Lodewyk F. A. Wessels

According to our database, Lodewyk F. A. Wessels authored at least 47 papers between 1992 and 2023.

Collaborative distances:

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

2023

ecpc: an R-package for generic co-data models for high-dimensional prediction.

Mirrelijn M. van Nee, Lodewyk F. A. Wessels, Mark A. van de Wiel

BMC Bioinform., December, 2023

Percolate: An Exponential Family JIVE Model to Design DNA-Based Predictors of Drug Response.

Soufiane Mourragui, Marco Loog, Mirrelijn M. van Nee, Mark A. van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels

Proceedings of the Research in Computational Molecular Biology, 2023

2019

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors.

Soufiane Mourragui, Marco Loog, Mark A. van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels

Bioinform., 2019

Principal component analysis of binary genomics data.

Yipeng Song, Johan A. Westerhuis, Nanne Aben, Magali Michaut, Lodewyk F. A. Wessels, Age K. Smilde

Briefings Bioinform., 2019

2018

Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis.

Tycho Bismeijer, Sander Canisius, Lodewyk F. A. Wessels

PLoS Comput. Biol., 2018

Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates.

Bram Thijssen, Tjeerd Dijkstra, Tom Heskes, Lodewyk F. A. Wessels

Bioinform., 2018

Modelling signalling networks from perturbation data.

Mathurin Dorel, Bertram Klinger, Torsten Gross, Anja Sieber, Anirudh Prahallad, Evert Bosdriesz, Lodewyk F. A. Wessels, Nils Blüthgen

Bioinform., 2018

Comparative Network Reconstruction using mixed integer programming.

Evert Bosdriesz, Anirudh Prahallad, Bertram Klinger, Anja Sieber, Astrid Bosma, René Bernards, Nils Blüthgen, Lodewyk F. A. Wessels

Bioinform., 2018

iTOP: inferring the topology of omics data.

Nanne Aben, Johan A. Westerhuis, Yipeng Song, Henk A. L. Kiers, Magali Michaut, Age K. Smilde, Lodewyk F. A. Wessels

Bioinform., 2018

2016

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

Bram Thijssen, T. M. H. Dijkstra, Tom Heskes, Lodewyk F. A. Wessels

BMC Syst. Biol., 2016

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.

Nanne Aben, Daniel J. Vis, Magali Michaut, Lodewyk F. A. Wessels

Bioinform., 2016

2015

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus T. Dittrich, Tobias Müller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk F. A. Wessels, Gunnar W. Klau

Bioinform., 2015

2013

Mutational Genomics for Cancer Pathway Discovery.

Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Johann de Jong, Alistair G. Rust, Anton Berns, Maarten van Lohuizen, David J. Adams, Lodewyk F. A. Wessels, Marcel J. T. Reinders

Proceedings of the Pattern Recognition in Bioinformatics, 2013

proSQLite: Prolog File Based Databases via an SQLite Interface.

Sander Canisius, Nicos Angelopoulos, Lodewyk F. A. Wessels

Proceedings of the Practical Aspects of Declarative Languages, 2013

Integrative Functional Statistics in Logic Programming.

Nicos Angelopoulos, Vítor Santos Costa, João Azevedo, Jan Wielemaker, Rui Camacho, Lodewyk F. A. Wessels

Proceedings of the Practical Aspects of Declarative Languages, 2013

2012

A regression model for estimating DNA copy number applied to capture sequencing data.

Guillem Rigaill, Sidney Cadot, Roelof J. C. Kluin, Zheng Xue, René Bernards, Ian J. Majewski, Lodewyk F. A. Wessels

Bioinform., 2012

2011

A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer

Christine Staiger, Sidney Cadot, R. Kooter, Marcus T. Dittrich, Tobias Müller, Gunnar W. Klau, Lodewyk F. A. Wessels

CoRR, 2011

On the organization of bioinformatics core services in biology-based research institutes.

Olli-P. Kallioniemi, Lodewyk F. A. Wessels, Alfonso Valencia

Bioinform., 2011

2010

Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach.

Christiaan Klijn, Jan Bot, David J. Adams, Marcel J. T. Reinders, Lodewyk F. A. Wessels, Jos Jonkers

PLoS Comput. Biol., 2010

Inferring combinatorial association logic networks in multimodal genome-wide screens.

Jeroen de Ridder, Alice Gerrits, Jan Bot, Gerald de Haan, Marcel J. T. Reinders, Lodewyk F. A. Wessels

Bioinform., 2010

2009

Knowledge driven decomposition of tumor expression profiles.

Martin H. van Vliet, Lodewyk F. A. Wessels, Marcel J. T. Reinders

BMC Bioinform., 2009

Analysis of mass spectrometry data using sub-spectra.

Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Lodewyk F. A. Wessels, Marcel J. T. Reinders

BMC Bioinform., 2009

Fewer permutations, more accurate <i>P</i>-values.

Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich

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

Biclustering Sparse Binary Genomic Data.

Miranda van Uitert, Wouter Meuleman, Lodewyk F. A. Wessels

J. Comput. Biol., 2008

Creating gene set activity profiles with time-series expression data.

Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders

Int. J. Bioinform. Res. Appl., 2008

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data.

Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Jos H. Beijnen, Marcel J. T. Reinders, Lodewyk F. A. Wessels

BMC Bioinform., 2008

Combinatorial influence of environmental parameters on transcription factor activity.

Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 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

SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets.

Carmen Lai, Hugo M. Horlings, Marc J. van de Vijver, Eric H. van Beers, Petra M. Nederlof, Lodewyk F. A. Wessels, Marcel J. T. Reinders

BMC Bioinform., 2007

Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes.

Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Lodewyk F. A. Wessels, Marcel J. T. Reinders

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

Random subspace method for multivariate feature selection.

Carmen Lai, Marcel J. T. Reinders, Lodewyk F. A. Wessels

Pattern Recognit. Lett., 2006

Artifacts of Markov blanket filtering based on discretized features in small sample size applications.

Theo A. Knijnenburg, Marcel J. T. Reinders, Lodewyk F. A. Wessels

Pattern Recognit. Lett., 2006

Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens.

Jeroen de Ridder, Anthony Uren, Jaap Kool, Marcel J. T. Reinders, Lodewyk F. A. Wessels

PLoS Comput. Biol., 2006

A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets.

Carmen Lai, Marcel J. T. Reinders, Laura J. van't Veer, Lodewyk F. A. Wessels

BMC Bioinform., 2006

Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast.

Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders

Proceedings of the Computational Methods in Systems Biology, International Conference, 2006

2005

A protocol for building and evaluating predictors of disease state based on microarray data.

Lodewyk F. A. Wessels, Marcel J. T. Reinders, Augustinus A. M. Hart, Cor J. Veenman, Hongyue Dai, Yudong D. He, Laura J. van't Veer

Bioinform., 2005

Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae.

Theo A. Knijnenburg, Marcel J. T. Reinders, Jean-Marc Daran, Pascale A. S. Daran-Lapujade, Lodewyk F. A. Wessels

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

Predicting gene function by combining expression and interaction data.

Rogier J. P. van Berlo, Lodewyk F. A. Wessels, S. D. C. Martes, Marcel J. T. Reinders

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

Identifying Orthologs: Cycle Splitting on the Breakpoint Graph.

Rogier J. P. van Berlo, Lodewyk F. A. Wessels, S. D. C. Martes, Marcel J. T. Reinders

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

2003

Multi-criterion optimization for genetic network modeling.

Eugene P. van Someren, Lodewyk F. A. Wessels, Eric Backer, Marcel J. T. Reinders

Signal Process., 2003

2001

Determination of Binding Amino Acids Based on Random Peptide Array Screening Data.

Peter J. van der Veen, Lodewyk F. A. Wessels, J. W. Slootstra, R. H. Meloen, Marcel J. T. Reinders, Johannes Hellendoorn

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

A Comparison of Genetic Network Models.

Lodewyk F. A. Wessels, Eugene P. van Someren, Marcel J. T. Reinders

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

2000

Linear Modeling of Genetic Networks from Experimental Data.

Eugene P. van Someren, Lodewyk F. A. Wessels, Marcel J. T. Reinders

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999

Information processing for intelligent molecular diagnosis.

Lodewyk F. A. Wessels, Eugene P. van Someren, Marcel J. T. Reinders

Pattern Recognit. Lett., 1999

1992

Avoiding false local minima by proper initialization of connections.

Lodewyk F. A. Wessels, Etienne Barnard

IEEE Trans. Neural Networks, 1992