Solvated docking: introducing water into the modelling of biomolecular complexes. - Aalt D. J. van Dijk; Alexandre M. J. J. Bonvin (Bioinform., 2006)

Predicting sub-Golgi localization of type II membrane proteins. - Aalt D. J. van Dijk; D. Bosch; Cajo J. F. ter Braak; A. R. van der Krol; Roeland C. H. J. van Ham (Bioinform., 2008)

Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control. - Aalt D. J. van Dijk; Cajo J. F. ter Braak; Richard G. H. Immink; Gerco C. Angenent; Roeland C. H. J. van Ham (Bioinform., 2008)

SLIDER: Mining Correlated Motifs in Protein-Protein Interaction Networks. - Peter Boyen; Frank Neven; Dries Van Dyck; Aalt D. J. van Dijk; Roeland C. H. J. van Ham (ICDM, 2009)

Continuous-time modeling of cell fate determination in Arabidopsis flowers. - Simon van Mourik; Aalt D. J. van Dijk; Maarten de Gee; Richard G. H. Immink; Kerstin Kaufmann; Gerco C. Angenent; Roeland C. H. J. van Ham; Jaap Molenaar (BMC Syst. Biol., 2010)

Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction. - Aalt D. J. van Dijk; Giuseppa Morabito; Martijn Fiers; Roeland C. H. J. van Ham; Gerco C. Angenent; Richard G. H. Immink (PLoS Comput. Biol., 2010)

Correlated mutations via regularized multinomial regression. - Janrdanan Sreekumar; Cajo J. F. ter Braak; Roeland C. H. J. van Ham; Aalt D. J. van Dijk (BMC Bioinform., 2011)

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments. - Jose M. Muiño; Marlous Hoogstraat; Roeland C. H. J. van Ham; Aalt D. J. van Dijk (Nucleic Acids Res., 2011)

SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks. - Peter Boyen; Dries Van Dyck; Frank Neven; Roeland C. H. J. van Ham; Aalt D. J. van Dijk (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes. - Yiannis Kourmpetis; Aalt D. J. van Dijk; Cajo J. F. ter Braak (Algorithms Mol. Biol., 2013)

Mining Minimal Motif Pair Sets Maximally Covering Interactions in a Protein-Protein Interaction Network. - Peter Boyen; Frank Neven; Dries Van Dyck; Felipe L. Valentim; Aalt D. J. van Dijk (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016. - Aalt D. J. van Dijk; Harri Lähdesmäki; Dick de Ridder; Juho Rousu (BMC Bioinform., 2016)

Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis. - Miguel Correa Marrero; Richard G. H. Immink; Dick de Ridder; Aalt D. J. van Dijk (Bioinform., 2019)

Geometricus represents protein structures as shape-mers derived from moment invariants. - Janani Durairaj; Mehmet Akdel; Dick de Ridder; Aalt D. J. van Dijk (Bioinform., 2020)

Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines. - Yan Wang; Miguel Correa Marrero; Marnix H. Medema; Aalt D. J. van Dijk (Bioinform., 2020)

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. - Janani Durairaj; Elena Melillo; Harro J. Bouwmeester; Jules Beekwilder; Dick de Ridder; Aalt D. J. van Dijk (PLoS Comput. Biol., 2021)

Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics. - Aalt D. J. van Dijk; Shin-Han Shiu; Dick de Ridder (Frontiers Artif. Intell., 2022)

Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction. - João Capela; Maria Zimmermann-Kogadeeva; Aalt D. J. van Dijk; Dick de Ridder; Oscar Dias; Miguel Rocha 001 (BMC Bioinform., 2025)