D. Ridder

发表

Image processing with neural networks - a review

Michael Egmont-Petersen, Heinz Handels, Dick de Ridder, 2002, Pattern Recognit..

Tax Featureless pattern classification

D. Ridder, W. Duin, J. DavidM., 2015 .

The PLETHORAGene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis RootsOPEN

Ari Pekka Mähönen, S. V. Heesch, B. Snel, 2016 .

Adaptive methods of image processing

Dick de Ridder, D. Ridder, 2001 .

Modelling Handwitten Digit Data using Probabilistic Principal Component Analysis

Mohamed E. M. Musa, R. Duin, D. Ridder, 2001 .

Structural, Syntactic, and Statistical Pattern Recognition: Joint IAPR International Workshops, SSPR 2006 and SPR 2006, Hong Kong, China, August 17-19, ... (Lecture Notes in Computer Science)

Dit-Yan Yeung, Fabio Roli, James T. Kwok, 2006 .

BASE L ESS : LIGHTWEIGHT DETECTION OF SEQUENCES IN RAW M IN ION DATA

Carlos de Lannoy, V. Carrión, J. Raaijmakers, 2022 .

Feature Extraction and Selection

Robert P. W. Duin, David M. J. Tax, F. van der Heijden, 2005 .

A PATHWAY APPROACH TO ALIGN REGULATORY-METABOLIC NETWORKS

M. Reinders, J. Bot, D. Ridder, 2009 .

Ectopic retroviral expression of LMO2, but not IL2Rγ, blocks human T-cell development from CD34+ cells: implications for leukemogenesis in gene therapy

M. Reinders, F. Weerkamp, J. Dongen, 2007, Leukemia.

Detection and Classification

Robert P. W. Duin, David M. J. Tax, F. van der Heijden, 2005 .

On the Application of Neural Networks to Non-Linear Image Processing Tasks

Robert P. W. Duin, Lucas J. van Vliet, Piet W. Verbeek, 1998, ICONIP.

A Matlab Toolbox for Pattern Recognition

Robert P. W. Duin, Elzbieta Pekalska, David M. J. Tax, 2004 .

A new measure for the effect of sharpening and smoothing filters on images

Robert P. W. Duin, Piet W. Verbeek, Ian T. Young, 1999 .

State Estimation in Practice

Robert P. W. Duin, David M. J. Tax, F. van der Heijden, 2005 .

Worked out Examples

Robert P. W. Duin, David M. J. Tax, D. de Ridder, 2005 .

Structural, Syntactic, And Statistical Pattern Recognition: Joint Iapr International Workshops, Sspr 2004 And Spr 2004, Lisbon, Portugal, August 18-20 ... oceedings (Lecture Notes in Computer Science)

Robert P. W. Duin, Terry Caelli, Dick de Ridder, 2004 .

Zeolites for nitrosamine and pharmaceutical removal from demineralised and surface water: Mechanisms and efficacy

J. V. Dijk, G. Amy, J. Verberk, 2012 .

BIOINFORMATICS Integrating genome assemblies with MAIA

M. Reinders, J. Daran, W. Winterbach, 2010 .

Influence of HPO42-, H4SiO4, Ca2+, Mg2+ on Fe floc growth and As(III) removal in aerated, natural groundwater

T. V. Dijk, D. Halem, D. Ridder, 2018 .

Influence of particle properties on iron flocculation

D. Halem, D. Ridder, 2018 .

Adsorption of organic micropollutants onto activated carbon and zeolites

D. D. Ridder, D. Ridder, 2012 .

Topology of molecular interaction networks

Piet Van Mieghem, Marcel J. T. Reinders, Dick de Ridder, 2013, BMC Systems Biology.

Metabolic network destruction: Relating topology to robustness

Piet Van Mieghem, Marcel J. T. Reinders, Dick de Ridder, 2010, Nano Commun. Networks.

Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks

Marcel J. T. Reinders, Dick de Ridder, Domenico Bellomo, 2008, EURASIP J. Bioinform. Syst. Biol..

Stability cannot be derived from local structure in biochemical networks

Marcel J. T. Reinders, Dick de Ridder, Domenico Bellomo, 2008, BIONETICS.

Magnetic separation and characterization of vivianite from digested sewage sludge

M. Loosdrecht, A. Bouderbala, T. Prot, 2019, Separation and Purification Technology.

Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription

I. Artsimovitch, E. Abbondanzieri, N. Dekker, 2018, Cell.

clones mark "stemness" pathways Retroviral vector insertion sites associated with dominant hematopoietic

C. Shaw, F. Staal, D. de Ridder, 2010 .

Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study

Richard Finkers, Dick de Ridder, Chris Maliepaard, 2017, Briefings Bioinform..

Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

Eran Segal, Dick de Ridder, Alexey A. Gritsenko, 2017, PLoS Comput. Biol..

Predicting functional effect of human missense mutations

Marcel J. T. Reinders, Dick de Ridder, Jm Thornton, 2013 .

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

Dick de Ridder, Sander Peters, Edouard Severing, 2015, BMC Bioinformatics.

Genome-wide expression analysis of paired diagnosis–relapse samples in ALL indicates involvement of pathways related to DNA replication, cell cycle and DNA repair, independent of immune phenotype

F. Staal, T. Szczepański, V. Velden, 2010, Leukemia.

Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing.

Linda V. Bakker, E. Schijlen, S. Peters, 2019, The Plant journal : for cell and molecular biology.

CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations

Cleo C. van Diemen, Birgit Sikkema-Raddatz, Kristin M. Abbott, 2019, Genome Medicine.

Laboratory evolution of new lactate transporter genes in a jen1Δ mutant of Saccharomyces cerevisiae and their identification as ADY2 alleles by whole-genome resequencing and transcriptome analysis

Dick de Ridder, Jack T. Pronk, Jurgen F. Nijkamp, 2012 .

Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction

M.J.T. Reinders, M. Hulsman, D. de Ridder, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

LYMPHOID NEOPLASIA B-cell prolymphocytic leukemia : a speci fi c subgroup of mantle cell lymphoma

A. Órfão, J. Dongen, A. Langerak, 2014 .

Metabolic Pathway Alignment (M-Pal) Reveals Diversity and Alternatives in Conserved Networks

Marcel J. T. Reinders, Dick de Ridder, Yunlei Li, 2007, APBC.

Making the difference: integrating structural variation detection tools

Guusje Bonnema, Dick de Ridder, Ke Lin, 2015, Briefings Bioinform..

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals

Richard Finkers, Dick de Ridder, Susan Thomson, 2018, Bioinform..

TriPoly: a haplotype estimation approach for polyploids using sequencing data of related individuals

D. D. Ridder, R. Finkers, C. Maliepaard, 2017, bioRxiv.

Purity for clarity: the need for purification of tumor cells in DNA microarray studies

M J T Reinders, M. Reinders, F. Staal, 2005, Leukemia.

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

Marcel J. T. Reinders, Mihai Pop, Dick de Ridder, 2013, Bioinform..

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

Marcel J. T. Reinders, Dick de Ridder, Alexey A. Gritsenko, 2013, PRIB.

Persistent polyclonal B-cell lymphocytosis: extensively proliferated CD27+IgM+IgD+ memory B cells with a distinctive immunophenotype

D. D. Ridder, A. Órfão, J. Dongen, 2014, Leukemia.

SPiCE: a web-based tool for sequence-based protein classification and exploration

Marcel J. T. Reinders, Dick de Ridder, Johannes A. Roubos, 2014, BMC Bioinformatics.

Pattern recognition in bioinformatics

Marcel J. T. Reinders, Dick de Ridder, Jeroen de Ridder, 2013, Briefings Bioinform..

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

Marcel J. T. Reinders, Dick de Ridder, Jurgen F. Nijkamp, 2012, Bioinform..

Integration of prior knowledge of measurement noise in kernel density classification

Marcel J. T. Reinders, Robert P. W. Duin, Dick de Ridder, 2008, Pattern Recognit..

Sequence-based analysis of protein degradation rates.

D. D. Ridder, M. Marrero, A. V. Dijk, 2017 .

protein metabolism , protein turnover , proteolysis , intrinsic disorder , sequence analysis , machine learning , support vector machine , multivariate regression , data mining

Miguel Correa Marrero, D. D. Ridder, M. Marrero, 2017 .

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

Marcel J. T. Reinders, Dick de Ridder, Marc Hulsman, 2015, PLoS Comput. Biol..

The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

Marcel J. T. Reinders, Dick de Ridder, Frank J. T. Staal, 2006, BMC Bioinformatics.

De novo detection of copy number variation by co-assembly

Marcel J. T. Reinders, Dick de Ridder, Jurgen F. Nijkamp, 2012, Bioinform..

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

Dick de Ridder, Siavash Sheikhizadeh, M. Eric Schranz, 2016, Bioinform..

The Applicability of Neural Networks to Non-linear Image Processing

Robert P. W. Duin, Piet W. Verbeek, Dick de Ridder, 1999, Pattern Analysis & Applications.

A new measure for the e ect of sharpening and smoothing lters on images

Piet W. Verbeek, Dick de Ridder, Jan Walraven, 1999 .

The Adaptive Subspace Map for Image Description and Image Database Retrieval

Josef Kittler, Robert P. W. Duin, Dick de Ridder, 2000, SSPR/SPR.

Supplementary Information for “ Deriving unbiased quantitative models of protein translation from ribosome profiling data ”

D. D. Ridder, M. Reinders, M. Hulsman, 2015 .

Classification in the presence of class noise using a probabilistic Kernel Fisher method

Marcel J. T. Reinders, Lodewyk F. A. Wessels, Dick de Ridder, 2007, Pattern Recognit..

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

Marcel J. T. Reinders, Rogier J. P. van Berlo, Dick de Ridder, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Shared Weights Neural Networks in Image Analysis

Dick de Ridder, D. Ridder, 1996 .

Nonlinear image processing using artificial neural networks

Robert P. W. Duin, Michael Egmont-Petersen, Piet W. Verbeek, 2003 .

Neural network experiences between perceptrons and support vectors

Robert P. W. Duin, Dick de Ridder, R. Duin, 1997, BMVC.

Gene therapy: Is IL2RG oncogenic in T-cell development?

M. Reinders, F. Weerkamp, J. Dongen, 2006, Nature.

Supervised Locally Linear Embedding

Matti Pietikäinen, Robert P. W. Duin, Dick de Ridder, 2003, ICANN.

Locally linear embedding for classification

D. D. Ridder, D. Ridder, 2002 .

Metabolite and reaction inference based on enzyme specificities

Marcel J. T. Reinders, Rogier J. P. van Berlo, Dick de Ridder, 2009, Bioinform..

Classification, Parameter Estimation and State Estimation: An Engineering Approach Using MATLAB, 2nd Edition

Bangjun Lei, Ferdinand van der Heijden, David M. J. Tax, 2017 .

A note on core research issues for statistical pattern recognition

Fabio Roli, Robert P. W. Duin, Dick de Ridder, 2002, Pattern Recognit. Lett..

Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction

Marcel J. T. Reinders, Dick de Ridder, Marc Hulsman, 2009, IEEE/ACM Transactions on Computational Biology & Bioinformatics.

Protein Complex Prediction Using an Integrative Bioinformatics Approach

Marcel J. T. Reinders, Lodewyk F. A. Wessels, Rogier J. P. van Berlo, 2007, J. Bioinform. Comput. Biol..

Proceedings of the 6th IAPR international conference on Pattern recognition in bioinformatics

Marcel J. T. Reinders, Marco Loog, Lodewyk F. A. Wessels, 2011 .

Genome-wide characterization of Phytophthora infestans 1 metabolism : a systems biology approach 2

D. D. Ridder, Sander Y. A. Rodenburg, M. Seidl, 2017 .

Integrating genome assemblies with MAIA

Marcel J. T. Reinders, Dick de Ridder, Wynand Winterbach, 2010, Bioinform..

In fl uence of particle properties on iron fl occulation

D. Halem, D. Ridder, 2018 .

Metabolic pathway alignment between species using a comprehensive and flexible similarity measure

Marcel J. T. Reinders, Dick de Ridder, Yunlei Li, 2008, BMC Systems Biology.

Adaptive Texture Representation Methods for Automatic Target Recognition

Josef Kittler, Kieron Messer, Dick de Ridder, 1999, BMVC.

Sequence-Based Prediction of Protein Secretion Success in Aspergillus niger

Marcel J. T. Reinders, Dick de Ridder, Johannes Andries Roubos, 2010, PRIB.

Robust subspace mixture models using t-distributions

Vojtech Franc, Dick de Ridder, Vojtech Franc, 2003, BMVC.

ACE: accurate correction of errors using K-mer tries

Dick de Ridder, Siavash Sheikhizadeh, D. Ridder, 2015, Bioinform..

The adaptive subspace map for texture segmentation

Josef Kittler, Robert P. W. Duin, Dick de Ridder, 2000, Proceedings 15th International Conference on Pattern Recognition. ICPR-2000.

Modeling equilibrium adsorption of organic micropollutants onto activated carbon.

J. V. Dijk, G. Amy, S. Heijman, 2010, Water research.

Retroviral vector insertion sites associated with dominant hematopoietic clones mark “stemness” pathways

C. Shaw, F. Staal, M. Goodell, 2007 .

Retroviral vector insertion sites associated with dominant hematopoietic clones mark “stemness” pathways

C. Shaw, F. Staal, M. Goodell, 2007 .

Maximum significance clustering of oligonucleotide microarrays

Marcel J. T. Reinders, Dick de Ridder, Frank J. T. Staal, 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

Locally linear embedding for classification

R. Duin, D. Ridder, 2002 .

Robust manifold learning

D. Ridder, 2003 .

Retroviral vector insertion sites associated with dominant hematopoietic clones mark “stemness” pathways

C. Shaw, F. Staal, M. Goodell, 2007 .

Retroviral vector insertion sites associated with dominant hematopoietic clones mark “stemness” pathways

F. Staal, M. Goodell, B. Fehse, 2007 .

Retroviral vector insertion sites associated with dominant hematopoietic clones mark “stemness” pathways

F. Staal, M. Goodell, B. Fehse, 2007 .

Retroviral vector insertion sites associated with dominant hematopoietic clones mark “stemness” pathways

F. Staal, M. Goodell, B. Fehse, 2007 .

Retroviral vector insertion sites associated with dominant hematopoietic clones mark “stemness” pathways

F. Staal, M. Goodell, B. Fehse, 2007 .

Gammaretrovirus-mediated correction of SCID-X1 is associated with skewed vector integration site distribution in vivo.

Christine Kinnon, Christof von Kalle, Dick de Ridder, 2007, The Journal of clinical investigation.

Integrating genome assemblies with MAIA

Jurgen F. Nijkamp, M. Reinders, J. Daran, 2010, Bioinform..

The economics of classification: error vs. complexity

Robert P. W. Duin, Elzbieta Pekalska, Dick de Ridder, 2002, Object recognition supported by user interaction for service robots.

B-cell prolymphocytic leukemia: a specific subgroup of mantle cell lymphoma.

M. V. van Zelm, A. Órfão, J. V. van Dongen, 2014, Blood.

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

Jurgen F. Nijkamp, M. Reinders, D. Ridder, 2013, Bioinform..

Almost autonomous training of mixtures of principal component analyzers

Robert P. W. Duin, Volkan Atalay, Dick de Ridder, 2004, Pattern Recognit. Lett..

Fast and adaptive protein structure representations for machine learning

A. V. Dijk, D. Ridder, Mehmet Akdel, 2021, bioRxiv.

Modeling equilibrium adsorption of organic micropollutants onto activated carbon.

L. Villacorte, J. Verberk, D. Ridder, 2010, Water research.

Development of a predictive model to determine micropollutant removal using granular activated carbon

D. D. Ridder, L. Rietveld, J. V. Dijk, 2009 .

Experiments with a featureless approach to pattern recognition

Robert P. W. Duin, David M. J. Tax, Dick de Ridder, 1997, Pattern Recognit. Lett..

GeneNoteBook, a collaborative notebook for comparative genomics

Rens Holmer, Dick de Ridder, Ton Bisseling, 2019, Bioinform..

Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis

Miguel Correa Marrero, A. V. Dijk, R. Immink, 2018, Bioinform..

Influence of natural organic matter on equilibrium adsorption of neutral and charged pharmaceuticals onto activated carbon.

L. Rietveld, J. V. Dijk, G. Amy, 2011, Water Science and Technology.

Metabolite and reaction inference based on enzyme specificities

M. Reinders, W. A. Winden, D. Ridder, 2009, Bioinform..

PanTools v3: functional annotation, classification and phylogenomics

S. Smit, D. de Ridder, T. A. van der Lee, 2022, Bioinform..