Mark A. van de Wiel, publications

Please, contact me (mark.vdwiel[at]vumc.nl) when interested in any of my (submitted) publications, or check whether it is availlable via my profile on Research Gate.

PhD-Thesis

Van de Wiel MA (2000) Exact distributions of distribution-free test statistics, Eindhoven University of Technology, The Netherlands. ISBN 90-386-0791-1, PDF version . Review: MathSciNet Review

Book Chapters

Riebler A, Robinson MD,  van de Wiel MA (2014). Analysis of Next Generation Sequencing Data Using Integrated Nested Laplace Approximation (INLA). In Statistical Analysis of Next Generation Sequencing Data (pp. 75-91). Springer International Publishing.

Chakraborti S,  van de Wiel MA (2008) A nonparametric control chart based on the Mann-Whitney statistic. In: Beyond parametrics in interdisciplinary research: Festschrift in honor of professor Pranab K. Sen.  Edited by Balakrishnan N, Peña EA, Silvapulle MJ. Institute of Mathematical Statistics Collections, Vol. 1. 

van de Wiel MA, Holden M, Glad IK, Lyng H, Frigessi A (2006) Bayesian process-based modeling of two-channel microarray experiments: estimating absolute mRNA concentrations. In: Bayesian inference for gene expression and proteomics. Edited by Mueller P,  Do K-A, Vannucci M. Cambridge University Press.

Published and accepted papers (Statistics; see below for Software and Biomedical)

  1. van de Wiel MA, te Beest DE, Münch M (2018). Learning from a lot: Empirical Bayes in high-dimensional model-based prediction settings. To appear in Scand J Stat. arXiv preprint arXiv:1709.04192.
  2. van Wieringen WN, Peeters CFW, De Menezes RX, van de Wiel MA (2018). Testing for pathway (in)activation using Gaussian graphical models. To appear in JRSS-C.
  3. Te Beest DE, Mes SW, Wilting SM, Brakenhoff RH,  Van de Wiel MA (2017). Improved high-dimensional prediction with Random Forests by the use of co-data. BMC Bioinformatics, 18 (1), 584.
  4. Eekhout I, Van de Wiel MA,  Heymans, MW (2017). Methods for significance testing of categorical covariates in logistic regression models after multiple imputation: power and applicability analysis. BMC Medical Research Methodology: 17(1), 129.
  5. Kpogbezan GB, Van der Vaart AW, Van Wieringen WN, Leday GGR, Van de Wiel MA (2017). An empirical Bayes approach to network recovery using external knowledge. Biom J. 59: 932–947.
  6. Leday GGR, de Gunst M, Kpogbezan GB, Van der Vaart AW, Van Wieringen WN,  Van de Wiel MA (2017). Gene network reconstruction using global-local shrinkage priors. Ann Appl Statist. 11, 41-68.
  7. Rauschenberger A, Jonker MA, van de Wiel MA, Menezes RX (2016), Testing for association between RNA-Seq and high-dimensional data. BMC Bioinformatics, 17: 118. R package: globalSeq.
  8. Van de Wiel MA, Lien TG, Verlaat W, Van Wieringen WN, Wilting SM (2016).  Better prediction by use of co-data: Adaptive group-regularized ridge regression. Stat Med. 35, 368-381. Preliminary version (arXiv). R package: GRridge.
  9. Obulkasim A, Meijer GA, van de Wiel MA (2014). Semi-supervised adaptive-height snipping of the hierarchical clustering tree. BMC Bioinformatics 16: 15. R package: HCsnip
  10. Miok V, Wilting SM, van de Wiel MA, Jaspers A, van Noort PI, Brakenhoff RH, Snijders PJ, Steenbergen RD, van Wieringen WN (2014). tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities. BMC Bioinformatics. 15(1):327. R package: tigaR.
  11.  van Wieringen WN, van de Wiel MA (2014). Penalized differential pathway analysis of integrative oncogenomics studies. Stat Appl Genet Mol Biol. 13(2): 141-58.
  12.  Van Iterson M, Van de Wiel MA, Boer JM, de Menezes RX (2013). General power and sample size calculations for high-dimensional genomic data. Stat Appl Genet Mol Biol. ;12(4):449-67. R package: SSPA.
  13.  Leday GGR, Van der Vaart AW, Van Wieringen WN, Van de Wiel MA (2013). Modeling association between DNA copy number and gene expression with constrained piecewise linear regression splines. Ann Appl Statist, 7, 823–845. R package: PLRS.
  14. Van de Wiel MA,  De Menezes RX, Siebring E, Van Beusechem VW (2013). Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening. BMC Med Genom, 6 (Suppl 2), S1. R package: ShrinkBayes.
  15. Van de Wiel MA, Leday GGR, Pardo L, Rue H, Van der Vaart AW, Van Wieringen WN (2013). Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors Freely available as Top 10 Cited. Biostatistics 14, 113-128. R package: ShrinkBayes. 
  16. Hothorn T, Hornik K, van de Wiel MA,  Zeileis A (2012). A Lego system for conditional inference. The American Statistician.
  17. Obulkasim A, Meijer GA, van de Wiel MA. Stepwise classification of cancer samples using clinical and molecular data (2011). BMC Bioinformatics, 12, 422. R package: stepwiseCM.
  18. Gerds TA, van de Wiel MA. Confidence scores for prediction models (2011). Biom J, 53, 259-74.
  19. van Wieringen, WN,  van de Wiel MA (2011). Exploratory factor analysis of pathway copy number data with an application towards the integration with gene expression data, J Comput Biol,18, 729-41.  
  20. van de Wiel MA, Picard F, van Wieringen WN, Ylstra B (2011). Preprocessing and downstream analysis of microarray DNA copy number profiles. Briefings in Bioinformatics,12,10-21.
  21. Kim, KI, Roquain E, van de Wiel MA (2010). Spatial clustering of array CGH features in combination with hierarchical multiple testing. Stat Appl Genet Mol Biol, 9, Article 40.  R package: dnaCplusT.
  22. van Wieringen WN, Berkhof J, van de Wiel, MA (2010). A random coefficients model for regional co-expression associated with DNA copy number, Stat Appl Genet Mol Biol, 9, 25. R package: sigaR.
  23. Scheinin I, Ferreira JA, Knuutila S, Meijer GA, van de Wiel MA, Ylstra B (2010). CGHpower: exploring sample size calculations for chromosomal copy number experiments. BMC Bioinformatics, 11, 331.
  24. Bossers K, Ylstra  B, Brakenhoff RH, Smeets SJ, Verhaagen J, van de Wiel MA (2010). Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility. BMC Genomics,  11, 112.
  25. Roquain E, van de Wiel MA (2009). Optimal weighting for false discovery rate control. Electron J Statist, 3, 678-711.
  26. van de Wiel MA, Berkhof J, van Wieringen WN (2009). Testing the prediction error difference between two predictors. Biostatistics,10,  550–560. Received Honorary Mention,  Dutch Biometry Award 2010.
  27. van de Wiel MA, Brosens R, Eilers PHC, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B (2009). Smoothing waves in array CGH tumor profiles. Bioinformatics,  25, 1099-1104.  R package: NoWaves.
  28. van Wieringen, WN, Van de Wiel, MA (2009). Nonparametric testing for DNA copy number induced differential mRNA gene expression, Biometrics, 65, 19-29. Received Honorary Mention,  Dutch Biometry Award 2010. R package: sigaR.
  29. van Wieringen WN,  van de Wiel MA, van der Vaart AW (2008). A test for partial differential expression. J Amer Statist Assoc, 103, 1039-1049. R package: PDGEtest.
  30. van Wieringen WN,  van de Wiel MA,  Ylstra B (2008). Weighted clustering of called aCGH data. Biostatistics, 9: 484-500. R package: WECCA.
  31. Kim KI, van de Wiel MA (2008). Effects of dependence in high-dimensional multiple testing problems. BMC Bioinformatics, 9:114.
  32. Pham TV, van de Wiel MA, Jimenez CR (2008). Support vector machine approach to separate control and breast cancer serum samples. Statist Appl Genet Mol Biol, 7(2), Article 11. 
  33. van Wieringen WN,  van de Wiel MA, Ylstra B (2007), Normalized, segmented or called aCGH data.  Cancer Informatics, 3, 331–337.
  34. Bar-Hen A, Kim KI, van de Wiel MA (2007), Some comments on false discovery rate. Journal of Bioinformatics and Computational Biology, 8, 1-4.
  35. van de Wiel MA,  Kim KI (2007), Estimating the False Discovery Rate using nonparametric deconvolution,  Biometrics, 63, 806-815.
  36. van de Wiel MA, Kim KI, Vosse SJ, van Wieringen WN,  Wilting SM, Ylstra B (2007), CGHcall: an algorithm for calling aberrations for multiple array CGH tumor profiles.  Bioinformatics, 23, 892–894. R package: CGHcall.
  37. van de Wiel MA, van Wieringen WN (2007), CGHregions: dimension reduction for array CGH data with minimal information loss,  Cancer Informatics, 2, 55-63. R package: CGHregions.
  38. Hothorn T, Hornik K, van de Wiel MA, Zeileis A (2006), A Lego System for Conditional Inference, The American Statistician, 60, 257-263.
  39. Chakraborti S, van de Wiel MA, Hong B (2006), A note on sample size determination for a nonparametric test of location, Technometrics,  48, 88-94.
  40. van de Wiel MA, Costa JL, Smid K, Oudejans CB, Bergman AM, Meijer GA, Peters GJ, Ylstra B (2005),  Expression microarray analysis and oligo array CGH of acquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations, Cancer Research, 65, 10208-10213.
  41. Frigessi A, van de Wiel MA, Holden M, Svendsrud DH, Glad IK, Lyng H (2005), Genome-wide estimation of transcript concentrations from spotted cDNA microarray data, Nucleic Acids Research - Methods Online, 33, e143.
  42. van de Wiel MA, Smeets SJ, Brakenhoff RH, Ylstra B (2005), CGHMultiArray: Exact p-values for multi-array CGH-data, Bioinformatics, 21, 3193-3194.
  43. van de Wiel MA (2005), The null distribution of Kendall's rank correlation statistic in the presence of ties, Journal of Nonparametric Statistics, 17, 269-275.
  44. Di Bucchianico A, van de Wiel MA (2005), Exact null distributions of distribution-free quadratic t-sample statistics, Journal of Statistical Planning and Inference, 127, 1-21.
  45. Armstrong NJ, van de Wiel MA (2004),  Microarray data analysis: from hypotheses to conclusions using gene expression data, Cellular Oncology, 26, 279-290
  46. Chakraborti S, van der Laan P, van de Wiel MA (2004), A class of distribution-free control charts, J. Roy. Statist. Soc.  C - Applied Statistics, 53, 443-462.
  47. van de Wiel MA (2004), Significance analysis of microarrays using rank scores, Kwantitatieve Methoden (The Netherlands Electronic Journal of Quantitative Methods), 71, 25-37.
  48. van de Wiel MA (2004), Exact null distributions of quadratic distribution-free statistics for two-way classification, Journal of Statistical Planning and Inference, 109, 29-40.
  49. van de Wiel MA (2002), Exact distributions of multiple comparisons rank statistics, Journal of the American Statistical Association, 97, 1081-1089.
  50. van de Wiel MA (2001), Exact non-null distributions of rank statistics, Communications Statistics: Simulation and Computation, 16, 1011-1028.
  51. van de Wiel MA (2001), The split-up algorithm: a fast symbolic method for computing p-values of rank statistics, Computational Statistics, 16, 519-538.
  52. van de Wiel MA  and Di Bucchianico A (2001), Fast computation of the exact null distribution of Spearman's rho and Page's L statistic for samples with and without ties, Journal of Statistical Planning and Inference, 92,133-145.
  53. van de Wiel MA, Di Bucchianico A, van der Laan P (1999), Exact distributions of nonparametric test statistics and computer algebra, J. Roy. Statist. Soc. D The Statistician, 48, 507-516.

Published and accepted papers (Software)
  1. Novianti PW, Snoek B, Wilting SM, van de Wiel MA (2017). Better diagnostic signatures from RNAseq data through use of auxiliary co-data. Bioinformatics, 33, 1572-1574.  R package: GRridge 
  2. van den Broek E, van Lieshout S, Rausch C, Ylstra B, van de Wiel MA, Meijer GA, Fijneman RJA, Abeln S (2017). GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes [version 2; referees: 2 approved]. F1000Research, 5:2340. R package: GeneBreak
  3. Obulkasim A, van de Wiel MA (2015). HCsnip: An R Package for Semi-supervised Snipping of the Hierarchical Clustering Tree. Cancer Inform.14:1-19.
  4. Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B. (2014). DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 24(12):2022-32. R package: QDNAseq.
  5. van de Wiel MA, Neerincx M, Buffart TE, Sie D, Verheul HMW (2014).ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs. BMC Bioinformatics. 15(1):116
  6. Krijgsman O, Benner C, Meijer GA, van de Wiel MA, Ylstra B. FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations. Cancer Inform. 2014 13:153-6
  7. Obulkasim A, van de Wiel MA (2014) stepwiseCM: An R Package for Stepwise Classification of Cancer Samples Using Multiple Heterogeneous Data Sets. Cancer Inform. 13:1-11.
  8. Leday GGR, van de Wiel MA (2013). PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data. Bioinformatics 29,1081-1082.
  9. van Wieringen WN, Unger K, Leday GGR, Krijgsman O, De Menezes RX, Ylstra B., van de Wiel MA (2012). Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses, BMC Bioinformatics, 13:80. R package: sigaR.
  10. Zeileis A, van de Wiel MA, Hornik K,  Hothorn T.  (2008). Implementing a class of permutation pests: the coin package. J Statist. Software, 28, Issue 8.

 Published and accepted papers (Biomedical)
  1. Snoek BC, Verlaat W, Novianti PW, Van de Wiel MA, Wilting SM,  van Trommel NE, Bleeker MCG, . Massuger LFAG, Melchers WJG, Sie D,  Heideman DAM, Snijders PJF, Meijer CJLM, Steenbergen RDM (2018). Genome-wide microRNA analysis of HPV-positive self-samples yields novel 1 triage markers for early detection of cervical cancer. Accepted for Int J Cancer.
  2. Verlaat W, Snoek BC,  Heideman DAM, Wilting SM,  Snijders PJF,  Novianti PW,  van Splunter AP, Peeters CWF, van Trommel NE,  Massuger LFAG, Bekkers RLM, Melchers WJG,  van Kemenade FJ, Berkhof J, van de Wiel MA,  Meijer CJLM, Steenbergen RDM (2018),
    Identification and validation of a 3-gene methylation classifier for HPV-based cervical screening on self-samples. Clin Cancer Res, 9.
  3. Babion I, Snoek BC, van de Wiel MA, Wilting SM, and Steenbergen RD (2017). A Strategy to Find Suitable Reference Genes for miRNA Quantitative PCR Analysis and Its Application to Cervical Specimens. The Journal of Molecular Diagnostics, 19(5), 625-637.
  4. de Leeuw FA, Peeters CFW, Kester MI et al. (2017). Blood-based metabolic signatures in Alzheimer's disease. Alzheimers Dement., 8, 196–207.
  5. Obulkasim A, Ylstra B, van Essen HF, Benner C, Stenning S, Langley R, Allum W, Cunningham D, Inam I, Hewitt LC, West NP, Meijer GA, van de Wiel MA, Grabsch HI (2016). Reduced genomic tumor heterogeneity after neoadjuvant chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma. Oncotargett, 7, 44084
  6. Willemse EA, van Uffelen KW, Yener L, van de Wiel MA,  Teunissen, CE (2016). Quality indicators of pre-analytical variation in cerebrospinal fluid detected with aptamer screening. Alzheimer's & Dementia, 12(7), P481.
  7. Goos JA, Coupé VM, van de Wiel MA, Diosdado B, Delis-Van Diemen PM, Hiemstra AC, de Cuba EM, Beliën JA, Menke-van der Houven van Oordt CW, Geldof AA, Meijer GA, Hoekstra OS, Fijneman RJ; DeCoDe PET Group. A prognostic classifier for patients with colorectal cancer liver metastasis, based on AURKA, PTGS2 and MMP9. Oncotarget. 2016, 7:2123-34.
  8. Goos JA, Verbeek J, Geldof AA, Hiemstra AC, van de Wiel MA, Adamzek KA, Delis-Van Diemen PM, Stroud SG, Bradley DP, Meijer GA, Hoekstra OS, Fijneman RJ, Windhorst AD. Molecular imaging of aurora kinase A (AURKA) expression: Synthesis and preclinical evaluation of radiolabeled alisertib (MLN8237). Nucl Med Biol. 2016, 43: 63-72.
  9. Neerincx M, Sie DL, van de Wiel MA, van Grieken NC, Burggraaf JD, Dekker H, Eijk PP, Ylstra B, Verhoef C, Meijer GA, Buffart TE, Verheul HM. MiR expression profiles of paired primary colorectal cancer and metastases by next-generation sequencing. Oncogenesis. 2015, 4:e170.
  10. van den Broek E, Dijkstra MJ, Krijgsman O, Sie D, Haan JC, Traets JJ, van de Wiel MA, Nagtegaal ID, Punt CJ, Carvalho B, Ylstra B, Abeln S, Meijer GA, Fijneman RJ. High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer. PLoS One. 2015, 10:e0138141.
  11. Haan JC, Labots M, Rausch C, Koopman M, Tol J, Mekenkamp LJ, van de Wiel MA, Israeli D, van Essen HF, van Grieken NC, Voorham QJ, Bosch LJ, Qu X, Kabbarah O, Verheul HM, Nagtegaal ID, Punt CJ, Ylstra B, Meijer GA (2014).  Genomic landscape of metastatic colorectal cancer. Nat Commun. 5: 5457.
  12. van Thuijl HF, Scheinin I, Sie D, Alentorn A, van Essen HF, Cordes M, Fleischeuer R, Gijtenbeek AM, Beute G, van den Brink WA, Meijer GA, Havenith M, Idbaih A, Hoang-Xuan K, Mokhtari K, Verhaak R, van der Valk P, van de Wiel MA, Heimans JJ, Aronica E, Reijneveld JC, Wesseling P, Ylstra B. (2014). Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas. Genome Biol. 15(9):471.
  13. Nota B, Ndika JD, van de Kamp JM, Kanhai WA, van Dooren SJ, van de Wiel MA, Pals G, Salomons GS (2014) RNA sequencing of creatine transporter (SLC6A8) deficient fibroblasts reveals impairment of the extracellular matrix. Hum Mutat. 35(9):1128-35.
  14. van Boerdonk RA, Daniels JM, Snijders PJ, Grünberg K, Thunnissen E, van de Wiel MA, Ylstra B, Postmus PE, Meijer CJ, Meijer GA, Smit EF, Sutedja TG, Heideman DA (2014). DNA copy number aberrations in endobronchial lesions: a validated predictor for cancer. Thorax. 69:451-7
  15. Blits M, Jansen G, Assaraf YG, Van de Wiel MA, Lems WF, Nurmohamed MT, van Schaardenburg D, Voskuyl AE, Wolbink GJ, Vosslamber S, Verweij CL(2013). Methotrexate normalizes up-regulated folate pathway genes in rheumatoid arthritis. Arthritis Rheum. 65(11):2791-802
  16. Kamieniak MM, Muñoz-Repeto I, Rico D, Osorio A, Urioste M, García-Donas J, Hernando S, Robles-Díaz L, Ramón Y Cajal T, Cazorla A, Sáez R, García-Bueno JM, Domingo S, Borrego S, Palacios J, van de Wiel MA, Ylstra B, Benítez J, García MJ (2013). DNA copy number profiling reveals extensive genomic loss in hereditary BRCA1 and BRCA2 ovarian carcinomas. Br J Cancer. 108,1732-42.
  17. Pardo LM, Rizzu P, Francescatto M, Vitezic M, Leday GG, Sanchez JS, Khamis A, Takahashi H, van de Berg WD, Medvedeva YA, van de Wiel MA, Daub CO, Carninci P, Heutink P (2013). Regional differences in gene expression and promoter usage in aged human brains. Neurobiol Aging. 34(7):1825-36
  18. Voorham QJ, Carvalho B, Spiertz AJ, Claes B, Mongera S, van Grieken NC, Grabsch H, Kliment M, Rembacken B,  Van de Wiel MA, Quirke P, Mulder CJ, Lambrechts D, van Engeland M, Meijer GA. Comprehensive mutation analysis in colorectal flat adenomas. PLoS One. 2012;7(7):e41963
  19. Groenendijk MR, Thunnissen E, Ylstra B, van de Wiel MA, Eijk PP, Paul MA, Smit EF, Postmus PE (2012). An 82-year-old woman with small-cell lung cancer: relapse after 9 years or a new primary?J Thorac Oncol. 7:e3-5
  20. Voorham QJ, Carvalho B, Spiertz AJ, van Grieken NC, Mongera S, Rondagh EJ, van de Wiel MA, Jordanova ES, Ylstra B, Kliment M, Grabsch H, Rembacken B, Arai T, de Bruine AP, Sanduleanu S, Quirke P, Mulder CJ, van Engeland M, Meijer GA (2012). Chromosome 5q loss in colorectal flat adenomas. Clin Cancer Res.18:4560-9.
  21. Bierkens M, Wilting SM, Van Wieringen WN, Van Kemenade FJ, Bleeker MCG, Jordanova ES, Bekker-Lettink M, van de Wiel MA, Ylstra B, Meijer CJLM, Snijders PJF, Steenbergen RDM (2012), Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infection, International Journal of Cancer, 131: E579-85.
  22. Sillars-Hardebol AH, Carvalho B, Tijssen M, Beliën JA, de Wit M, Delis-van Diemen PM, Pontén F, van de Wiel MA, Fijneman RJ, Meijer GA (2012). TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progression. Gut.
  23. Wilting SM, Snijders PJ, Verlaat W, Jaspers A, van de Wiel MA, van Wieringen WN, Meijer GA, Kenter GG, Yi Y, le Sage C, Agami R, Meijer CJ, Steenbergen RD (2013). Altered microRNA expression associated with chromosomal changes contributes to cervical carcinogenesis. Oncogene, 32:106-16.
  24. Bierkens M, Wilting SM, van Wieringen WN, van de Wiel MA, Ylstra B, Meijer CJ, Snijders PJ, Steenbergen RD (2012) HPV type-related chromosomal profiles in high-grade cervical intraepithelial neoplasia. BMC Cancer. 12: 36
  25. Sillars-Hardebol AH, Carvalho B, Beliën JA, de Wit M, Delis-van Diemen PM, Tijssen M, van de Wiel MA, Pontén F, Fijneman RJ, Meijer GA. BCL2L1 has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain (2012). J Pathol. 226:442-50
  26. van Boerdonk RA, Sutedja TG, Snijders PJ, Reinen E, Wilting SM, van de Wiel MA, Thunnissen FE, Duin S, Kooi C, Ylstra B, Meijer CJ, Meijer GA, Grünberg K, Daniels JM, Postmus PE, Smit EF, Heideman DA. DNA copy number alterations in endobronchial squamous metaplastic lesions predict lung cancer (2011). Am J Respir Crit Care Med. 184:948-56.
  27. Bierkens M, Wilting SM, van Wieringen WN, van Kemenade FJ, Bleeker MC, Jordanova ES, Bekker-Lettink M, van de Wiel MA, Ylstra B, Meijer CJ, Snijders PJ, Steenbergen RD (2011). Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infection. Int J Cancer.  
  28. Haan JC, Buffart TE, Eijk PP, van de Wiel MA, van Wieringen WN, Howdle PD, Mulder CJ, van de Velde CJ, Quirke P, Nagtegaal ID, van Grieken NC, Grabsch H, Meijer GA, Ylstra B (2011). Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers. Ann Oncol. 23:367-74.
  29. Sombekke MH, Arteta D, van de Wiel MA, Crusius JB, Tejedor D, Killestein J, Martínez A, Peña AS, Polman CH, Uitdehaag BM (2010). Analysis of multiple candidate genes in association with phenotypes of multiple sclerosis. Mult Scler, 16, 652-9.
  30. Sillars-Hardebol AH, Carvalho B, de Wit M, Postma C, Delis-van Diemen PM, Mongera S, Ylstra B, van de Wiel MA, Meijer GA, Fijneman RJ (2010). Identification of key genes for carcinogenic pathways associated with colorectal adenoma-to-carcinoma progression. Tumour Biol, 31, 89-96.
  31. Costa JL, Eijk PP, van de Wiel MA, ten Berge D, Schmitt F, Narvaez CJ, Welsh J, Ylstra B (2009). Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-down. BMC Genomics, 10, 499.
  32. Fijneman RJ, Bade LK, Peham JR, van de Wiel MA, van Hinsbergh VW, Meijer GA, O'Sullivan MG, Cormier RT (2009). Pla2g2a attenuates colon tumorigenesis in azoxymethane-treated C57BL/6 mice; expression studies reveal Pla2g2a target genes and pathways. Cell Oncol, 31, 345-56.
  33. Diosdado B, van de Wiel MA, Terhaar Sive Droste JS, Mongera S, Postma C,  Meijerink WJHJ, Carvalho B, Meijer GA (2009). MiR-17-92 cluster is associated with 13q gain and c-myc expression during colorectal adenoma to adenocarcinoma progression. Br J Cancer, 101, 707-714.
  34. Buffart TE, Tijssen M, El-Bchiri J, Duval A, van de Wiel MA, Ylstra B, Meijer GA, Carvalho B. (2009). NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines. BMC Med Genetics, 29, 39.
  35. Smeets SJ, Brakenhoff RH, Ylstra, B, Van Wieringen WN, Van de Wiel MA, Leemans CR, Braakhuis BJM (2009), Genetic classification of oral and oropharyngeal carcinomas identifies subgroups with a different prognosis", Cellular Oncology, 39, 291-300.
  36. Wilting SM, Smeets SJ, Snijders PJ, van Wieringen WN, van de Wiel MA, Meijer GA, Ylstra B, Leemans CR, Meijer CJ, Brakenhoff RH, Braakhuis BJ, Steenbergen RD (2009). Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck. BMC Med Genetics, 2, 32. 
  37. Wilting SM, Steenbergen RDM, Tijssen M, Van Wieringen WN, Helmerhorst TJM, Van Kemenade FJ, Bleeker MCG, Van de Wiel MA, Carvalho B, Meijer GA, Ylstra B, Meijer CJLM, Snijders PF (2009), Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas, Cancer Research, 69, 647-655.
  38. Vékony H, Röser K, Löning T, Ylstra B, Meijer GA, van Wieringen WN, van de Wiel MA, Carvalho B, Kok K, René Leemans C, van der Waal I, Bloemena E. (2009). Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomas. Genes Chromosomes Cancer, 48, 202-12.
  39. Carvalho B, Postma C, Mongera S, Hopmans E, Diskin S, van de Wiel MA, van Criekinge W, Thas O, Matthäi A, Cuesta MA, Terhaar Sive Droste JS, Craanen M, Schröck E, Ylstra B, Meijer GA. (2009). Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression. Gut, 58, 79-89.
  40. Coffa J, van de Wiel MA, Diosdado B, Carvalho B, Schouten J, Meijer GA (2008). MLPAnalyzer: Data analysis tool for reliable automated normalization of MLPA fragment data. Cell Oncol, 30(4):323-35.
  41. Nygaard V, Liu F, Holden M, Kuo WP, Trimarchi J, Ohno-Machado L, Cepko CL, Frigessi A, Glad IK, van de Wiel MA, Hovig E, Lyng H (2008). Validation of oligoarrays for quantitative exploration of the transcriptome. BMC Genomics, 9(1):258.
  42. de Wilde J, Wilting SM, Meijer CJ, van de Wiel MA, Ylstra B, Snijders PJ, Steenbergen RD (2008). Gene expression profiling to identify markers associated with deregulated hTERT in HPV-transformed keratinocytes and cervical cancer. Int J Cancer.  122(4):877-88.
  43. Cillessen SA, Hess CJ, Hooijberg E, Castricum KC, Kortman P, Denkers F, Vos W, van de Wiel MA, Schuurhuis GJ, Ossenkoppele GJ, Meijer CJ, Oudejans JJ (2007). Inhibition of the intrinsic apoptosis pathway downstream of caspase-9 activation causes chemotherapy resistance in diffuse large B-cell lymphoma. Clin Cancer Res. 13(23):7012-21
  44. Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, van de Wiel MA, Green AR, Ellis IO, Porter PL, Tavare S, Brenton JD, Ylstra B, Caldas C. (2007) High-resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biology, 8, R215.
  45. Vekony H, Ylstra B, Wilting SM, Meijer GA, Van de Wiel MA, Leemans CR, Van der Waal I, Bloemena E (2007), DNA Copy Number Gains at Loci of Growth Factors and Their Receptors in Salivary Gland Adenoid Cystic Carcinoma. Clin Cancer Res, 13, 3133-3139.
  46. Muris JJ, Ylstra B, Cillessen SA, Ossenkoppele GJ, Kluin-Nelemans JC, Eijk PP, Nota B, Tijssen M, de Boer WP, van de Wiel M, van den IJssel PR, Jansen P, de Bruin PC, van Krieken JH, Meijer GA, Meijer CJ, Oudejans JJ (2007),Profiling of apoptosis genes allows for clinical stratification of primary nodal diffuse large B-cell lymphomas. Br J Haematol,136, 38-47.
  47. Wilting SM, Snijders PJ, Meijer GA, Ylstra B, van den Ijssel PR, Snijders AM, Albertson DG, Coffa J, Schouten JP, van de Wiel MA, Meijer CJ, Steenbergen RD (2006) Frequent gene copy number increases at chromosome 20q in both squamous cell carcinomas and adenocarcinomas of the cervix, Journal of Pathology, 209, 220-230.
  48. Smeets SJ, Braakhuis BJ, Abbas S, Snijders PJ, Ylstra B, van de Wiel MA, Meijer GA, Leemans CR, Brakenhoff RH (2006) Genome wide DNA copy number alterations in head and neck squamous cell carcinomas with or without biologically active human papillomavirus, Oncogene, 25, 2558-2564.
  49. Greijer AE, van der Groep P, Kemming D, Shvarts A, Semenza GL, Meijer GA, van de Wiel MA, Belien JA, van Diest PJ, van der Wall E (2005), Up-regulation of gene expression by hypoxia is mediated predominantly by hypoxia-inducible factor 1 (HIF-1), Journal of Pathology, 206, 291-304.
  50. van Sighem AI, van de Wiel MA, Ghani AC, Jambroes M, Reiss P, Gyssens IC, Brinkman K, Lange JM, de Wolf F; ATHENA Cohort Study Group (2003), Mortality and progression to AIDS after starting Highly Active Antiretroviral Therapy, AIDS, 17, 1-10.
  51. Delsing DJ, Jukema JW, van de Wiel MA, Emeis JJ, van der Laarse A, Havekes LM, Princen HM (2003), Differential effects of amlodipine and atorvastatin treatment and their combination on atherosclerosis in ApoE*3-Leiden transgenic mice, Journal of Cardiovascular Pharmacology, 42, 63-70.