Lodewyk F. A. Wessels - researchr alias

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Viewing Publication 1 - 43 from 43

2023

Percolate: An Exponential Family JIVE Model to Design DNA-Based Predictors of Drug ResponseSoufiane Mourragui, Marco Loog, Mirrelijn M. van Nee, Mark A. van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels. recomb 2023: 120-138 [doi]

ecpc: an R-package for generic co-data models for high-dimensional predictionMirrelijn M. van Nee, Lodewyk F. A. Wessels, Mark A. van de Wiel. bmcbi, 24(1):172, December 2023. [doi]

2019

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumorsSoufiane Mourragui, Marco Loog, Mark A van de Wiel, Marcel J. T. Reinders, Lodewyk F. A. Wessels. bioinformatics, 35(14), 2019. [doi]

Principal component analysis of binary genomics dataYipeng Song, Johan A. Westerhuis, Nanne Aben, Magali Michaut, Lodewyk F. A. Wessels, Age K. Smilde. bib, 20(1):317-329, 2019. [doi]

2018

iTOP: inferring the topology of omics dataNanne Aben, Johan A. Westerhuis, Yipeng Song, Henk A. L. Kiers, Magali Michaut, Age K. Smilde, Lodewyk F. A. Wessels. bioinformatics, 34(17), 2018. [doi]

Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysisTycho Bismeijer, Sander Canisius, Lodewyk F. A. Wessels. ploscb, 14(10), 2018. [doi]

Comparative Network Reconstruction using mixed integer programmingEvert Bosdriesz, Anirudh Prahallad, Bertram Klinger, Anja Sieber, Astrid Bosma, René Bernards, Nils Blüthgen, Lodewyk F. A. Wessels. bioinformatics, 34(17), 2018. [doi]

Modelling signalling networks from perturbation dataMathurin Dorel, Bertram Klinger, Torsten Gross, Anja Sieber, Anirudh Prahallad, Evert Bosdriesz, Lodewyk F. A. Wessels, Nils Blüthgen. bioinformatics, 34(23):4079-4086, 2018. [doi]

Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimatesBram Thijssen, Tjeerd Dijkstra, Tom Heskes, Lodewyk F. A. Wessels. bioinformatics, 34(5):803-811, 2018. [doi]

2016

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data typesNanne Aben, Daniel J. Vis, Magali Michaut, Lodewyk F. A. Wessels. bioinformatics, 32(17):413-420, 2016. [doi]

BCM: toolkit for Bayesian analysis of Computational Models using samplersBram Thijssen, T. M. H. Dijkstra, Tom Heskes, Lodewyk F. A. Wessels. bmcsb, 10:100, 2016. [doi]

2015

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation modelMohammed 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. bioinformatics, 31(19):3147-3155, 2015. [doi]

2013

Mutational Genomics for Cancer Pathway DiscoveryJeroen 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: 35-46 [doi]

2012

A regression model for estimating DNA copy number applied to capture sequencing dataGuillem Rigaill, Sidney Cadot, Roelof J. C. Kluin, Zheng Xue, Rene Bernards, Ian J. Majewski, Lodewyk F. A. Wessels. bioinformatics, 28(18):2357-2365, 2012. [doi]

2010

Inferring combinatorial association logic networks in multimodal genome-wide screensJeroen de Ridder, Alice Gerrits, Jan Bot, Gerald de Haan, Marcel J. T. Reinders, Lodewyk F. A. Wessels. bioinformatics, 26(12):149-157, 2010. [doi]

Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring ApproachChristiaan Klijn, Jan Bot, David J. Adams, Marcel J. T. Reinders, Lodewyk F. A. Wessels, Jos Jonkers. ploscb, 6(1), 2010. [doi]

2009

2008

Creating gene set activity profiles with time-series expression dataTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders. ijbra, 4(3):306-323, 2008. [doi]

Combinatorial influence of environmental parameters on transcription factor activityTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders. ismb 2008: 172-181 [doi]

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. PR, 41(3):1214, 2008. [doi]

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry dataWouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Jos H. Beijnen, Marcel J. T. Reinders, Lodewyk F. A. Wessels. bmcbi, 9, 2008. [doi]

Biclustering Sparse Binary Genomic DataMiranda van Uitert, Wouter Meuleman, Lodewyk F. A. Wessels. jcb, 15(10):1329-1345, 2008. [doi]

2007

2006

Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis ScreensJeroen de Ridder, Anthony Uren, Jaap Kool, Marcel J. T. Reinders, Lodewyk F. A. Wessels. ploscb, 2(12), 2006. [doi]

Artifacts of Markov blanket filtering based on discretized features in small sample size applicationsTheo A. Knijnenburg, Marcel J. T. Reinders, Lodewyk F. A. Wessels. prl, 27(7):709-714, 2006. [doi]

Condition Transition Analysis Reveals TF Activity Related to Nutrient-Limitation-Specific Effects of Oxygen Presence in YeastTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders. cmsb 2006: 271-284 [doi]

Random subspace method for multivariate feature selectionCarmen Lai, Marcel J. T. Reinders, Lodewyk F. A. Wessels. prl, 27(10):1067-1076, 2006. [doi]

A comparison of univariate and multivariate gene selection techniques for classification of cancer datasetsCarmen Lai, Marcel J. T. Reinders, Laura J. van t Veer, Lodewyk F. A. Wessels. bmcbi, 7:235, 2006. [doi]

2005

Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiaeTheo A. Knijnenburg, Marcel J. T. Reinders, J. M. Daran, P. Daran-Lapujade, Lodewyk F. A. Wessels. csb 2005: 71-72 [doi]

Identifying Orthologs: Cycle Splitting on the Breakpoint GraphRogier J. P. van Berlo, Lodewyk F. A. Wessels, S. D. C. Martes, Marcel J. T. Reinders. csb 2005: 65-68 [doi]

Predicting gene function by combining expression and interaction dataRogier J. P. van Berlo, Lodewyk F. A. Wessels, S. D. C. Martes, Marcel J. T. Reinders. csb 2005: 166-167 [doi]

A protocol for building and evaluating predictors of disease state based on microarray dataLodewyk F. A. Wessels, Marcel J. T. Reinders, Augustinus A. M. Hart, Cor J. Veenman, Hongyue Dai, Yudong D. He, Laura J. van t Veer. bioinformatics, 21(19):3755-3762, 2005. [doi]

2003

Multi-criterion optimization for genetic network modelingEugene P. van Someren, Lodewyk F. A. Wessels, Eric Backer, Marcel J. T. Reinders. sigpro, 83(4):763-775, 2003. [doi]

2001

Determination of Binding Amino Acids Based on Random Peptide Array Screening DataPeter J. van der Veen, Lodewyk F. A. Wessels, J. W. Slootstra, R. H. Meloen, Marcel J. T. Reinders, J. Hellendoorn. wabi 2001: 264-277 [doi]

A Comparison of Genetic Network ModelsLodewyk F. A. Wessels, Eugene P. van Someren, Marcel J. T. Reinders. psb 2001: 508-519 [doi]

2000

Linear Modeling of Genetic Networks from Experimental DataEugene P. van Someren, Lodewyk F. A. Wessels, Marcel J. T. Reinders. ismb 2000: 355-366

1999

Information processing for intelligent molecular diagnosisLodewyk F. A. Wessels, Eugene P. van Someren, Marcel J. T. Reinders. prl, 20(11-13):1457-1465, 1999. [doi]

1992

Avoiding false local minima by proper initialization of connectionsLodewyk F. A. Wessels, Etienne Barnard. tnn, 3(6):899-905, 1992. [doi]

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Publications by 'Lodewyk F. A. Wessels'

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2023

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2010

2009

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1992

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