Publications

Peer-reviewed publications

Selected publications

Özçelik R, De Ruiter S, Criscuolo E, Grisoni F (2024). Chemical Language Modeling with Structured State Space Models. Nature Communications 15, 6176.

van Tilborg, D, Brinkmann H, Criscuolo E, Rossen L, Özçelik R, Grisoni F (2024). Deep learning for low-data drug discovery: hurdles and opportunities. Current Opinion in Structural Biology, 86, 102818.

Grisoni F (2023). Chemical language models for de novo drug design: Challenges and opportunities. Current Opinion in Structural Biology 79, 102527.

van Tilborg D, Alenicheva A and Grisoni F (2022). Exposing the limitations of molecular machine learning with activity cliffs. Journal of Chemical Information and Modeling 62, 5938.

2024

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Özçelik R, De Ruiter S, Criscuolo E, Grisoni F (2024). Chemical Language Modeling with Structured State Space Models. Nature Communications 15, 6176.

van Tilborg, D, Brinkmann H, Criscuolo E, Rossen L, Özçelik R, Grisoni F (2024). Deep learning for low-data drug discovery: hurdles and opportunities. Current Opinion in Structural Biology, 86, 102818.

Teukam, YGN, Zipoli F, Laino T, Criscuolo E, Grisoni F, Manica M (2024). Integrating Genetic Algorithms and Language Models for Enhanced Enzyme Design. Briefings in Bioinformatics (just accepted).

Ortiz-Perez A+, van Tilborg D+, van der Meel, R, Grisoni F, Albertazzi L (2024). Machine learning-guided high throughput nanoparticle design. Digital Discovery 3, 1280.

van der Meel R, Grisoni F, Mulder WJ (2024). Lipid discovery for mRNA delivery guided by machine learning. Nature Materials 23, 880.

Faquetti ML, Slappendel L, Bigonne H, Aichinger G, Grisoni F, Schneider P, Schneider G, Burden A, Sturla S (2024). Baricitinib and tofacitinib off-target profile, with a focus on Alzheimer’s disease. Alzheimer’s & Dementia: Translational Research & Clinical Interventions, 10.

2023

Boldini D, Ballabio D, Consonni V, Todeschini R, Grisoni F, Sieber S (2023). Effectiveness of molecular fingerprints for exploring the chemical space of natural products. Journal of Cheminformatics 16, 35.

Moret M, Pachon Angona I, Cotos L, Yan S, Atz K, Brunner C, Baumgartner M, Grisoni F, Schneider G (2023). Leveraging molecular structure and bioactivity with chemical language models for de novo drug design. Nature Communications 14, 114.

Mullowney MW, Duncan KR, Elsayed SS, et al. (2023). Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery 1, 22.

Boldini D, Grisoni F, Kuhn D, Friedrich L and Sieber AS (2023). Practical guidelines for the use of gradient boosting for molecular property prediction. J. Cheminform. 15, 73.

Grisoni F (2023). Chemical language models for de novo drug design: Challenges and opportunities. Current Opinion in Structural Biology 79, 102527.

Ballarotto M, Willems S, Stiller T, Nawa F, Marschner JA, Grisoni F and Merk D (2023). De Novo Design of Nurr1 Agonists via Fragment-Augmented Generative Deep Learning in Low-Data Regime. Journal of Medicinal Chemistry 66, 12.

Özçelik R, van Tilborg D, Jiménez-Luna J and Grisoni F (2023). Structure‐based Drug discovery with Deep Learning. ChemBioChem e202200776.

Deckers J, Anbergen T, Hokke AM, de Dreu A, Schrijver DP, de Bruin K, Toner YC, Beldman, TJ, Spangler JB, de Greef TF, Grisoni F, van der Meel R, Joosten LAB, Merkx M, Netea MG and Mulder WJM (2023). Engineering cytokine therapeutics. Nature Reviews Bioengineering 1, 286.

Volkamer A, Riniker S, Nittinger E, Lanini J, Grisoni F, Evertsson E, Schneider N (2023). Machine Learning for Small Molecule Drug Discovery in Academia and Industry. Artificial Intelligence in the Life Sciences, 100056.

2022

van Tilborg D, Alenicheva A and Grisoni F (2022). Exposing the limitations of molecular machine learning with activity cliffs. Journal of Chemical Information and Modeling 62, 5938.

Ortiz-Perez A, Izquierdo-Lozano C, Meijers R, Grisoni F and Albertazzi L (2023). Identification of fluorescently-barcoded nanoparticles using machine learning. Nanoscale Advances 5, 2307.

2021

Grisoni F, Huisman BJ, Button AL, Moret M, Atz K, Merk D, Schneider G. (2021). Combining generative artificial intelligence and on-chip synthesis for de novo drug design. Science Advances 7 , e3338.

Moret M, Helmstädter M, Grisoni F, Schneider G, Merk D (2021). Beam search for automated design and scoring of novel ROR ligands with machine intelligence. Angewandte Chemie International Edition 60, 19477.

Faquetti, M. L., Grisoni, F., Schneider, P., Schneider, G., & Burden, A. M. (2022). Identification of novel off targets of baricitinib and tofacitinib by machine learning with a focus on thrombosis and viral infection. Scientific reports, 12(1), 7843.

Preprints (under review)

Mastrolorito, F., Ciriaco, F., Togo, M. V., Gambacorta, N., Trisciuzzi, D., Altomare, C. D., Grisoni, F. & Nicolotti, O. (2024). fragSMILES: A Chemical String Notation for Advanced Fragment and Chirality Representation. ChemRxiv.

Özçelik, R., & Grisoni, F. (2024). A Hitchhiker’s Guide to Deep Chemical Language Processing for Bioactivity Prediction. arXiv preprint arXiv:2407.12152.

Birolo, R., Özçelik, R., Aramini, A., Gobetto, R., Chierotti, M. R., & Grisoni, F. (2024). Leveraging Deep Chemical Language Processing for Co-crystal Prediction. ChemRxiv.

Özçelik, R., van Weesep, L., de Ruiter, S., & Grisoni, F. (2024). peptidy: A light-weight Python library for peptide representation in machine learning. ChemRxiv.

Izquierdo-Lozano, C., van Noort, N., van Veen, S., Tholen, M. M., Grisoni, F., & Albertazzi, L. (2024). nanoFeatures: a cross-platform application to characterize nanoparticles from super-resolution microscopy images. bioRxiv, 2024-02.

van Tilborg, D., & Grisoni, F. (2023). Traversing chemical space with active deep learning. ChemRxiv.

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