A Searchable Map of PubChem. - Ruud van Deursen; Lorenz C. Blum; Jean-Louis Reymond (J. Chem. Inf. Model., 2010)

Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. - Lorenz C. Blum; Ruud van Deursen; Jean-Louis Reymond (J. Comput. Aided Mol. Des., 2011)

Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem. - Ruud van Deursen; Lorenz C. Blum; Jean-Louis Reymond (J. Comput. Aided Mol. Des., 2011)

Discovery of α7-Nicotinic Receptor Ligands by Virtual Screening of the Chemical Universe Database GDB-13. - Lorenz C. Blum; Ruud van Deursen; Sonia Bertrand; Milena Mayer; Justus J. Bürgi; Daniel Bertrand; Jean-Louis Reymond (J. Chem. Inf. Model., 2011)

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17. - Lars Ruddigkeit; Ruud van Deursen; Lorenz C. Blum; Jean-Louis Reymond (J. Chem. Inf. Model., 2012)

MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13. - Mahendra Awale; Ruud van Deursen; Jean-Louis Reymond (J. Chem. Inf. Model., 2013)

Deep Generative Model for Sparse Graphs using Text-Based Learning with Augmentation in Generative Examination Networks. - Ruud van Deursen; Guillaume Godin (CoRR, 2019)

Multitask Learning On Graph Neural Networks Applied To Molecular Property Predictions. - Fabio Capela; Vincent Nouchi; Ruud van Deursen; Igor V. Tetko; Guillaume Godin (CoRR, 2019)

Augmented Transformer Achieves 97% and 85% for Top5 Prediction of Direct and Classical Retro-Synthesis. - Igor V. Tetko; Pavel Karpov; Ruud van Deursen; Guillaume Godin (CoRR, 2020)

Beyond Chemical 1D knowledge using Transformers. - Ruud van Deursen; Igor V. Tetko; Guillaume Godin (CoRR, 2020)

GEN: highly efficient SMILES explorer using autodidactic generative examination networks. - Ruud van Deursen; Peter Ertl; Igor V. Tetko; Guillaume Godin (J. Cheminformatics, 2020)

Machine Learning Predicts Degree of Aromaticity from Structural Fingerprints. - David J. Ponting; Ruud van Deursen; Martin A. Ott (J. Chem. Inf. Model., 2020)

Be aware of overfitting by hyperparameter optimization! - Igor V. Tetko; Ruud van Deursen; Guillaume Godin (J. Cheminformatics, 2024)

Data-driven federated learning in drug discovery with knowledge distillation. - Thierry Hanser; Ernst Ahlberg; Alexander Amberg; Lennart T. Anger; Chris Barber; Richard J. Brennan; Alessandro Brigo; Annie Delaunois; Susanne Glowienke; Nigel Greene; Laura Johnston; Daniel Kuhn; et al. (Nat. Mac. Intell., 2025)