* = equal contribution
' = co-corresponding

Journal

Endowing protein language models Endowing protein language models with structural knowledge
Philip Hartout*, Dexiong Chen*, Paolo Pellizzoni, Carlos Oliver, and Karsten Borgwardt
Bioinformatics, 41(11):btaf582, 2025 (preprint) (article)
Protein Structure-Function Graphs
RNAmigos2 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
Multimodal learning in clinical proteomics Multimodal learning in clinical proteomics: enhancing antimicrobial resistance models with chemical information
Giovanni Visonà*, Diane Duroux*, Lucas Miranda, Emese Sükei, Yiran Li, Karsten Borgwardt', and Carlos Oliver'
Bioinformatics (2023) (paper)
Drug Discovery
RNAGlib RNAGlib: A Python Package for RNA 2.5D Graphs
Vincent Mallet, Carlos Oliver, Jonathan Broadbent, William L. Hamilton, Jerome Waldispuhl
Bioinformatics (2021) (preprint | article)
RNA Structure-Function Graphs
OptiMol OptiMol: Optimization of binding affinities in chemical space for drug discovery
Jacques Boitreaud, Vincent Mallet, Carlos Oliver, Jerome Waldispuhl
ACS JCIM (2020) (article | preprint)
Drug Discovery Graphs
Augmented RNA base pairing Augmented RNA base pairing networks imprint small molecule binding preferences
Carlos Oliver, Vincent Mallet, Roman Sarrazin Gendron, Vladimir Reinharz, William L. Hamilton, Nicolas Moitessier, Jerome Waldispuhl
Nucleic Acids Research (2020) (article | preprint)
RNA Structure-Function Drug Discovery
Difficulty Scaling in Proof of Work Difficulty Scaling in Proof of Work for Decentralized Problem Solving
Pericles Philippopoulos, Alessandro Ricottone, Carlos Oliver
Ledger Journal (2020) (article)

Perspectives

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

Reviews

RNA drug design 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

Conference

Structure-and function-aware substitution Structure-and function-aware substitution matrices via learnable graph matching
Paolo Pellizzoni*, Carlos Oliver*, Karsten Borgwardt
RECOMB (2024) (proceedings)
Protein Structure-Function Graphs
ProteinShake ProteinShake: Building Datasets and Benchmarks for Deep Learning on Protein Structures
Tim Kucera*, Carlos Oliver*, Dexiong Chen, Karsten Borgwardt
NeurIPS Datasets and Benchmarks (2023) (preprint)
Protein Structure-Function Benchmarks
Unsupervised Manifold Alignment Unsupervised Manifold Alignment with Joint Multidimensional Scaling
Dexiong Chen, Bowen Fan, Carlos Oliver, Karsten Borgwardt
ICLR 2022 (preprint)
Graphs
VeRNAl VeRNAl: A tool for fuzzy network motif mining in RNA
Carlos Oliver, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton, Jerome Waldispuhl
RECOMB 2021 & Bioinformatics (preprint | article)
RNA Structure-Function Motif Mining
Stochastic Sampling Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification
Roman Sarrazin Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos Oliver, Yann Pony, Jerome Waldispuhl
Accepted at RECOMB 2020 (preprint)
RNA Structure-Function Motif Mining

Workshop

BioBlobs 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
RNA 3D Structure-Function benchmark 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 ENSEMBITS: an alphabet of protein conformational ensembles
Kaiwen Shi, Carlos Oliver
Submitted, NeurIPS 2026 (preprint)
Protein Dynamics
BioBlobs 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
3D-based RNA function prediction 3D-based RNA function prediction with rnaglib
Carlos Oliver, Vincent Mallet, and Jerome Waldispuhl
arXiV (2024), to appear as book chapter in Springer Nature: Methods in Molecular Biology (preprint)
RNA Structure-Function Graphs
Approximate Network Motif Mining Approximate Network Motif Mining via Graph Learning
Carlos Oliver, Dexiong Chen, Vincent Mallet, Pericles Philippopoulos, Karsten Borgwardt
ArXiV (2022) (preprint)
Graphs Motif Mining
Edge Similarity-Aware GNNs Edge Similarity-Aware Graph Neural Networks
Vincent Mallet, Carlos Oliver, William L. Hamilton
arXiv (2021) (preprint)
Graphs
Leveraging binding site structure Leveraging binding site structure for drug discovery with point-cloud methods
Vincent Mallet, Carlos Oliver, Nicolas Moitessier, Jerome Waldispuhl
arXiv (2019) (preprint)
Drug Discovery Protein Structure-Function