Publications

This is a list of papers published since starting the lab in January 2025. For a full list of my publications go here.

* = equal contribution

' = co-corresponding

Journal

	Endowing protein language models with structural knowledge Philip Hartout*, Dexiong Chen*, Paolo Pellizzoni, Carlos Oliver, Karsten Borgwardt Bioinformatics, 41(11):btaf582, 2025 (preprint) (article) Protein Structure-Function Graphs
	RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning Juan G. Carvajal Patiño*, Vincent Mallet*, David Becerra, L. Fernando Niño V, Carlos Oliver', Jerome Waldispuhl' Nature Communications 2025 (preprint) (article) RNA Structure-Function Drug Discovery Graphs

Perspectives

What's so hard about RNA-targeting drug discovery? Carlos Oliver, Jerome Waldispuhl Nature Computational Science, 2025 (article) RNA Structure-Function Drug Discovery

Reviews

Machine learning for RNA-targeting drug design Wissam Karroucha, Carlos Oliver, Veronique Stoven, Vincent Mallet Journal of Chemical Information and Modeling (in revision), 2025 (preprint) RNA Structure-Function Drug Discovery

Workshop

	BioBlobs: Unsupervised Discovery of Functional Substructures for Protein Function Prediction Xin (Allen) Wang, Kaiwen Shi, Carlos Oliver Workshop on Machine Learning for Structural Biology, 2025 (Accepted) (preprint) Protein Structure-Function Motif Mining
	A Comprehensive Benchmark for RNA 3D Structure-Function Modeling Luis Wyss*, Vincent Mallet*, Wissam Karroucha, Karsten Borgwardt', Carlos Oliver' ICLR 2025 Workshop on AI for Nucleic Acids (preprint) RNA Structure-Function Benchmarks

Preprints

	ENSEMBITS: an alphabet of protein conformational ensembles Kaiwen Shi, Carlos Oliver Submitted, NeurIPS 2026 (preprint) Protein Dynamics
	BioBlobs: Unsupervised Discovery of Functional Substructures for Protein Function Prediction Xin (Allen) Wang, Kaiwen Shi, Carlos Oliver Submitted, NeurIPS 2026 (preprint) Protein Structure-Function Motif Mining