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2020 – today
- 2022
[j46]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:
PanTools v3: functional annotation, classification and phylogenomics. Bioinform. 38(18): 4403-4405 (2022)- [j45]Aalt D. J. van Dijk, Shin-Han Shiu, Dick de Ridder:
Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics. Frontiers Artif. Intell. 5 (2022) - 2021
- [j44]Janani Durairaj, Elena Melillo, Harro J. Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D. J. van Dijk:
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. PLoS Comput. Biol. 17(3) (2021) - 2020
- [j43]Basten L. Snoek, Mark G. Sterken, Margi Hartanto, Albert-Jan van Zuilichem, Jan E. Kammenga, Dick de Ridder, Harm Nijveen:
WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans. Database J. Biol. Databases Curation 2020: baz149 (2020) - [j42]Sina Majidian, Mohammad Hossein Kahaei, Dick de Ridder:
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads. BMC Bioinform. 21(1): 253 (2020)
2010 – 2019
- 2019
- [j41]Miguel Correa Marrero, Richard G. H. Immink, Dick de Ridder, Aalt D. J. van Dijk:
Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis. Bioinform. 35(12): 2036-2042 (2019) - [j40]Carlos de Lannoy, Judith Risse, Dick de Ridder:
poreTally: run and publish de novo nanopore assembler benchmarks. Bioinform. 35(15): 2663-2664 (2019) - [j39]Rens Holmer, Robin van Velzen, René Geurts, Ton Bisseling, Dick de Ridder, Sandra Smit:
GeneNoteBook, a collaborative notebook for comparative genomics. Bioinform. 35(22): 4779-4781 (2019) - 2018
- [j38]Ehsan Motazedi, Richard Finkers, Chris Maliepaard, Dick de Ridder:
Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study. Briefings Bioinform. 19(3): 387-403 (2018) - [j37]Ehsan Motazedi, Dick de Ridder, Richard Finkers, Samantha J. Baldwin, Susan Thomson, Katrina Monaghan, Chris Maliepaard:
TriPoly: haplotype estimation for polyploids using sequencing data of related individuals. Bioinform. 34(22): 3864-3872 (2018) - [j36]Siavash Sheikhizadeh, Dick de Ridder, M. Eric Schranz, Sandra Smit:
Efficient inference of homologs in large eukaryotic pan-proteomes. BMC Bioinform. 19(1): 340:1-340:11 (2018) - 2017
- [j35]Alexey A. Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal:
Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity. PLoS Comput. Biol. 13(9) (2017) - 2016
- [j34]Siavash Sheikhizadeh, M. Eric Schranz, Mehmet Akdel, Dick de Ridder, Sandra Smit:
PanTools: representation, storage and exploration of pan-genomic data. Bioinform. 32(17): 487-493 (2016) - [j33]Aalt D. J. van Dijk, Harri Lähdesmäki, Dick de Ridder, Juho Rousu:
Selected proceedings of Machine Learning in Systems Biology: MLSB 2016. BMC Bioinform. 17(S-16): 51-52 (2016) - [i1]Maria Cecília D. Costa, Thijs Slijkhuis, Wilco Ligterink, Henk W. M. Hilhorst, Dick de Ridder, Harm Nijveen:
CyLineUp: A Cytoscape app for visualizing data in network small multiples. F1000Research 5: 635 (2016) - 2015
- [j32]Ke Lin, Sandra Smit, Guusje Bonnema, Gabino Sanchez-Perez, Dick de Ridder:
Making the difference: integrating structural variation detection tools. Briefings Bioinform. 16(5): 852-864 (2015) - [j31]Siavash Sheikhizadeh, Dick de Ridder:
ACE: accurate correction of errors using K-mer tries. Bioinform. 31(19): 3216-3218 (2015) - [j30]Saulo Aflitos, Edouard Severing, Gabino Sanchez-Perez, Sander Peters, Hans de Jong, Dick de Ridder:
Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data. BMC Bioinform. 16: 352:1-352:10 (2015) - [j29]Alexey A. Gritsenko, Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder:
Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data. PLoS Comput. Biol. 11(8) (2015) - 2014
- [j28]Bastiaan A. van den Berg, Marcel J. T. Reinders, Johannes A. Roubos, Dick de Ridder:
SPiCE: a web-based tool for sequence-based protein classification and exploration. BMC Bioinform. 15: 93 (2014) - 2013
- [j27]Dick de Ridder, Jeroen de Ridder, Marcel J. T. Reinders:
Pattern recognition in bioinformatics. Briefings Bioinform. 14(5): 633-647 (2013) - [j26]Jurgen F. Nijkamp, Mihai Pop, Marcel J. T. Reinders, Dick de Ridder:
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinform. 29(22): 2826-2834 (2013) - [j25]Wynand Winterbach, Piet Van Mieghem, Marcel J. T. Reinders, Huijuan Wang, Dick de Ridder:
Topology of molecular interaction networks. BMC Syst. Biol. 7: 90 (2013) - [j24]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:
Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels. Int. J. Bioinform. Res. Appl. 9(4): 407-432 (2013) - [c20]Wynand Winterbach, Piet Van Mieghem, Marcel J. T. Reinders, Huijuan Wang, Dick de Ridder:
Local Topological Signatures for Network-Based Prediction of Biological Function. PRIB 2013: 23-34 - [c19]Alexey A. Gritsenko, Marcel J. T. Reinders, Dick de Ridder:
Using Predictive Models to Engineer Biology: A Case Study in Codon Optimization. PRIB 2013: 159-171 - [c18]Thies Gehrmann, Marco Loog, Marcel J. T. Reinders, Dick de Ridder:
Conditional Random Fields for Protein Function Prediction. PRIB 2013: 184-195 - 2012
- [j23]Alexey A. Gritsenko, Jurgen F. Nijkamp, Marcel J. T. Reinders, Dick de Ridder:
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinform. 28(11): 1429-1437 (2012) - [j22]Jurgen F. Nijkamp, Marcel van den Broek, Jan-Maarten A. Geertman, Marcel J. T. Reinders, Jean-Marc Daran, Dick de Ridder:
De novo detection of copy number variation by co-assembly. Bioinform. 28(24): 3195-3202 (2012) - 2011
- [j21]Wynand Winterbach, Huijuan Wang, Marcel J. T. Reinders, Piet Van Mieghem, Dick de Ridder:
Metabolic network destruction: Relating topology to robustness. Nano Commun. Networks 2(2-3): 88-98 (2011) - [j20]Rogier J. P. van Berlo, Dick de Ridder, Jean-Marc Daran, Pascale A. S. Daran-Lapujade, Bas Teusink, Marcel J. T. Reinders:
Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints. IEEE ACM Trans. Comput. Biol. Bioinform. 8(1): 206-216 (2011) - [e4]Marco Loog, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Dick de Ridder:
Pattern Recognition in Bioinformatics - 6th IAPR International Conference, PRIB 2011, Delft, The Netherlands, November 2-4, 2011. Proceedings. Lecture Notes in Computer Science 7036, Springer 2011, ISBN 978-3-642-24854-2 [contents] - 2010
- [j19]Jurgen F. Nijkamp, Wynand Winterbach, Marcel van den Broek, Jean-Marc Daran, Marcel J. T. Reinders, Dick de Ridder:
Integrating genome assemblies with MAIA. Bioinform. 26(18) (2010) - [c17]Bastiaan A. van den Berg, Jurgen F. Nijkamp, Marcel J. T. Reinders, Liang Wu, Herman J. Pel, Johannes A. Roubos, Dick de Ridder:
Sequence-Based Prediction of Protein Secretion Success in Aspergillus niger. PRIB 2010: 3-14
2000 – 2009
- 2009
- [j18]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:
Metabolite and reaction inference based on enzyme specificities. Bioinform. 25(22): 2975-2982 (2009) - [j17]Peter van Nes, Domenico Bellomo, Marcel J. T. Reinders, Dick de Ridder:
Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks. EURASIP J. Bioinform. Syst. Biol. 2009 (2009) - [j16]Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder:
Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 6(3): 427-437 (2009) - 2008
- [j15]Yunlei Li, Dick de Ridder, Marco J. L. de Groot, Marcel J. T. Reinders:
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. BMC Syst. Biol. 2: 111 (2008) - [j14]Yunlei Li, Dick de Ridder, Robert P. W. Duin, Marcel J. T. Reinders:
Integration of prior knowledge of measurement noise in kernel density classification. Pattern Recognit. 41(1): 320-330 (2008) - [j13]Yunlei Li, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders:
Erratum to "Classification in the presence of class noise using a probabilistic kernel fisher method": [Pattern Recognition 40 (12) 3349-3357]. Pattern Recognit. 41(3): 1214 (2008) - [c16]Yunlei Li, Dick de Ridder, Marco J. L. de Groot, Marcel J. T. Reinders:
Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks. APBC 2008: 273-286 - [c15]Domenico Bellomo, Peter van Nes, Marcel J. T. Reinders, Dick de Ridder:
Stability cannot be derived from local structure in biochemical networks. BIONETICS 2008: 3 - 2007
- [j12]Rogier J. P. van Berlo, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders:
Protein Complex Prediction Using an Integrative Bioinformatics Approach. J. Bioinform. Comput. Biol. 5(4): 839-864 (2007) - [j11]Yunlei Li, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders:
Classification in the presence of class noise using a probabilistic Kernel Fisher method. Pattern Recognit. 40(12): 3349-3357 (2007) - 2006
- [j10]Dick de Ridder, Frank J. T. Staal, Jacques J. M. van Dongen, Marcel J. T. Reinders:
Maximum significance clustering of oligonucleotide microarrays. Bioinform. 22(3): 326-331 (2006) - [j9]Roel G. W. Verhaak, Frank J. T. Staal, Peter J. M. Valk, Bob Löwenberg, Marcel J. T. Reinders, Dick de Ridder:
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. BMC Bioinform. 7: 105 (2006) - [c14]Marco Loog, Dick de Ridder:
Local Discriminant Analysis. ICPR (3) 2006: 328-331 - [e3]Dit-Yan Yeung, James T. Kwok, Ana L. N. Fred, Fabio Roli, Dick de Ridder:
Structural, Syntactic, and Statistical Pattern Recognition, Joint IAPR International Workshops, SSPR 2006 and SPR 2006, Hong Kong, China, August 17-19, 2006, Proceedings. Lecture Notes in Computer Science 4109, Springer 2006, ISBN 3-540-37236-9 [contents] - 2005
- [c13]Dick de Ridder, Marcel J. T. Reinders, Frank J. T. Staal, Jacques J. M. van Dongen:
Maximum signi.cance clustering of oligonucleotide microarrays. CSB Workshops 2005: 93-94 - 2004
- [j8]Mohamed E. M. Musa, Dick de Ridder, Robert P. W. Duin, Volkan Atalay:
Almost autonomous training of mixtures of principal component analyzers. Pattern Recognit. Lett. 25(9): 1085-1095 (2004) - [c12]Dick de Ridder, Marco Loog, Marcel J. T. Reinders:
Local Fisher Embedding. ICPR (2) 2004: 295-298 - [e2]Ana L. N. Fred, Terry Caelli, Robert P. W. Duin, Aurélio C. Campilho, Dick de Ridder:
Structural, Syntactic, and Statistical Pattern Recognition, Joint IAPR International Workshops, SSPR 2004 and SPR 2004, Lisbon, Portugal, August 18-20, 2004 Proceedings. Lecture Notes in Computer Science 3138, Springer 2004, ISBN 3-540-22570-6 [contents] - 2003
- [c11]Dick de Ridder, Vojtech Franc:
Robust subspace mixture models using t-distributions. BMVC 2003: 1-10 - [c10]Dick de Ridder, Olga Kouropteva, Oleg Okun, Matti Pietikäinen, Robert P. W. Duin:
Supervised Locally Linear Embedding. ICANN 2003: 333-341 - [c9]Mohamed E. M. Musa, Robert P. W. Duin, Dick de Ridder, Volkan Atalay:
Texture Segmentation Using the Mixtures of Principal Component Analyzers. ISCIS 2003: 505-512 - 2002
- [j7]Michael Egmont-Petersen, Dick de Ridder, Heinz Handels:
Image processing with neural networks - a review. Pattern Recognit. 35(10): 2279-2301 (2002) - [j6]Robert P. W. Duin, Fabio Roli, Dick de Ridder:
A note on core research issues for statistical pattern recognition. Pattern Recognit. Lett. 23(4): 493-499 (2002) - [c8]Dick de Ridder, Elzbieta Pekalska, Robert P. W. Duin:
The Economics of Classification: Error vs. Complexity. ICPR (2) 2002: 244-247 - [c7]Dick de Ridder, Robert P. W. Duin, Josef Kittler:
Texture Description by Independent Components. SSPR/SPR 2002: 587-596 - [e1]Terry Caelli, Adnan Amin, Robert P. W. Duin, Mohamed S. Kamel, Dick de Ridder:
Structural, Syntactic, and Statistical Pattern Recognition, Joint IAPR International Workshops SSPR 2002 and SPR 2002, Windsor, Ontario, Canada, August 6-9, 2002, Proceedings. Lecture Notes in Computer Science 2396, Springer 2002, ISBN 3-540-44011-9 [contents] - 2000
- [c6]Dick de Ridder, Josef Kittler, Robert P. W. Duin:
Probabilistic PCA and ICA Subspace Mixture Models for Image Segmentation. BMVC 2000: 1-10 - [c5]Dick de Ridder, Josef Kittler, Olaf Lemmers, Robert P. W. Duin:
The Adaptive Subspace Map for Texture Segmentation. ICPR 2000: 1216-1220 - [c4]Dick de Ridder, Olaf Lemmers, Robert P. W. Duin, Josef Kittler:
The Adaptive Subspace Map for Image Description and Image Database Retrieval. SSPR/SPR 2000: 94-103
1990 – 1999
- 1999
- [j5]Dick de Ridder, Robert P. W. Duin, Piet W. Verbeek:
The Applicability of Neural Networks to Non-linear Image Processing. Pattern Anal. Appl. 2(2): 111-128 (1999) - [j4]Robert P. W. Duin, Elzbieta Pekalska, Dick de Ridder:
Relational discriminant analysis. Pattern Recognit. Lett. 20(11-13): 1175-1181 (1999) - [c3]Kieron Messer, Dick de Ridder, Josef Kittler:
Adaptive Texture Representation Methods for Automatic Target Recognition. BMVC 1999: 1-10 - 1998
- [j3]Robert P. W. Duin, Dick de Ridder, David M. J. Tax:
Featureless pattern classification. Kybernetika 34(4): 399-404 (1998) - [c2]Dick de Ridder, Robert P. W. Duin, Piet W. Verbeek, Lucas J. van Vliet:
On the Application of Neural Networks to Non-Linear Image Processing Tasks. ICONIP 1998: 161-165 - 1997
- [j2]Robert P. W. Duin, Dick de Ridder, David M. J. Tax:
Experiments with a featureless approach to pattern recognition. Pattern Recognit. Lett. 18(11-13): 1159-1166 (1997) - [j1]Dick de Ridder, Robert P. W. Duin:
Sammon's mapping using neural networks: A comparison. Pattern Recognit. Lett. 18(11-13): 1307-1316 (1997) - [c1]Robert P. W. Duin, Dick de Ridder:
Neural network experiences between perceptrons and support vectors. BMVC 1997
Coauthor Index
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