</h1> <p>Fri, 01 Feb 2019 00:00:00 +0000</p> </article> </main></body></html>