Dick de Ridder

According to our database, Dick de Ridder authored at least 67 papers between 1997 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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

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

2021

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

2020

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads.

Sina Majidian, Mohammad Hossein Kahaei, Dick de Ridder

BMC Bioinform., 2020

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

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

poreTally: run and publish de novo nanopore assembler benchmarks.

Carlos de Lannoy, Judith Risse, Dick de Ridder

Bioinform., 2019

GeneNoteBook, a collaborative notebook for comparative genomics.

Rens Holmer, Robin van Velzen, René Geurts, Ton Bisseling, Dick de Ridder, Sandra Smit

Bioinform., 2019

2018

Efficient inference of homologs in large eukaryotic pan-proteomes.

Siavash Sheikhizadeh, Dick de Ridder, M. Eric Schranz, Sandra Smit

BMC 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, Katrina Monaghan, Chris Maliepaard

Bioinform., 2018

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

2017

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

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

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

PanTools: representation, storage and exploration of pan-genomic data.

Siavash Sheikhizadeh, M. Eric Schranz, Mehmet Akdel, Dick de Ridder, Sandra Smit

Bioinform., 2016

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

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

ACE: accurate correction of errors using <i>K</i>-mer tries.

Siavash Sheikhizadeh, Dick de Ridder

Bioinform., 2015

Making the difference: integrating structural variation detection tools.

Ke Lin, Sandra Smit, Guusje Bonnema, Gabino Sanchez-Perez, Dick de Ridder

Briefings Bioinform., 2015

2014

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

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, Peter J. T. Verheijen, Marcel J. T. Reinders, Dick de Ridder

Int. J. Bioinform. Res. Appl., 2013

Topology of molecular interaction networks.

Wynand Winterbach, Piet Van Mieghem, Marcel J. T. Reinders, Huijuan Wang, Dick de Ridder

BMC Syst. Biol., 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

Pattern recognition in bioinformatics.

Dick de Ridder, Jeroen de Ridder, Marcel J. T. Reinders

Briefings Bioinform., 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

Proceedings of the Pattern Recognition in Bioinformatics, 2013

Using Predictive Models to Engineer Biology: A Case Study in Codon Optimization.

Alexey A. Gritsenko, Marcel J. T. Reinders, Dick de Ridder

Proceedings of the Pattern Recognition in Bioinformatics, 2013

Conditional Random Fields for Protein Function Prediction.

Thies Gehrmann, Marco Loog, Marcel J. T. Reinders, Dick de Ridder

Proceedings of the Pattern Recognition in Bioinformatics, 2013

2012

<i>De novo</i> 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

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

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

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

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

Sequence-Based Prediction of Protein Secretion Success in <i>Aspergillus niger</i>.

Bastiaan A. van den Berg, Jurgen F. Nijkamp, Marcel J. T. Reinders, Liang Wu, Herman J. Pel, Johannes A. Roubos, Dick de Ridder

Proceedings of the Pattern Recognition in Bioinformatics, 2010

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

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

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

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

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

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

Stability cannot be derived from local structure in biochemical networks.

Domenico Bellomo, Peter van Nes, Marcel J. T. Reinders, Dick de Ridder

Proceedings of the 3rd International ICST Conference on Bio-Inspired Models of Network, 2008

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

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

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

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

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

Maximum significance clustering of oligonucleotide microarrays.

Dick de Ridder, Frank J. T. Staal, Jacques J. M. van Dongen, Marcel J. T. Reinders

Bioinform., 2006

Local Discriminant Analysis.

Marco Loog, Dick de Ridder

Proceedings of the 18th International Conference on Pattern Recognition (ICPR 2006), 2006

2005

Maximum signi.cance clustering of oligonucleotide microarrays.

Dick de Ridder, Marcel J. T. Reinders, Frank J. T. Staal, Jacques J. M. van Dongen

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

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

Local Fisher Embedding.

Dick de Ridder, Marco Loog, Marcel J. T. Reinders

Proceedings of the 17th International Conference on Pattern Recognition, 2004

2003

Texture Segmentation Using the Mixtures of Principal Component Analyzers.

Mohamed E. M. Musa, Robert P. W. Duin, Dick de Ridder, Volkan Atalay

Proceedings of the Computer and Information Sciences, 2003

Supervised Locally Linear Embedding.

Dick de Ridder, Olga Kouropteva, Oleg Okun, Matti Pietikäinen, Robert P. W. Duin

Proceedings of the Artificial Neural Networks and Neural Information Processing, 2003

Robust subspace mixture models using t-distributions.

Dick de Ridder, Vojtech Franc

Proceedings of the British Machine Vision Conference, 2003

2002

A note on core research issues for statistical pattern recognition.

Robert P. W. Duin, Fabio Roli, Dick de Ridder

Pattern Recognit. Lett., 2002

Image processing with neural networks - a review.

Michael Egmont-Petersen, Dick de Ridder, Heinz Handels

Pattern Recognit., 2002

Texture Description by Independent Components.

Dick de Ridder, Robert P. W. Duin, Josef Kittler

Proceedings of the Structural, 2002

The Economics of Classification: Error vs. Complexity.

Dick de Ridder, Elzbieta Pekalska, Robert P. W. Duin

Proceedings of the 16th International Conference on Pattern Recognition, 2002

2000

The Adaptive Subspace Map for Image Description and Image Database Retrieval.

Dick de Ridder, Olaf Lemmers, Robert P. W. Duin, Josef Kittler

Proceedings of the Advances in Pattern Recognition, Joint IAPR International Workshops SSPR 2000 and SPR 2000, [8th International Workshop on Structural and Syntactic Pattern Recognition, 3rd International Workshop on Statistical Techniques in Pattern Recognition], Alicante, Spain, August 30, 2000

The Adaptive Subspace Map for Texture Segmentation.

Dick de Ridder, Josef Kittler, Olaf Lemmers, Robert P. W. Duin

Proceedings of the 15th International Conference on Pattern Recognition, 2000

Probabilistic PCA and ICA Subspace Mixture Models for Image Segmentation.

Dick de Ridder, Josef Kittler, Robert P. W. Duin

Proceedings of the British Machine Vision Conference 2000, 2000

1999

Relational discriminant analysis.

Robert P. W. Duin, Elzbieta Pekalska, Dick de Ridder

Pattern Recognit. Lett., 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

Adaptive Texture Representation Methods for Automatic Target Recognition.

Kieron Messer, Dick de Ridder, Josef Kittler

Proceedings of the British Machine Vision Conference 1999, 1999

1998

Featureless pattern classification.

Robert P. W. Duin, Dick de Ridder, David M. J. Tax

Kybernetika, 1998

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

Proceedings of the Fifth International Conference on Neural Information Processing, 1998

1997

Sammon's mapping using neural networks: A comparison.

Dick de Ridder, Robert P. W. Duin

Pattern Recognit. Lett., 1997

Experiments with a featureless approach to pattern recognition.

Robert P. W. Duin, Dick de Ridder, David M. J. Tax

Pattern Recognit. Lett., 1997

Neural network experiences between perceptrons and support vectors.

Robert P. W. Duin, Dick de Ridder

Proceedings of the British Machine Vision Conference 1997, 1997