* = equal contribution
' = co-corresponding
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)
Endowing protein language models with structural knowledge
Dexiong Chen*, Philip Hartout*, Paolo Pellizzoni, Carlos Oliver, and Karsten Borgwardt
arXiV (2024) (preprint)
Structure-and function-aware substitution matrices via learnable graph matching.
Paolo Pellizzoni*, Carlos Oliver*, Karsten Borgwardt
RECOMB (2024) (proceedings)
Semi-supervised learning and large-scale docking data accelerate RNA virtual screening
Juan G. Carvajal Patiño*, Vincent Mallet*, David Becerra, L. Fernando Niño V, Carlos Oliver', Jerome Waldispuhl'
bioRxiv (2023) (preprint)
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)
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)
Unsupervised Manifold Alignment with Joint Multidimensional Scaling
Dexiong Chen, Bowen Fan, Carlos Oliver, Karsten Borgwardt
ICLR 2022(preprint)
Approximate Network Motif Mining via Graph Learning
Carlos Oliver, Dexiong Chen, Vincent Mallet, Pericles Philippopoulos, Karsten Borgwardt
ArXiV (2022) (preprint)
RNAGlib: A Python Package for RNA 2.5D Graphs.
Vincent Mallet, Carlos Oliver, Jonathan Broadbent, William L. Hamilton, Jerome Waldispuhl
Bioinformatics (2021) (preprint | article)
Edge Similarity-Aware Graph Neural Networks.
Vincent Mallet, Carlos Oliver, William L. Hamilton
arXiv (2021)(preprint)
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)
OptiMol: Optimization of binding affinities in chemical space for drug discovery.
Jacques Boitreaud, Vincent Mallet, Carlos Oliver, Jerome Waldispuhl
ACM JCIM (2020) (article | preprint)
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)
Difficulty Scaling in Proof of Work for Decentralized Problem Solving.
Pericles Philippopoulos, Alessandro Ricottone, Carlos Oliver
Ledger Journal (2020) (article)
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)
Leveraging binding site structure for drug discovery with point-cloud methods
Vincent Mallet, Carlos Oliver, Nicolas Moitessier, Jerome Waldispuhl
ArXiv (2019) (preprint)
Automated, customizable and efficient identification of 3D base pair modules with BayesPairing
Roman Sarrazin Gendron, Vladimir Reinharz, Carlos Oliver, Nicolas Moitessier, Jerome Waldispuhl
Nucleic Acids Research (2019) (article)
On the emergence of structural complexity in RNA replicators.
Carlos Oliver, Vladimir Reinharz, Jerome Waldispuhl
RNA (2018) (article)
Proposal for a fully decentralized blockchain and proof-of-work algorithm for solving NP-complete problems
Carlos Oliver, Alessandro Ricottone, Pericles Philippopoulos
ArXiv (2017)(preprint)
Concerted millisecond timescale dynamics in the intrinsically disordered carboxyl terminus of gamma‐tubulin induced by mutation of a conserved tyrosine residue
Jason Harris, Maria Shadrina, Carlos Oliver, Anthony Mittermaier, Jackie Vogel
Protein Science (2018) (article)
The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts
Jonathan Bouchard, Carlos Oliver, Paul Harrison
BMC Genomics (2015) (article)