Avoiding false local minima by proper initialization of connections. - Lodewyk F. A. Wessels; Etienne Barnard (IEEE Trans. Neural Networks, 1992)

Information processing for intelligent molecular diagnosis. - Lodewyk F. A. Wessels; Eugene P. van Someren; Marcel J. T. Reinders (Pattern Recognit. Lett., 1999)

Linear Modeling of Genetic Networks from Experimental Data. - Eugene P. van Someren; Lodewyk F. A. Wessels; Marcel J. T. Reinders (ISMB, 2000)

A Comparison of Genetic Network Models. - Lodewyk F. A. Wessels; Eugene P. van Someren; Marcel J. T. Reinders (Pacific Symposium on Biocomputing, 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 (WABI, 2001)

Multi-criterion optimization for genetic network modeling. - Eugene P. van Someren; Lodewyk F. A. Wessels; Eric Backer; Marcel J. T. Reinders (Signal Process., 2003)

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 (CSB Workshops, 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 (CSB Workshops, 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 (CSB Workshops, 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)

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 (CMSB, 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)

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)

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)

Random subspace method for multivariate feature selection. - Carmen Lai; Marcel J. T. Reinders; Lodewyk F. A. Wessels (Pattern Recognit. Lett., 2006)

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 (ISMB/ECCB (Supplement of Bioinformatics), 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)

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)

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)

Combinatorial influence of environmental parameters on transcription factor activity. - Theo A. Knijnenburg; Lodewyk F. A. Wessels; Marcel J. T. Reinders (ISMB, 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)

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)

Biclustering Sparse Binary Genomic Data. - Miranda van Uitert; Wouter Meuleman; Lodewyk F. A. Wessels (J. Comput. Biol., 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)

Fewer permutations, more accurate P-values. - Theo A. Knijnenburg; Lodewyk F. A. Wessels; Marcel J. T. Reinders; Ilya Shmulevich (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)

Knowledge driven decomposition of tumor expression profiles. - Martin H. van Vliet; Lodewyk F. A. Wessels; Marcel J. T. Reinders (BMC Bioinform., 2009)

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)

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)

On the organization of bioinformatics core services in biology-based research institutes. - Olli-P. Kallioniemi; Lodewyk F. A. Wessels; Alfonso Valencia (Bioinform., 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 001; Gunnar W. Klau; Lodewyk F. A. Wessels (CoRR, 2011)

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)

Integrative Functional Statistics in Logic Programming. - Nicos Angelopoulos; Vítor Santos Costa; João Azevedo; Jan Wielemaker; Rui Camacho; Lodewyk F. A. Wessels (PADL, 2013)

proSQLite: Prolog File Based Databases via an SQLite Interface. - Sander Canisius; Nicos Angelopoulos; Lodewyk F. A. Wessels (PADL, 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 (PRIB, 2013)

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 001; Guillaume Blin; Jaap Heringa; Macha Nikolski; Lodewyk F. A. Wessels; Gunnar W. Klau (Bioinform., 2015)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 (RECOMB, 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., 2023)

Foundation Models in Medical Imaging - A Review and Outlook. - Vivien van Veldhuizen; Vanessa Botha; Chunyao Lu; Melis Erdal Cesur; Kevin Groot Lipman; Edwin D. de Jong; Hugo M. Horlings; Clarisa I. Sánchez; Cees G. M. Snoek; Lodewyk F. A. Wessels; Ritse Mann; Eric Marcus; et al. (CoRR, 2025)