Mark A van de Wiel

Summary

Affiliation: VU University Medical Center
Country: The Netherlands

Publications

  1. ncbi request reprint ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs
    Mark A van de Wiel
    Department of Epidemiology and Biostatistics, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
    BMC Bioinformatics 15:116. 2014
  2. pmc The interferon type I signature towards prediction of non-response to rituximab in rheumatoid arthritis patients
    Hennie G Raterman
    Department of Rheumatology, VU University Medical Center, De Boelelaan 1117, Amsterdam, 1081HV, The Netherlands
    Arthritis Res Ther 14:R95. 2012
  3. pmc Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening
    Mark A van de Wiel
    Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
    BMC Med Genomics 6:S1. 2013
  4. doi request reprint Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors
    Mark 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
  5. pmc CGHregions: dimension reduction for array CGH data with minimal information loss
    Mark 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
  6. doi request reprint Preprocessing and downstream analysis of microarray DNA copy number profiles
    Mark A van de Wiel
    Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
    Brief Bioinform 12:10-21. 2011
  7. doi request reprint Smoothing waves in array CGH tumor profiles
    Mark 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
  8. ncbi request reprint Estimating the false discovery rate using nonparametric deconvolution
    Mark A van de Wiel
    Department of Mathematics, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands
    Biometrics 63:806-15. 2007
  9. ncbi request reprint CGHcall: calling aberrations for array CGH tumor profiles
    Mark A van de Wiel
    Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands
    Bioinformatics 23:892-4. 2007
  10. doi request reprint Testing the prediction error difference between 2 predictors
    Mark 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

Collaborators

Detail Information

Publications44

  1. ncbi request reprint ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs
    Mark A van de Wiel
    Department of Epidemiology and Biostatistics, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
    BMC Bioinformatics 15:116. 2014
    ..Moreover, when sample sizes are small, inference is likely to be too liberal when, in a Bayesian setting, applying a non-appropriate prior or to lack power when not carefully borrowing information across features...
  2. pmc The interferon type I signature towards prediction of non-response to rituximab in rheumatoid arthritis patients
    Hennie G Raterman
    Department of Rheumatology, VU University Medical Center, De Boelelaan 1117, Amsterdam, 1081HV, The Netherlands
    Arthritis Res Ther 14:R95. 2012
    ..However, approximately 40% to 50% of rituximab (RTX) treated RA patients have a poor response. We investigated whether baseline gene expression levels can discriminate between clinical non-responders and responders to RTX...
  3. pmc Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening
    Mark A van de Wiel
    Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
    BMC Med Genomics 6:S1. 2013
    ..These were not detected by limma. In the context of gene-targeted (conjugate) treatment, these are interesting candidates for further research...
  4. doi request reprint Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors
    Mark 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...
  5. pmc CGHregions: dimension reduction for array CGH data with minimal information loss
    Mark 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...
  6. doi request reprint Preprocessing and downstream analysis of microarray DNA copy number profiles
    Mark 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?..
  7. doi request reprint Smoothing waves in array CGH tumor profiles
    Mark 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...
  8. ncbi request reprint Estimating the false discovery rate using nonparametric deconvolution
    Mark 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...
  9. ncbi request reprint CGHcall: calling aberrations for array CGH tumor profiles
    Mark A van de Wiel
    Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands
    Bioinformatics 23:892-4. 2007
    ..By incorporating more than three classes, CGHcall improves detection of single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome arm information...
  10. doi request reprint Testing the prediction error difference between 2 predictors
    Mark 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...
  11. pmc High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
    Suet 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...
  12. pmc NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines
    Tineke 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...
  13. pmc Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility
    Koen 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...
  14. pmc Validation of oligoarrays for quantitative exploration of the transcriptome
    Vigdis 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...
  15. pmc Effects of dependence in high-dimensional multiple testing problems
    Kyung 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...
  16. ncbi request reprint TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progression
    Anke 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...
  17. doi request reprint CSE1L, DIDO1 and RBM39 in colorectal adenoma to carcinoma progression
    Anke 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...
  18. doi request reprint Identification of genes putatively involved in the pathogenesis of diffuse large B-cell lymphomas by integrative genomics
    Joost 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...
  19. ncbi request reprint Chromosome 5q loss in colorectal flat adenomas
    Quirinus 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...
  20. doi request reprint Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas
    Saskia 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...
  21. ncbi request reprint DNA copy number aberrations in endobronchial lesions: a validated predictor for cancer
    Robert A A van Boerdonk
    Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
    Thorax 69:451-7. 2014
    ..This classifier could assist in selecting subjects with endobronchial lesions who might benefit from more aggressive therapeutic intervention or surveillance. ..
  22. doi request reprint Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infection
    Mariska 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...
  23. pmc HPV type-related chromosomal profiles in high-grade cervical intraepithelial neoplasia
    Mariska 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...
  24. ncbi request reprint BCL2L1 has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain
    Anke 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...
  25. doi request reprint Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomas
    Hedy 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...
  26. pmc Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses
    Wessel 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...
  27. ncbi request reprint Weighted clustering of called array CGH data
    Wessel 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...
  28. pmc CGHpower: exploring sample size calculations for chromosomal copy number experiments
    Ilari 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)...
  29. pmc Identification of key genes for carcinogenic pathways associated with colorectal adenoma-to-carcinoma progression
    Anke 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
    ....
  30. pmc Comprehensive mutation analysis in colorectal flat adenomas
    Quirinus 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...
  31. pmc Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck
    Saskia 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...
  32. doi request reprint Nonparametric testing for DNA copy number induced differential mRNA gene expression
    Wessel 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...
  33. ncbi request reprint MLPAnalyzer: data analysis tool for reliable automated normalization of MLPA fragment data
    Jordy 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...
  34. doi request reprint Exploratory factor analysis of pathway copy number data with an application towards the integration with gene expression data
    Wessel N van Wieringen
    Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
    J Comput Biol 18:729-41. 2011
    ....
  35. pmc Stepwise classification of cancer samples using clinical and molecular data
    Askar 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...
  36. doi request reprint DNA copy number alterations in endobronchial squamous metaplastic lesions predict lung cancer
    Robert 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...
  37. doi request reprint Pla2g2a attenuates colon tumorigenesis in azoxymethane-treated C57BL/6 mice; expression studies reveal Pla2g2a target genes and pathways
    Remond 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...
  38. ncbi request reprint PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data
    Gwenaël G R Leday
    Department of Mathematics, VU University, De Boelelaan 1081a, Amsterdam, The Netherlands
    Bioinformatics 29:1081-2. 2013
    ..Moreover, it tests the strength of the association and provides confidence intervals. We illustrate PLRS using glioblastoma data from The Cancer Genome Atlas...
  39. ncbi request reprint Gene expression profiling to identify markers associated with deregulated hTERT in HPV-transformed keratinocytes and cervical cancer
    Jillian 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...
  40. ncbi request reprint Genetic classification of oral and oropharyngeal carcinomas identifies subgroups with a different prognosis
    Serge 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...
  41. ncbi request reprint Microarray data analysis: from hypotheses to conclusions using gene expression data
    Nicola 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...
  42. pmc Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-down
    Jose 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)...
  43. pmc 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...
  44. ncbi request reprint Analysis of multiple candidate genes in association with phenotypes of multiple sclerosis
    Madeleine 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...