Neural network experiences between perceptrons and support vectors. - Robert P. W. Duin; Dick de Ridder (BMVC, 1997)

Experiments with a featureless approach to pattern recognition. - Robert P. W. Duin; Dick de Ridder; David M. J. Tax (Pattern Recognit. Lett., 1997)

Sammon's mapping using neural networks: A comparison. - Dick de Ridder; Robert P. W. Duin (Pattern Recognit. Lett., 1997)

On the Application of Neural Networks to Non-Linear Image Processing Tasks. - Dick de Ridder; Robert P. W. Duin; Piet W. Verbeek; Lucas J. van Vliet (ICONIP, 1998)

Featureless pattern classification. - Robert P. W. Duin; Dick de Ridder; David M. J. Tax (Kybernetika, 1998)

Adaptive Texture Representation Methods for Automatic Target Recognition. - Kieron Messer; Dick de Ridder; Josef Kittler (BMVC, 1999)

The Applicability of Neural Networks to Non-linear Image Processing. - Dick de Ridder; Robert P. W. Duin; Piet W. Verbeek (Pattern Anal. Appl., 1999)

Relational discriminant analysis. - Robert P. W. Duin; Elzbieta Pekalska; Dick de Ridder (Pattern Recognit. Lett., 1999)

Probabilistic PCA and ICA Subspace Mixture Models for Image Segmentation. - Dick de Ridder; Josef Kittler; Robert P. W. Duin (BMVC, 2000)

The Adaptive Subspace Map for Texture Segmentation. - Dick de Ridder; Josef Kittler; Olaf Lemmers; Robert P. W. Duin (ICPR, 2000)

The Adaptive Subspace Map for Image Description and Image Database Retrieval. - Dick de Ridder; Olaf Lemmers; Robert P. W. Duin; Josef Kittler (SSPR/SPR, 2000)

The Economics of Classification: Error vs. Complexity. - Dick de Ridder; Elzbieta Pekalska; Robert P. W. Duin (ICPR (2), 2002)

Texture Description by Independent Components. - Dick de Ridder; Robert P. W. Duin; Josef Kittler (SSPR/SPR, 2002)

Image processing with neural networks - a review. - Michael Egmont-Petersen; Dick de Ridder; Heinz Handels (Pattern Recognit., 2002)

A note on core research issues for statistical pattern recognition. - Robert P. W. Duin; Fabio Roli; Dick de Ridder (Pattern Recognit. Lett., 2002)

Robust subspace mixture models using t-distributions. - Dick de Ridder; Vojtech Franc (BMVC, 2003)

Supervised Locally Linear Embedding. - Dick de Ridder; Olga Kouropteva; Oleg Okun; Matti Pietikäinen; Robert P. W. Duin (ICANN, 2003)

Texture Segmentation Using the Mixtures of Principal Component Analyzers. - Mohamed E. M. Musa; Robert P. W. Duin; Dick de Ridder; Volkan Atalay (ISCIS, 2003)

Local Fisher Embedding. - Dick de Ridder; Marco Loog; Marcel J. T. Reinders (ICPR (2), 2004)

Almost autonomous training of mixtures of principal component analyzers. - Mohamed E. M. Musa; Dick de Ridder; Robert P. W. Duin; Volkan Atalay (Pattern Recognit. Lett., 2004)

Maximum signi.cance clustering of oligonucleotide microarrays. - Dick de Ridder; Marcel J. T. Reinders; Frank J. T. Staal; Jacques J. M. van Dongen (CSB Workshops, 2005)

Local Discriminant Analysis. - Marco Loog; Dick de Ridder (ICPR (3), 2006)

Maximum significance clustering of oligonucleotide microarrays. - Dick de Ridder; Frank J. T. Staal; Jacques J. M. van Dongen; Marcel J. T. Reinders (Bioinform., 2006)

The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. - Roel G. W. Verhaak; Frank J. T. Staal; Peter J. M. Valk; Bob Löwenberg; Marcel J. T. Reinders; Dick de Ridder (BMC Bioinform., 2006)

Protein Complex Prediction Using an Integrative Bioinformatics Approach. - Rogier J. P. van Berlo; Lodewyk F. A. Wessels; Dick de Ridder; Marcel J. T. Reinders (J. Bioinform. Comput. Biol., 2007)

Classification in the presence of class noise using a probabilistic Kernel Fisher method. - Yunlei Li; Lodewyk F. A. Wessels; Dick de Ridder; Marcel J. T. Reinders (Pattern Recognit., 2007)

Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks. - Yunlei Li; Dick de Ridder; Marco J. L. de Groot; Marcel J. T. Reinders (APBC, 2008)

Stability cannot be derived from local structure in biochemical networks. - Domenico Bellomo; Peter van Nes; Marcel J. T. Reinders; Dick de Ridder (BIONETICS, 2008)

Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. - Yunlei Li; Dick de Ridder; Marco J. L. de Groot; Marcel J. T. Reinders (BMC Syst. Biol., 2008)

Integration of prior knowledge of measurement noise in kernel density classification. - Yunlei Li; Dick de Ridder; Robert P. W. Duin; Marcel J. T. Reinders (Pattern Recognit., 2008)

Erratum to "Classification in the presence of class noise using a probabilistic kernel fisher method": [Pattern Recognition 40 (12) 3349-3357]. - Yunlei Li; Lodewyk F. A. Wessels; Dick de Ridder; Marcel J. T. Reinders (Pattern Recognit., 2008)

Metabolite and reaction inference based on enzyme specificities. - Marco J. L. de Groot; Rogier J. P. van Berlo; Wouter A. van Winden; Peter J. T. Verheijen; Marcel J. T. Reinders; Dick de Ridder (Bioinform., 2009)

Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks. - Peter van Nes; Domenico Bellomo; Marcel J. T. Reinders; Dick de Ridder (EURASIP J. Bioinform. Syst. Biol., 2009)

Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction. - Marc Hulsman; Marcel J. T. Reinders; Dick de Ridder (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Sequence-Based Prediction of Protein Secretion Success in Aspergillus niger. - Bastiaan A. van den Berg; Jurgen F. Nijkamp; Marcel J. T. Reinders; Liang Wu; Herman J. Pel; Johannes A. Roubos; Dick de Ridder (PRIB, 2010)

Integrating genome assemblies with MAIA. - Jurgen F. Nijkamp; Wynand Winterbach; Marcel van den Broek; Jean-Marc Daran; Marcel J. T. Reinders; Dick de Ridder (Bioinform., 2010)

Metabolic network destruction: Relating topology to robustness. - Wynand Winterbach; Huijuan Wang; Marcel J. T. Reinders; Piet Van Mieghem; Dick de Ridder (Nano Commun. Networks, 2011)

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints. - Rogier J. P. van Berlo; Dick de Ridder; Jean-Marc Daran; Pascale A. S. Daran-Lapujade; Bas Teusink; Marcel J. T. Reinders (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. - Alexey A. Gritsenko; Jurgen F. Nijkamp; Marcel J. T. Reinders; Dick de Ridder (Bioinform., 2012)

De novo detection of copy number variation by co-assembly. - Jurgen F. Nijkamp; Marcel van den Broek; Jan-Maarten A. Geertman; Marcel J. T. Reinders; Jean-Marc Daran; Dick de Ridder (Bioinform., 2012)

Conditional Random Fields for Protein Function Prediction. - Thies Gehrmann; Marco Loog; Marcel J. T. Reinders; Dick de Ridder (PRIB, 2013)

Using Predictive Models to Engineer Biology: A Case Study in Codon Optimization. - Alexey A. Gritsenko; Marcel J. T. Reinders; Dick de Ridder (PRIB, 2013)

Local Topological Signatures for Network-Based Prediction of Biological Function. - Wynand Winterbach; Piet Van Mieghem; Marcel J. T. Reinders; Huijuan Wang; Dick de Ridder (PRIB, 2013)

Pattern recognition in bioinformatics. - Dick de Ridder; Jeroen de Ridder; Marcel J. T. Reinders (Briefings Bioinform., 2013)

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. - Jurgen F. Nijkamp; Mihai Pop; Marcel J. T. Reinders; Dick de Ridder (Bioinform., 2013)

Topology of molecular interaction networks. - Wynand Winterbach; Piet Van Mieghem; Marcel J. T. Reinders; Huijuan Wang; Dick de Ridder (BMC Syst. Biol., 2013)

Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels. - Rogier J. P. van Berlo; Wynand Winterbach; Marco J. L. de Groot; Andreas Bender 002; Peter J. T. Verheijen; Marcel J. T. Reinders; Dick de Ridder (Int. J. Bioinform. Res. Appl., 2013)

SPiCE: a web-based tool for sequence-based protein classification and exploration. - Bastiaan A. van den Berg; Marcel J. T. Reinders; Johannes A. Roubos; Dick de Ridder (BMC Bioinform., 2014)

Making the difference: integrating structural variation detection tools. - Ke Lin; Sandra Smit; Guusje Bonnema; Gabino Sanchez-Perez; Dick de Ridder (Briefings Bioinform., 2015)

ACE: accurate correction of errors using K-mer tries. - Siavash Sheikhizadeh; Dick de Ridder (Bioinform., 2015)

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data. - Saulo Aflitos; Edouard Severing; Gabino Sanchez-Perez; Sander Peters; Hans de Jong; Dick de Ridder (BMC Bioinform., 2015)

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data. - Alexey A. Gritsenko; Marc Hulsman; Marcel J. T. Reinders; Dick de Ridder (PLoS Comput. Biol., 2015)

PanTools: representation, storage and exploration of pan-genomic data. - Siavash Sheikhizadeh; M. Eric Schranz; Mehmet Akdel; Dick de Ridder; Sandra Smit (Bioinform., 2016)

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)

CyLineUp: A Cytoscape app for visualizing data in network small multiples. - Maria Cecília D. Costa; Thijs Slijkhuis; Wilco Ligterink; Henk W. M. Hilhorst; Dick de Ridder; Harm Nijveen (F1000Research, 2016)

Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity. - Alexey A. Gritsenko; Shira Weingarten-Gabbay; Shani Elias-Kirma; Ronit Nir; Dick de Ridder; Eran Segal (PLoS Comput. Biol., 2017)

Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study. - Ehsan Motazedi; Richard Finkers; Chris Maliepaard; Dick de Ridder (Briefings Bioinform., 2018)

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals. - Ehsan Motazedi; Dick de Ridder; Richard Finkers; Samantha J. Baldwin; Susan Thomson 003; Katrina Monaghan; Chris Maliepaard (Bioinform., 2018)

Efficient inference of homologs in large eukaryotic pan-proteomes. - Siavash Sheikhizadeh; Dick de Ridder; M. Eric Schranz; Sandra Smit (BMC Bioinform., 2018)

GeneNoteBook, a collaborative notebook for comparative genomics. - Rens Holmer; Robin van Velzen; René Geurts; Ton Bisseling; Dick de Ridder; Sandra Smit (Bioinform., 2019)

poreTally: run and publish de novo nanopore assembler benchmarks. - Carlos de Lannoy; Judith Risse; Dick de Ridder (Bioinform., 2019)

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)

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans. - Basten L. Snoek; Mark G. Sterken; Margi Hartanto; Albert-Jan van Zuilichem; Jan E. Kammenga; Dick de Ridder; Harm Nijveen (Database J. Biol. Databases Curation, 2020)

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)

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads. - Sina Majidian; Mohammad Hossein Kahaei; Dick de Ridder (BMC 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)

Analysis results of the paper baseLess: Lightweight detection of sequences in raw MinION data. - Ben Noordijk; Reindert Nijland; Victor J. Carrion; Jos M. Raaijmakers; Dick de Ridder; Carlos de Lannoy (4TU.Federation, 2022)

PanTools v3: functional annotation, classification and phylogenomics. - Eef M. Jonkheer; Dirk-Jan M. van Workum; Siavash Sheikhizadeh Anari; Balázs Brankovics; Jorn R. de Haan; Lidija Berke; Theo A. J. van der Lee; Dick de Ridder; Sandra Smit (Bioinform., 2022)

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)