Research Topics
Genomes and Genes | Mark A van de WielSummaryAffiliation: VU University Medical Center Country: The Netherlands Publications
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Publications
Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priorsMark A van de Wiel
Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
Biostatistics 14:113-28. 2013..Finally, compared with other methods, the results on small sample subsets are more reproducible when validated on their large sample complements, illustrating the importance of the type of shrinkage...- Smoothing waves in array CGH tumor profilesMark A van de Wiel
Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands
Bioinformatics 25:1099-104. 2009..Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult... 
CGHcall: calling aberrations for array CGH tumor profilesMark A van de Wiel
Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands
Bioinformatics 23:892-4. 2007..AVAILABILITY: An R-package (GUI), a manual and an example data set are available at http://www.few.vu.nl/~mavdwiel/CGHcall.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...- Estimating the false discovery rate using nonparametric deconvolutionMark A van de Wiel
Department of Mathematics, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands
Biometrics 63:806-15. 2007..We improve the naive estimator by using deconvolution. That is, the density of the parameter of interest is recovered from the data. We study performance of the methods using simulations and real data... - Testing the prediction error difference between 2 predictorsMark A van de Wiel
Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
Biostatistics 10:550-60. 2009..The framework easily accommodates any prediction paradigm and allows comparing any 2, possibly nonmodel-based, prediction procedures... - Preprocessing and downstream analysis of microarray DNA copy number profilesMark A van de Wiel
Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
Brief Bioinform 12:10-21. 2011..Finally, we look ahead: what should we prepare for and which methodology-related topics may deserve attention in the near future?.. 
CGHregions: dimension reduction for array CGH data with minimal information lossMark A van de Wiel
Department of Pathology and Department of Biostatistics KEB, VU University Medical Center, Amsterdam, The Netherlands
Cancer Inform 3:55-63. 2007..The algorithm, named CGHregions, is available as an easy-to-use script in R...- High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancerSuet F Chin
Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
Genome Biol 8:R215. 2007..To date, most genome-wide array comparative genomic hybridization studies have used tumor panels of relatively large tumor size and high Nottingham Prognostic Index (NPI) that are not as representative of breast cancer demographics... - NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell linesTineke E Buffart
Dept Pathology, VU University Medical Center, Amsterdam, The Netherlands
BMC Med Genomics 2:39. 2009..Our results show that the GINI strategy leads to a high number of false positives... - Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibilityKoen Bossers
Neuroregeneration Laboratory, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands
BMC Genomics 11:112. 2010..Furthermore, we compared performance of both ratio- and intensity-based analyses in terms of reproducibility and sensitivity for differential gene expression... - Validation of oligoarrays for quantitative exploration of the transcriptomeVigdis Nygaard
Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, Oslo, Norway
BMC Genomics 9:258. 2008..105. Our aim was to investigate whether the less resource demanding and more widespread oligoarray technique could provide data that were correlated to and had the same absolute scale as those obtained with MPSS and SAGE... - Effects of dependence in high-dimensional multiple testing problemsKyung In Kim
Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands
BMC Bioinformatics 9:114. 2008..Our aim is to systematically study effects of several network features like sparsity and correlation strength by imposing dependence structures among variables using random correlation matrices... - TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progressionAnke H Sillars-Hardebol
VU University Medical Center, Department of Pathology, De Boelelaan 1117, Amsterdam, The Netherlands
Gut 61:1568-75. 2012..The aim of this study was to identify genes located on the 20q amplicon that promote progression of colorectal adenoma to carcinoma... - CSE1L, DIDO1 and RBM39 in colorectal adenoma to carcinoma progressionAnke H Sillars-Hardebol
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
Cell Oncol (Dordr) 35:293-300. 2012..This study aimed to investigate whether CSE1L, DIDO1 and RBM39 may drive 20q amplification... - Identification of genes putatively involved in the pathogenesis of diffuse large B-cell lymphomas by integrative genomicsJoost J Oudejans
Department of Pathology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
Genes Chromosomes Cancer 48:250-60. 2009..In summary, using integrative genomics novel onco and tumor suppressor genes were identified in DLBCL that were not recognized by expression profiling alone... - Chromosome 5q loss in colorectal flat adenomasQuirinus J M Voorham
Departments of Pathology, Epidemiology and Biostatistics, Gynaecology, and Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands
Clin Cancer Res 18:4560-9. 2012..Here, we aimed to compare one of the molecular changes most explicitly associated with adenoma to carcinoma progression, that is, chromosomal instability, between flat and polypoid colorectal adenomas... - Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomasSaskia M Wilting
Departments of Pathology and Mathematics, VU University Medical Center, Amsterdam, The Netherlands, and Department of Obstetrics and Gynaecology, Erasmus University Medical Center, Rotterdam, The Netherlands
Cancer Res 69:647-55. 2009..These findings suggest that biomarkers associated with gains at chromosomes 1, 3q, and 20 are potential hallmarks of advanced p16(INK4a)-positive CIN2/3 lesions with a high short-term risk of progression... - Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infectionMariska Bierkens
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
Int J Cancer 131:E579-85. 2012..Hence, CIN3 with a longer duration of existence are likely more prone to have an increased short-term risk of cervical cancer... - HPV type-related chromosomal profiles in high-grade cervical intraepithelial neoplasiaMariska Bierkens
Department of Pathology, Unit of Molecular Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
BMC Cancer 12:36. 2012..The current study aimed to investigate whether CIN2/3 with different hrHPV types vary with respect to their chromosomal profiles, both in terms of the number of aberrations and chromosomal loci affected... - BCL2L1 has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gainAnke H Sillars-Hardebol
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
J Pathol 226:442-50. 2012..Therefore, even though BCL2L1 affects CRC biology in a 20q gain-dependent manner, it is not likely to be a driver of chromosome 20q gain associated adenoma-to-carcinoma progression... - Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomasHedy Vékony
Department of Oral and Maxillofacial Surgery Oral Pathology, Academic Centre for Dentistry ACTA, VU University Medical Center, Amsterdam, The Netherlands
Genes Chromosomes Cancer 48:202-12. 2009..Both unsupervised and supervised analysis of the genomic profiles revealed chromosome arm 8q to be involved in the malignant phenotype of salivary gland myoepitheliomas... - Weighted clustering of called array CGH dataWessel N van Wieringen
Department of Mathematics, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands
Biostatistics 9:484-500. 2008..We illustrate WECCA using an application to a breast cancer data set, where WECCA finds a clustering that relates better with survival than the original one... - CGHpower: exploring sample size calculations for chromosomal copy number experimentsIlari Scheinin
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
BMC Bioinformatics 11:331. 2010..Several approaches for sample size determination have been developed for expression array studies, but so far none has been proposed for array comparative genomic hybridization (aCGH)... - Identification of key genes for carcinogenic pathways associated with colorectal adenoma-to-carcinoma progressionAnke H Sillars-Hardebol
Department of Pathology Tumor Profiling Unit, VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands
Tumour Biol 31:89-96. 2010.... - Comprehensive mutation analysis in colorectal flat adenomasQuirinus J M Voorham
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
PLoS ONE 7:e41963. 2012..In the present study, we aimed to compare the mutation spectrum of 14 cancer genes, between these two phenotypes... - Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neckSaskia M Wilting
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
BMC Med Genomics 2:32. 2009..The existence of hrHPV-specific alterations in SCCs of different anatomical origin, suggests that these alterations are crucial for hrHPV-mediated carcinogenesis... - Nonparametric testing for DNA copy number induced differential mRNA gene expressionWessel N van Wieringen
Department of Mathematics, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands
Biometrics 65:19-29. 2009..The method is illustrated on breast cancer data, in which it confirms previously reported findings, now with a more profound statistical underpinning... - Exploratory factor analysis of pathway copy number data with an application towards the integration with gene expression dataWessel N van Wieringen
Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
J Comput Biol 18:729-41. 2011.... - MLPAnalyzer: data analysis tool for reliable automated normalization of MLPA fragment dataJordy Coffa
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
Cell Oncol 30:323-35. 2008..We therefore set out to develop an MLPA data analysis strategy and tool that is simple to use, while still taking into account the above-mentioned sources of variation... - Stepwise classification of cancer samples using clinical and molecular dataAskar Obulkasim
Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
BMC Bioinformatics 12:422. 2011..Second, the need to measure both data types for all patients may be both unpractical and (cost) inefficient... - DNA copy number alterations in endobronchial squamous metaplastic lesions predict lung cancerRobert A A van Boerdonk
VU University Medical Center, Department of Pathology, De Boelelaan 1117, Amsterdam, The Netherlands
Am J Respir Crit Care Med 184:948-56. 2011..Autofluorescence bronchoscopy (AFB) is a valid strategy for detecting premalignant endobronchial lesions. However, no biomarker can reliably predict lung cancer risk of subjects with AFB-visualized premalignant lesions... - Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analysesWessel N van Wieringen
Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
BMC Bioinformatics 13:80. 2012..Often such analyses require knowledge of which elements of one platform link to those of another. Although important, many integrative analyses do not or insufficiently detail the matching of the platforms... - Genetic classification of oral and oropharyngeal carcinomas identifies subgroups with a different prognosisSerge J Smeets
Section Tumor Biology, Department of Otolaryngology Head Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands
Cell Oncol 31:291-300. 2009..In conclusion, the discovery of these new classes of oral and oropharyngeal cancer with unique genetic and clinical characteristics has important consequences for future basic and clinical studies... - Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-downJose L Costa
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
BMC Genomics 10:499. 2009..In contrast, the molecular mechanism of 1,25D for the regulation of calcium homeostasis has principally been resolved, demonstrating a pivotal role for the vitamin D receptor (VDR)... - Gene expression profiling to identify markers associated with deregulated hTERT in HPV-transformed keratinocytes and cervical cancerJillian de Wilde
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
Int J Cancer 122:877-88. 2008..In summary, we identified 32 candidate biomarkers for deregulated hTERT mRNA expression, which may enable the identification of cervical premalignant lesions that are at highest risk to progress to invasive cancer... - Microarray data analysis: from hypotheses to conclusions using gene expression dataNicola J Armstrong
Department of Mathematics, Vrije Universiteit, Amsterdam, The Netherlands
Cell Oncol 26:279-90. 2004..We finish with some remarks on literature and software. The emphasis in this paper is on the philosophy behind several statistical issues and on a critical interpretation of microarray related analysis methods... - Pla2g2a attenuates colon tumorigenesis in azoxymethane-treated C57BL/6 mice; expression studies reveal Pla2g2a target genes and pathwaysRemond J A Fijneman
Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
Cell Oncol 31:345-56. 2009..However, it is unclear how Pla2g2a exerts its tumor-suppressive effects and whether its mode of action depends on Apc-germline mutations... - Normalized, segmented or called aCGH data?Wessel N van Wieringen
Department of Mathematics, Vrije Universiteit De Boelelaan 1081A, Amsterdam, The Netherlands
Cancer Inform 3:321-7. 2007..We discuss several issues that should be taken into account when deciding on which data are to be used. We express the believe that called data are best used, but would welcome opposing views... - PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression dataGwenaël G R Leday
Department of Mathematics, VU University, De Boelelaan 1081a, 1081HV Amsterdam and Department of Epidemiology and Biostatistics, VU University Medical Center, 1007MB Amsterdam, The Netherlands
Bioinformatics 29:1081-2. 2013..Availability and implementation: PLRS is implemented as an R package and available from Bioconductor (as of version 2.12; http://bioconductor.org). Additional code for parallel computations is available as Supplementary Material... - Analysis of multiple candidate genes in association with phenotypes of multiple sclerosisMadeleine H Sombekke
Department of Neurology, VU University Medical Center, Amsterdam, The Netherlands
Mult Scler 16:652-9. 2010..These results support our hypothesis that disease severity is determined by clinical variables and genetic influences (through several genes with small effects) in concert...