C.F. Seale, Marco Barazas, Robin van Schendel, Marcel Tijsterman, Joana P. Gonçalves (2025), MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis.

C.F. Seale, Joana P. Gonçalves (2025), X-CRISP: Domain-Adaptable and Interpretable CRISPR Repair Outcome Prediction.

Sanjay Jain, Liming Pei, Joana P. Gonçalves, Huiping Liu, Paul Robson, Raf Van de Plas, Roy Lardenoije, Lukasz G. Migas, Roger Moens, More Authors (2024), Correction to: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP) (Nature Cell Biology, (2023), 25, 8, (1089-1100), 10.1038/s41556-023-01194-w).

Y.I. Tepeli, Joana P. Gonçalves (2024), DCAST: Diverse Class-Aware Self-Training Mitigates Selection Bias for Fairer Learning.

Y.I. Tepeli, M.J. de Wolf, Joana P. Gonçalves (2024), Metric-DST: Mitigating Selection Bias Through Diversity-Guided Semi-Supervised Metric Learning.

A.C.H. Goossens, Y.I. Tepeli, C.F. Seale, Joana P. Gonçalves (2024), SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies.

Debora L. Gisch, Michelle Brennan, Blue B. Lake, Jeannine Basta, Mark S. Keller, Joana P. Gonçalves, L.G. Migas, Raf Van de Plas, R. Lardenoije, More Authors (2024), The chromatin landscape of healthy and injured cell types in the human kidney, In Nature Communications Volume 15.

Sanjay Jain, Liming Pei, Jeffrey M. Spraggins, Michael Angelo, Joana P. Gonçalves, Raf Van de Plas, R. Lardenoije, L.G. Migas, R.A.R. Moens, More Authors (2023), Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP), In Nature Cell Biology Volume 25 p.1089-1100.

Y.I. Tepeli, C.F. Seale, Joana P. Gonçalves (2023), ELISL: early-late integrated synthetic lethality prediction in cancer, In Bioinformatics Volume 40.

Colm Seale, Yasin Tepeli, Joana P. Gonçalves (2022), Overcoming Selection Bias in Synthetic Lethality Prediction, In Bioinformatics Volume 38 p.4360–4368.