Publications

H. Rafique, Anthony Baptista, E. Parisini, I. Wall, A. Grigoriadis (2026). Spatial gene expression inference from histology using feature-level fusion of pathology foundation models. ECCB 2026.
Anthony Baptista, R. Nuamah, C. Chiappini, A. Grigoriadis (2026). MOSAIK: Multi-Origin Spatial Transcriptomics Analysis and Integration Kit. JOSS.
Anthony Baptista
Equal contribution
, M. Niedostatek
Equal contribution
, J. Yamamoto, B. McArthur, J. Kurths, R. J. Sánchez-García, G. Bianconi (2025). Mining higher-order triadic interactions. Nat. Commun..
G. Verghese
Equal contribution
, Anthony Baptista
Equal contribution
, C. Eke
Equal contribution
, H. Rafique
Equal contribution
, M. Li, F. Mohamed, A. Bhalla, L. Ryan, M. Pitcher, E. Parisini, C. Piazzese, L. Simmons, A. Grigoriadis (2025). PySlyde: A Lightweight, Open-Source Toolkit for Pathology Preprocessing. arXiv:2511.05183.
PDF
I. Wall
Equal contribution
, Anthony Baptista
Equal contribution
, J. Quist
Equal contribution
, H. Rafique, M. Li, L. Ryan, G. Verghese, S. Marcotti, T. A. Phillips, C. Owczarek, S. Clausen, T. Tramm, G. Booker, A. Mera, J. Timbres, E. Sawyer, C. Gillet, S. Irshad, S. Pinder, M. Parsons, A. Grigoriadis (2025). SMART: A Spatio-Molecular Atlas of Response Trajectories in Triple-Negative Breast Cancer. Nat. Cancer.
L. R. Orozco, A. E. Weaver, C. C. Pauli, C. J. Grassa, D. Vergara, Anthony Baptista, K. White, B. F. Emery, N. R. M. Castro, R. F. Guerrero, B. C. Keegan, N. C. Kane (2025). Unraveling Cross-Cellular Communication in Cannabis sativa Sex Determination: A Network Ontology Transcript Annotation Analysis. Sci. Rep..
PDF DOI
Anthony Baptista, C. R. S. Banerji, A. Barp, T. Chakraborti, C. Harbron, B. D. MacArthur (2024). Deep Learning as Ricci Flow. Sci. Rep..
Anthony Baptista, B. D. MacArthur, C. R. S. Banerji (2024). Charting cellular differentiation trajectories with Ricci flow. Nat. Commun..
C. Beust, A. Valdeolivas, Anthony Baptista, G. Brière, N. Lévy, O. Ozisik, A. Baudot (2024). The molecular landscape of premature aging diseases defined by multilayer network exploration. Adv. Biol..
Anthony Baptista, G. Brière, A. Baudot (2024). Random Walk with Restart on multilayer networks: from node prioritisation to supervised link prediction and beyond. BMC Bioinformatics.