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Computational and Structural Biotechnology Journal|January 20, 2023
Beyond sequence: Structure-based machine learningJanani Durairaj, Dick de Ridder, Aalt D J van Dijk
Proteins|May 27, 2017
Sequence-based analysis of protein degradation ratesMiguel Correa Marrero, Aalt D J van Dijk, Dick de Ridder
Bioinformatics (Oxford, England)|December 31, 2020
Geometricus represents protein structures as shape-mers derived from moment invariantsJanani Durairaj, Mehmet Akdel, Dick de Ridder, et al.
Computational and Structural Biotechnology Journal|May 6, 2020
Caretta - A multiple protein structure alignment and feature extraction suiteMehmet Akdel, Janani Durairaj, Dick de Ridder, et al.
Quantitative Plant Biology|September 24, 2025
BADDADAN: Mechanistic modelling of time-series gene module expressionBen Noordijk, Marcel Reinders, Aalt D J van Dijk, et al.
The Plant Journal : for Cell and Molecular Biology|May 30, 2018
DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdomSevgin Demirci, Sander A Peters, Dick de Ridder, et al.
Molecular Biology and Evolution|October 1, 2021
Domestication Shapes Recombination Patterns in TomatoRoven Rommel Fuentes, Dick de Ridder, Aalt D J van Dijk, et al.
F1000Research|April 11, 2023
Genomic prediction in plants: opportunities for ensemble machine learning based approachesMuhammad Farooq, Aalt D J van Dijk, Harm Nijveen, et al.
Bioinformatics (Oxford, England)|November 7, 2018
Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysisMiguel Correa Marrero, Richard G H Immink, Dick de Ridder, et al.
BMC Bioinformatics|February 27, 2025
Comparative Assessment of Protein Large Language Models for Enzyme Commission Number PredictionJoão Capela, Maria Zimmermann-Kogadeeva, Aalt D J van Dijk, et al.
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