Lodewyk F. A. Wessels

50 papers A 2B 1C 3Misc 1Journal 36Unranked 6

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Reconstructing and comparing signal transduction networks from single-cell protein quantification data. Bioinform. Tim Stohn, Roderick A P. M. van Eijl, Klaas W. Mulder, Lodewyk F. A. Wessels, Evert Bosdriesz
2025	J	`jnl`	Foundation Models in Medical Imaging - A Review and Outlook. CoRR 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, Jonas Teuwen
2023	B	`conf`	Percolate: An Exponential Family JIVE Model to Design DNA-Based Predictors of Drug Response. RECOMB Soufiane Mourragui, Marco Loog, Mirrelijn M. van Nee, Mark A. van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2023	J	`jnl`	ecpc: an R-package for generic co-data models for high-dimensional prediction. BMC Bioinform. Mirrelijn M. van Nee, Lodewyk F. A. Wessels, Mark A. van de Wiel
2019	J	`jnl`	PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors. Bioinform. Soufiane Mourragui, Marco Loog, Mark A. van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2019	J	`jnl`	Principal component analysis of binary genomics data. Briefings Bioinform. Yipeng Song, Johan A. Westerhuis, Nanne Aben, Magali Michaut, Lodewyk F. A. Wessels, Age K. Smilde
2018	J	`jnl`	Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates. Bioinform. Bram Thijssen, Tjeerd Dijkstra, Tom Heskes, Lodewyk F. A. Wessels
2018	J	`jnl`	Comparative Network Reconstruction using mixed integer programming. Bioinform. Evert Bosdriesz, Anirudh Prahallad, Bertram Klinger, Anja Sieber, Astrid Bosma, René Bernards, Nils Blüthgen, Lodewyk F. A. Wessels
2018	J	`jnl`	Modelling signalling networks from perturbation data. Bioinform. Mathurin Dorel, Bertram Klinger, Torsten Gross, Anja Sieber, Anirudh Prahallad, Evert Bosdriesz, Lodewyk F. A. Wessels, Nils Blüthgen
2018	J	`jnl`	Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis. PLoS Comput. Biol. Tycho Bismeijer, Sander Canisius, Lodewyk F. A. Wessels
2018	J	`jnl`	iTOP: inferring the topology of omics data. Bioinform. Nanne Aben, Johan A. Westerhuis, Yipeng Song, Henk A. L. Kiers, Magali Michaut, Age K. Smilde, Lodewyk F. A. Wessels
2016	J	`jnl`	BCM: toolkit for Bayesian analysis of Computational Models using samplers. BMC Syst. Biol. Bram Thijssen, T. M. H. Dijkstra, Tom Heskes, Lodewyk F. A. Wessels
2016	J	`jnl`	TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types. Bioinform. Nanne Aben, Daniel J. Vis, Magali Michaut, Lodewyk F. A. Wessels
2015	J	`jnl`	xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinform. 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
2013	C	`conf`	Integrative Functional Statistics in Logic Programming. PADL Nicos Angelopoulos, Vítor Santos Costa, João Azevedo, Jan Wielemaker, Rui Camacho, Lodewyk F. A. Wessels
2013	—	`conf`	Mutational Genomics for Cancer Pathway Discovery. PRIB 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
2013	C	`conf`	proSQLite: Prolog File Based Databases via an SQLite Interface. PADL Sander Canisius, Nicos Angelopoulos, Lodewyk F. A. Wessels
2012	J	`jnl`	A regression model for estimating DNA copy number applied to capture sequencing data. Bioinform. Guillem Rigaill, Sidney Cadot, Roelof J. C. Kluin, Zheng Xue, René Bernards, Ian J. Majewski, Lodewyk F. A. Wessels
2011	J	`jnl`	A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer CoRR Christine Staiger, Sidney Cadot, R. Kooter, Marcus T. Dittrich, Tobias Müller, Gunnar W. Klau, Lodewyk F. A. Wessels
2011	J	`jnl`	On the organization of bioinformatics core services in biology-based research institutes. Bioinform. Olli-P. Kallioniemi, Lodewyk F. A. Wessels, Alfonso Valencia
2011	—	`ed.`	Pattern Recognition in Bioinformatics - 6th IAPR International Conference, PRIB 2011, Delft, The Netherlands, November 2-4, 2011. Proceedings PRIB Marco Loog, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Dick de Ridder
2010	J	`jnl`	Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach. PLoS Comput. Biol. Christiaan Klijn, Jan Bot, David J. Adams, Marcel J. T. Reinders, Lodewyk F. A. Wessels, Jos Jonkers
2010	J	`jnl`	Inferring combinatorial association logic networks in multimodal genome-wide screens. Bioinform. Jeroen de Ridder, Alice Gerrits, Jan Bot, Gerald de Haan, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2009	J	`jnl`	Analysis of mass spectrometry data using sub-spectra. BMC Bioinform. Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2009	J	`jnl`	Fewer permutations, more accurate Bioinform. Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich
2009	J	`jnl`	Knowledge driven decomposition of tumor expression profiles. BMC Bioinform. Martin H. van Vliet, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2008	J	`jnl`	Biclustering Sparse Binary Genomic Data. J. Comput. Biol. Miranda van Uitert, Wouter Meuleman, Lodewyk F. A. Wessels
2008	A	`conf`	Combinatorial influence of environmental parameters on transcription factor activity. ISMB Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2008	J	`jnl`	Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data. BMC Bioinform. Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Jos H. Beijnen, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2008	J	`jnl`	Creating gene set activity profiles with time-series expression data. Int. J. Bioinform. Res. Appl. Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2008	J	`jnl`	Erratum to "Classification in the presence of class noise using a probabilistic kernel fisher method": [Pattern Recognition 40 (12) 3349-3357]. Pattern Recognit. Yunlei Li, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders
2007	J	`jnl`	Classification in the presence of class noise using a probabilistic Kernel Fisher method. Pattern Recognit. Yunlei Li, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders
2007	—	`conf`	Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes. ISMB/ECCB (Supplement of Bioinformatics) Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2007	J	`jnl`	Protein Complex Prediction Using an Integrative Bioinformatics Approach. J. Bioinform. Comput. Biol. Rogier J. P. van Berlo, Lodewyk F. A. Wessels, Dick de Ridder, Marcel J. T. Reinders
2007	J	`jnl`	SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets. BMC Bioinform. 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
2006	J	`jnl`	A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets. BMC Bioinform. Carmen Lai, Marcel J. T. Reinders, Laura J. van't Veer, Lodewyk F. A. Wessels
2006	J	`jnl`	Artifacts of Markov blanket filtering based on discretized features in small sample size applications. Pattern Recognit. Lett. Theo A. Knijnenburg, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2006	—	`conf`	Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in Yeast. CMSB Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders
2006	J	`jnl`	Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens. PLoS Comput. Biol. Jeroen de Ridder, Anthony Uren, Jaap Kool, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2006	J	`jnl`	Random subspace method for multivariate feature selection. Pattern Recognit. Lett. Carmen Lai, Marcel J. T. Reinders, Lodewyk F. A. Wessels
2005	J	`jnl`	A protocol for building and evaluating predictors of disease state based on microarray data. Bioinform. 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
2005	—	`conf`	Identifying Orthologs: Cycle Splitting on the Breakpoint Graph. CSB Workshops Rogier J. P. van Berlo, Lodewyk F. A. Wessels, S. D. C. Martes, Marcel J. T. Reinders
2005	—	`conf`	Predicting gene function by combining expression and interaction data. CSB Workshops Rogier J. P. van Berlo, Lodewyk F. A. Wessels, S. D. C. Martes, Marcel J. T. Reinders
2005	—	`conf`	Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae. CSB Workshops Theo A. Knijnenburg, Marcel J. T. Reinders, Jean-Marc Daran, Pascale A. S. Daran-Lapujade, Lodewyk F. A. Wessels
2003	J	`jnl`	Multi-criterion optimization for genetic network modeling. Signal Process. Eugene P. van Someren, Lodewyk F. A. Wessels, Eric Backer, Marcel J. T. Reinders
2001	Misc	`conf`	A Comparison of Genetic Network Models. Pacific Symposium on Biocomputing Lodewyk F. A. Wessels, Eugene P. van Someren, Marcel J. T. Reinders
2001	C	`conf`	Determination of Binding Amino Acids Based on Random Peptide Array Screening Data. WABI Peter J. van der Veen, Lodewyk F. A. Wessels, J. W. Slootstra, R. H. Meloen, Marcel J. T. Reinders, Johannes Hellendoorn
2000	A	`conf`	Linear Modeling of Genetic Networks from Experimental Data. ISMB Eugene P. van Someren, Lodewyk F. A. Wessels, Marcel J. T. Reinders
1999	J	`jnl`	Information processing for intelligent molecular diagnosis. Pattern Recognit. Lett. Lodewyk F. A. Wessels, Eugene P. van Someren, Marcel J. T. Reinders
1992	J	`jnl`	Avoiding false local minima by proper initialization of connections. IEEE Trans. Neural Networks Lodewyk F. A. Wessels, Etienne Barnard