Dick de Ridder

73 papers A 4B 3C 1Journal 49Unranked 12
YearRankTypeTitle / Venue / Authors
2025 J jnl
Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction.
BMC Bioinform.
João Capela, Maria Zimmermann-Kogadeeva, Aalt D. J. van Dijk, Dick de Ridder, Oscar Dias, Miguel Rocha
2025 J jnl
Predicting precursors of plant specialized metabolites using DeepMol automated machine learning.
J. Integr. Bioinform.
João Capela, João Cheixo, Dick de Ridder, Oscar Dias, Miguel Rocha
2022 J jnl
Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics.
Frontiers Artif. Intell.
Aalt D. J. van Dijk, Shin-Han Shiu, Dick de Ridder
2022 J jnl
PanTools v3: functional annotation, classification and phylogenomics.
Bioinform.
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
2021 J jnl
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases.
PLoS Comput. Biol.
Janani Durairaj, Elena Melillo, Harro J. Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D. J. van Dijk
2020 J jnl
Geometricus represents protein structures as shape-mers derived from moment invariants.
Bioinform.
Janani Durairaj, Mehmet Akdel, Dick de Ridder, Aalt D. J. van Dijk
2020 J jnl
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads.
BMC Bioinform.
Sina Majidian, Mohammad Hossein Kahaei, Dick de Ridder
2020 J jnl
WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans.
Database J. Biol. Databases Curation
Basten L. Snoek, Mark G. Sterken, Margi Hartanto, Albert-Jan van Zuilichem, Jan E. Kammenga, Dick de Ridder, Harm Nijveen
2019 J jnl
GeneNoteBook, a collaborative notebook for comparative genomics.
Bioinform.
Rens Holmer, Robin van Velzen, René Geurts, Ton Bisseling, Dick de Ridder, Sandra Smit
2019 J jnl
Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis.
Bioinform.
Miguel Correa Marrero, Richard G. H. Immink, Dick de Ridder, Aalt D. J. van Dijk
2019 J jnl
poreTally: run and publish de novo nanopore assembler benchmarks.
Bioinform.
Carlos de Lannoy, Judith Risse, Dick de Ridder
2018 J jnl
Efficient inference of homologs in large eukaryotic pan-proteomes.
BMC Bioinform.
Siavash Sheikhizadeh, Dick de Ridder, M. Eric Schranz, Sandra Smit
2018 J jnl
Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study.
Briefings Bioinform.
Ehsan Motazedi, Richard Finkers, Chris Maliepaard, Dick de Ridder
2018 J jnl
TriPoly: haplotype estimation for polyploids using sequencing data of related individuals.
Bioinform.
Ehsan Motazedi, Dick de Ridder, Richard Finkers, Samantha J. Baldwin, Susan Thomson, Katrina Monaghan, Chris Maliepaard
2017 J jnl
Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity.
PLoS Comput. Biol.
Alexey A. Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal
2016 J jnl
CyLineUp: A Cytoscape app for visualizing data in network small multiples.
F1000Research
Maria Cecília D. Costa, Thijs Slijkhuis, Wilco Ligterink, Henk W. M. Hilhorst, Dick de Ridder, Harm Nijveen
2016 J jnl
PanTools: representation, storage and exploration of pan-genomic data.
Bioinform.
Siavash Sheikhizadeh, M. Eric Schranz, Mehmet Akdel, Dick de Ridder, Sandra Smit
2016 J jnl
Selected proceedings of Machine Learning in Systems Biology: MLSB 2016.
BMC Bioinform.
Aalt D. J. van Dijk, Harri Lähdesmäki, Dick de Ridder, Juho Rousu
2015 J jnl
ACE: accurate correction of errors using
Bioinform.
Siavash Sheikhizadeh, Dick de Ridder
2015 J jnl
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data.
BMC Bioinform.
Saulo Aflitos, Edouard Severing, Gabino Sanchez-Perez, Sander Peters, Hans de Jong, Dick de Ridder
2015 J jnl
Making the difference: integrating structural variation detection tools.
Briefings Bioinform.
Ke Lin, Sandra Smit, Guusje Bonnema, Gabino Sanchez-Perez, Dick de Ridder
2015 J jnl
Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.
PLoS Comput. Biol.
Alexey A. Gritsenko, Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder
2014 J jnl
SPiCE: a web-based tool for sequence-based protein classification and exploration.
BMC Bioinform.
Bastiaan A. van den Berg, Marcel J. T. Reinders, Johannes A. Roubos, Dick de Ridder
2013 — conf
Conditional Random Fields for Protein Function Prediction.
PRIB
Thies Gehrmann, Marco Loog, Marcel J. T. Reinders, Dick de Ridder
2013 J jnl
Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels.
Int. J. Bioinform. Res. Appl.
Rogier J. P. van Berlo, Wynand Winterbach, Marco J. L. de Groot, Andreas Bender, Peter J. T. Verheijen, Marcel J. T. Reinders, Dick de Ridder
2013 J jnl
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.
Bioinform.
Jurgen F. Nijkamp, Mihai Pop, Marcel J. T. Reinders, Dick de Ridder
2013 — conf
Local Topological Signatures for Network-Based Prediction of Biological Function.
PRIB
Wynand Winterbach, Piet Van Mieghem, Marcel J. T. Reinders, Huijuan Wang, Dick de Ridder
2013 J jnl
Pattern recognition in bioinformatics.
Briefings Bioinform.
Dick de Ridder, Jeroen de Ridder, Marcel J. T. Reinders
2013 J jnl
Topology of molecular interaction networks.
BMC Syst. Biol.
Wynand Winterbach, Piet Van Mieghem, Marcel J. T. Reinders, Huijuan Wang, Dick de Ridder
2013 — conf
Using Predictive Models to Engineer Biology: A Case Study in Codon Optimization.
PRIB
Alexey A. Gritsenko, Marcel J. T. Reinders, Dick de Ridder
2012 J jnl
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
Bioinform.
Alexey A. Gritsenko, Jurgen F. Nijkamp, Marcel J. T. Reinders, Dick de Ridder
2011 J jnl
Metabolic network destruction: Relating topology to robustness.
Nano Commun. Networks
Wynand Winterbach, Huijuan Wang, Marcel J. T. Reinders, Piet Van Mieghem, Dick de Ridder
2011 — ed.
Pattern Recognition in Bioinformatics - 6th IAPR International Conference, PRIB 2011, Delft, The Netherlands, November 2-4, 2011. Proceedings
PRIB
Marco Loog, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Dick de Ridder
2011 J jnl
Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints.
IEEE ACM Trans. Comput. Biol. Bioinform.
Rogier J. P. van Berlo, Dick de Ridder, Jean-Marc Daran, Pascale A. S. Daran-Lapujade, Bas Teusink, Marcel J. T. Reinders
2010 J jnl
Integrating genome assemblies with MAIA.
Bioinform.
Jurgen F. Nijkamp, Wynand Winterbach, Marcel van den Broek, Jean-Marc Daran, Marcel J. T. Reinders, Dick de Ridder
2010 — conf
Sequence-Based Prediction of Protein Secretion Success in
PRIB
Bastiaan A. van den Berg, Jurgen F. Nijkamp, Marcel J. T. Reinders, Liang Wu, Herman J. Pel, Johannes A. Roubos, Dick de Ridder
2009 J jnl
Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder
2009 J jnl
Metabolite and reaction inference based on enzyme specificities.
Bioinform.
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
2009 J jnl
Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks.
EURASIP J. Bioinform. Syst. Biol.
Peter van Nes, Domenico Bellomo, Marcel J. T. Reinders, Dick de Ridder
2008 J jnl
Erratum to "Classification in the presence of class noise using a probabilistic kernel fisher method": [Pattern Recognition 40 (12) 3349-3357].
Pattern Recognit.
Yunlei Li, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders
2008 J jnl
Integration of prior knowledge of measurement noise in kernel density classification.
Pattern Recognit.
Yunlei Li, Dick de Ridder, Robert P. W. Duin, Marcel J. T. Reinders
2008 B conf
Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks.
APBC
Yunlei Li, Dick de Ridder, Marco J. L. de Groot, Marcel J. T. Reinders
2008 J jnl
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure.
BMC Syst. Biol.
Yunlei Li, Dick de Ridder, Marco J. L. de Groot, Marcel J. T. Reinders
2008 — conf
Stability cannot be derived from local structure in biochemical networks.
BIONETICS
Domenico Bellomo, Peter van Nes, Marcel J. T. Reinders, Dick de Ridder
2007 J jnl
Classification in the presence of class noise using a probabilistic Kernel Fisher method.
Pattern Recognit.
Yunlei Li, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders
2007 J jnl
Protein Complex Prediction Using an Integrative Bioinformatics Approach.
J. Bioinform. Comput. Biol.
Rogier J. P. van Berlo, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders
2006 — conf
Local Discriminant Analysis.
ICPR (3)
Marco Loog, Dick de Ridder
2006 J jnl
Maximum significance clustering of oligonucleotide microarrays.
Bioinform.
Dick de Ridder, Frank J. T. Staal, Jacques J. M. van Dongen, Marcel J. T. Reinders
2006 — ed.
Structural, Syntactic, and Statistical Pattern Recognition, Joint IAPR International Workshops, SSPR 2006 and SPR 2006, Hong Kong, China, August 17-19, 2006, Proceedings
SSPR/SPR
Dit-Yan Yeung, James T. Kwok, Ana L. N. Fred, Fabio Roli, Dick de Ridder
2006 J jnl
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies.
BMC Bioinform.
Roel G. W. Verhaak, Frank J. T. Staal, Peter J. M. Valk, Bob Löwenberg, Marcel J. T. Reinders, Dick de Ridder
2005 — conf
Maximum signi.cance clustering of oligonucleotide microarrays.
CSB Workshops
Dick de Ridder, Marcel J. T. Reinders, Frank J. T. Staal, Jacques J. M. van Dongen
2004 J jnl
Almost autonomous training of mixtures of principal component analyzers.
Pattern Recognit. Lett.
Mohamed E. M. Musa, Dick de Ridder, Robert P. W. Duin, Volkan Atalay
2004 — conf
Local Fisher Embedding.
ICPR (2)
Dick de Ridder, Marco Loog, Marcel J. T. Reinders
2004 — ed.
Structural, Syntactic, and Statistical Pattern Recognition, Joint IAPR International Workshops, SSPR 2004 and SPR 2004, Lisbon, Portugal, August 18-20, 2004 Proceedings
SSPR/SPR
Ana L. N. Fred, Terry Caelli, Robert P. W. Duin, Aurélio C. Campilho, Dick de Ridder
2003 A conf
Robust subspace mixture models using t-distributions.
BMVC
Dick de Ridder, Vojtech Franc
2003 C conf
Supervised Locally Linear Embedding.
ICANN
Dick de Ridder, Olga Kouropteva, Oleg Okun, Matti Pietikäinen, Robert P. W. Duin
2003 — conf
Texture Segmentation Using the Mixtures of Principal Component Analyzers.
ISCIS
Mohamed E. M. Musa, Robert P. W. Duin, Dick de Ridder, Volkan Atalay
2002 J jnl
A note on core research issues for statistical pattern recognition.
Pattern Recognit. Lett.
Robert P. W. Duin, Fabio Roli, Dick de Ridder
2002 J jnl
Image processing with neural networks - a review.
Pattern Recognit.
Michael Egmont-Petersen, Dick de Ridder, Heinz Handels
2002 — ed.
Structural, Syntactic, and Statistical Pattern Recognition, Joint IAPR International Workshops SSPR 2002 and SPR 2002, Windsor, Ontario, Canada, August 6-9, 2002, Proceedings
SSPR/SPR
Terry Caelli, Adnan Amin, Robert P. W. Duin, Mohamed S. Kamel, Dick de Ridder
2002 — conf
Texture Description by Independent Components.
SSPR/SPR
Dick de Ridder, Robert P. W. Duin, Josef Kittler
2002 — conf
The Economics of Classification: Error vs. Complexity.
ICPR (2)
Dick de Ridder, Elzbieta Pekalska, Robert P. W. Duin
2000 A conf
Probabilistic PCA and ICA Subspace Mixture Models for Image Segmentation.
BMVC
Dick de Ridder, Josef Kittler, Robert P. W. Duin
2000 — conf
The Adaptive Subspace Map for Image Description and Image Database Retrieval.
SSPR/SPR
Dick de Ridder, Olaf Lemmers, Robert P. W. Duin, Josef Kittler
2000 B conf
The Adaptive Subspace Map for Texture Segmentation.
ICPR
Dick de Ridder, Josef Kittler, Olaf Lemmers, Robert P. W. Duin
1999 A conf
Adaptive Texture Representation Methods for Automatic Target Recognition.
BMVC
Kieron Messer, Dick de Ridder, Josef Kittler
1999 J jnl
Relational discriminant analysis.
Pattern Recognit. Lett.
Robert P. W. Duin, Elzbieta Pekalska, Dick de Ridder
1999 J jnl
The Applicability of Neural Networks to Non-linear Image Processing.
Pattern Anal. Appl.
Dick de Ridder, Robert P. W. Duin, Piet W. Verbeek
1998 J jnl
Featureless pattern classification.
Kybernetika
Robert P. W. Duin, Dick de Ridder, David M. J. Tax
1998 B conf
On the Application of Neural Networks to Non-Linear Image Processing Tasks.
ICONIP
Dick de Ridder, Robert P. W. Duin, Piet W. Verbeek, Lucas J. van Vliet
1997 J jnl
Experiments with a featureless approach to pattern recognition.
Pattern Recognit. Lett.
Robert P. W. Duin, Dick de Ridder, David M. J. Tax
1997 A conf
Neural network experiences between perceptrons and support vectors.
BMVC
Robert P. W. Duin, Dick de Ridder
1997 J jnl
Sammon's mapping using neural networks: A comparison.
Pattern Recognit. Lett.
Dick de Ridder, Robert P. W. Duin