Higher-order molecular organization as a source of biological function. - Thomas Gaudelet; Noël Malod-Dognin; Natasa Przulj (Bioinform., 2018)

Utilising Graph Machine Learning within Drug Discovery and Development. - Thomas Gaudelet; Ben Day; Arian R. Jamasb; Jyothish Soman; Cristian Regep; Gertrude Liu; Jeremy B. R. Hayter; Richard Vickers; Charles Roberts; Jian Tang 005; David Roblin; Tom L. Blundell; et al. (CoRR, 2020)

Utilizing graph machine learning within drug discovery and development. - Thomas Gaudelet; Ben Day; Arian R. Jamasb; Jyothish Soman; Cristian Regep; Gertrude Liu; Jeremy B. R. Hayter; Richard Vickers; Charles Roberts; Jian Tang 005; David Roblin; Tom L. Blundell; et al. (Briefings Bioinform., 2021)

Classification in biological networks with hypergraphlet kernels. - Jose Lugo-Martinez; Daniel Zeiberg; Thomas Gaudelet; Noël Malod-Dognin; Natasa Przulj; Predrag Radivojac (Bioinform., 2021)

RECOVER: sequential model optimization platform for combination drug repurposing identifies novel synergistic compounds in vitro. - Paul Bertin; Jarrid Rector-Brooks; Deepak Sharma; Thomas Gaudelet; Andrew Anighoro; Torsten Gross; Francisco Martinez-Pena; Eileen L. Tang; Suraj M. S; Cristian Regep; Jeremy B. R. Hayter; Maksym Korablyov; et al. (CoRR, 2022)

PyRelationAL: A Library for Active Learning Research and Development. - Paul Scherer; Thomas Gaudelet; Alison Pouplin; Suraj M. S; Jyothish Soman; Lindsay Edwards; Jake P. Taylor-King (CoRR, 2022)

Season combinatorial intervention predictions with Salt & Peper. - Thomas Gaudelet; Alice Del Vecchio; Eli M. Carrami; Juliana Cudini; Chantriolnt-Andreas Kapourani; Caroline Uhler; Lindsay Edwards (CoRR, 2024)

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery. - Peter St. John; Dejun Lin; Polina Binder; Malcolm Greaves; Vega Shah; John St. John; Adrian Lange; Patrick D. Hsu; Rajesh Illango; Arvind Ramanathan; Anima Anandkumar; David H. Brookes; et al. (CoRR, 2024)

No Foundations without Foundations - Why semi-mechanistic models are essential for regulatory biology. - Luka Kovacevic; Thomas Gaudelet; James Opzoomer; Hagen Triendl; John Whittaker; Caroline Uhler; Lindsay Edwards; Jake P. Taylor-King (CoRR, 2025)