Scientific publications by Wessel N. van Wieringen

  1. Lange, R., ter Heine, R., van Wieringen, W.N., Tromp, A.M., Paap, M., Bloemendal, H.J., de Klerk, J.M.H., Hendrikse, N.H., Geldof, A.A. (2016), "Cytotoxic Effects of the Therapeutic Radionuclide Rhenium-188 Combined with Taxanes in Human Prostate Carcinoma Cell Lines", Cancer Biotherapy and Radiopharmaceuticals, accepted.
  2. Korkmaz, H.I., Ulrich, M.M.W., van Wieringen, W.N., Vlig, M., Emmens, R.W., Meyer, K.W., Sinnige, P., Krijnen, P.A.J., van Zuijlen, P.P.M., Niessen, H.W.M. (2016), "The local and systemic inflammatory response in a pig burn wound model with a pivotal role for complement", Journal of Burn Care & Research, doi:10.1097/BCR.0000000000000486.
  3. Peeters, C.F.W., van de Wiel, M.A., van Wieringen, W.N. (2016) "The spectral condition number plot for regularization parameter determination", submitted, arXiv:1608.04123 [stat.CO].
  4. van Wieringen, W.N. Peeters, C.F.W., de Menezes, R.X., van de Wiel, M.A. (2016) "Testing for pathway (in)activation using Gaussian graphical models", submitted.
  5. Bilgrau, A.E., Peeters, C.F.W., Eriksen, P.S., Bogsted, M., van Wieringen, W.N. (2015), "Targeted fused ridge estimation of inverse covariance matrices from multiple high-dimensional data classes", arXiv:1509.07982 [stat.ME].
  6. Kpogbezan, G.B., van der Vaart, A.W., van Wieringen, W.N., Leday, G.G.R., van de Wiel, M.A. (2016), "An empirical Bayes approach to network recovery using external knowledge", Biometrical Journal, accepted.
  7. van Wieringen, W.N. (2017) "On the mean squared error of the ridge estimator of the covariance and precision matrix", Statistics and Probability Letters, 123, 88-92.
  8. Miok, V., Wilting, S.M., van Wieringen, W.N. (2017), "Ridge estimation of the VAR(1) model and its time series chain graph from multivariate time-course omics data", Biometrical Journal, 59(1), 172-191.
  9. Leday, G.G.R., de Gunst, M.C.M., Kpogbezan, G.B., van der Vaart, A.W., van Wieringen, W.N., van de Wiel, M.A. (2015), "Gene network reconstruction using global-local shrinkage priors", Annals of Applied Statistics, accepted, arXiv:1510.03771 [stat.ME].
  10. Mak-van der Vossen, M.C., van Mook, W.N.K.A., Kors, J.M., van Wieringen, W.N., Peerdeman, S.M., Croiset, G., Kusurkar, R.A. (2016), "Distinguishing three unprofessional behavior profiles of medical students using latent class analysis", Academic Medicine, 91(9), 1276-1283.
  11. Steenweg, M.E., Wolf, N.I., van Wieringen, W.N., Barkhof, F., van der Knaap, M.S., Pouwels, P.J. (2016), "Quantitative MRI in hypomyelinating disorders: correlation with motor handicap", Neurology, 87(8), 752-758.
  12. Wilting, S.M., Miok, V., Jaspers, A., Boon, D., Sorgard, H., Lando, M., Snoek, B.C., van Wieringen, W.N., Meijer, C.J., Lyng, H. and Snijders, P.J. (2016). "Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence", Oncotarget, 7(28), 43805-43819, DOI: 10.18632/oncotarget.9698. .
  13. van der Vaart, A.W., van Wieringen, W.N. (2016), "Statistics in high dimensions", Chapter 5 (p51-p70) in Mathematics and Society by W. Koenig (Editor).
  14. Van Wieringen, W.N., Peeters, C.F.W. (2016), "Ridge estimation of inverse covariance matrices from high-dimensional data", Computational Statistics and Data Analysis, 103, 284-303.
  15. Van de Wiel, M.A., Lien, T.G., Verlaat, W., Van Wieringen, W.N., Wilting, S.M. (2016), "Better prediction by use of co-data: Adaptive group-regularized ridge regression", Statistics in Medicine, 35(3), 368-381.
  16. Van Wieringen, W.N., Peeters, C.F.W. (2015), "Application of a new ridge estimator of the inverse covariance matrix to the reconstruction of gene-gene interaction networks", Lecture Notes in Computer Science, Vol. 8623, 170-179.
  17. Van Wieringen, W.N., Van der Vaart, A.W. (2015), "Transcriptomic heterogeneity in cancer as a consequence of dysregulation of the gene-gene interaction network", Bulletin of Mathematical Biology, 77(9), 1768-1786.
  18. Miok, V., Wilting, S.M., Van de Wiel, M.A., Jaspers, A., van Noort, P.I., Brakenhoff, R.H., Snijders, P.J.F., Steenbergen, R.D.M., Van Wieringen, W.N. (2014), " tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities", BMC Bioinformatics, 15, 327.
  19. Chaturvedi, N., Goeman, J. J., Boer, J. M., Van Wieringen, W. N., de Menezes, R. X. (2014), "A test for comparing two groups of samples when analyzing multiple omics profiles", BMC Bioinformatics, 15(1), 236.
  20. van Berge, L., Hamilton, E. M., Linnankivi, T., Uziel, G., Steenweg, M. E., Isohanni, P., Wolf, N.I., Krägeloh-Mann, I., Brautaset, N.J., Andrews, P.I., De Jong, B.A., Al Ghamdi, M. , Wessel N. van Wieringen, W.N., LBSL Research Group, Tannous, B.A., Hulleman, E., Würdinger, T., Van Berkel, C.G.M., Polder, E., Abbink, T.E.M., Struys, E.A., Scheper, G.C., Van der Knaap, M. S. (2014). Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation: clinical and genetic characterization and target for therapy. Brain, 137(4), 1019-1029.
  21. Van Wieringen, W.N., Van de Wiel, M.A.. (2014), "Penalized differential pathway analysis of integrative oncogenomics studies", Statistical Applications in Genetics and Molecular Biology, 13(2), 141-158.
  22. Lindenbergh-van der Plas, M., Martens-de Kemp, S.R., De Maaker, M., Van Wieringen, W.N., Ylstra, B., Agami, R., Cerisoli, F., Leemans, C.R., Braakhuis, B.J.M., Brakenhoff, R.H. (2013), "Identification of lethal microRNAs specific for head and neck cancer", Clinical Cancer Research, 19, 5647-5657.
  23. Van Wieringen, W.N., Ros, B.P., Wilting, S.M. (2013), "Modeling the DNA copy number aberration patterns in observational high-throughput cancer data", Statistical Applications in Genetics and Molecular Biology, 12(2), 143-174.
  24. Leday, G.G.R., Van der Vaart, A.W., Van Wieringen, W.N., Van de Wiel, M.A. (2013), "Modeling association between DNA copy number and gene expression with constrained piecewise linear regression splines", Annals of Applied Statistics, 7(2), 823-845.
  25. Martens-de Kemp, S.R., Brink, A., Stigter-van Walsum, M., Damen, M.A., Rustenburg, F., Wu, T., Van Wieringen, W.N., Schuurhuis, G.J., Braakhuis, B.J.M., Monique Slijper, M., Brakenhoff, R.H. (2013), "CD98 marks a subpopulation of head and neck squamous cell carcinoma cells with stem cell properties", Stem Cell Research, 10, 477-488.
  26. Braakhuis, B.L.M., Graveland, A.P., Dijk, F., Ylstra, B., Van Wieringen, W.N., Leemans, C.R., Brakenhoff, R.H.(2012), "Expression signature in peripheral blood cells for molecular diagnosis of head and neck squamous cell carcinoma", Oral Diseases, 19(5), 452-455.
  27. Van Wieringen, W.N., Van der Vaart, A.W.> (2013), "The cancer cell, its entropy, and high-dimensional molecular data", Chapter 14 (p261-p284) in Statistical Diagnostics for Cancer: Analyzing High-Dimensional Data by M. Dehmer and F. Emmert-Streib (Editors).
  28. Van de Wiel, M.A., Leday, G.G.R., Pardo, L., Rue, H., Van der Vaart, A.W., Van Wieringen, W.N. (2013), "Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors", Biostatistics, 14(1), 113-128.
  29. Wilting, S.M., Snijders, P.J.F., Verlaat, W., Jaspers, A., Van de Wiel, M.A., Van Wieringen, W.N., Meijer, G.A., Kenter, G.G., Yi, Y., le Sage, C., Agami, R., Meijer, C.J.L.M., R D M Steenbergen, R.D.M. (2013), "Altered microRNA expression associated with chromosomal changes contributes to cervical carcinogenesis", Oncogene, 32, 106-116
  30. Van der Lei, H.D.W., Steenweg, M.E., Bugiani, M., Pouwels, P.J.W., Vent, I.M., Barkhof, F., van Wieringen, W.N., van der Knaap, M.S. (2012), "Restricted diffusion in vanishing white matter", Archives of Neurology, 69(6), 723-727.
  31. Zaal, A., Peyrot, W.J., Berns, P.M., van der Burg, M.E., Veerbeek, J.H., Trimbos, J.B., Cadron, I., van Diest. P.J., van Wieringen, W.N., Krijgsman, O., Meijer, G.A., Piek, J.M., Timmers, P.J., Vergote, I., Verheijen, R.H., Ylstra, B., Zweemer, R.P.; EORTC GCG Translational Research Group (2012), "Genomic aberrations relate early and advanced stage ovarian cancer", Cellular Oncology, 35(3), 181-188.
  32. Bierkens, M., Wilting, S.M., Van Wieringen, W.N., Van Kemenade, F.J., Bleeker, M.C.G., Jordanova, E.S., Bekker-Lettink, M., Van de Wiel, M.A., Ylstra, B., Meijer, C.J.L.M., Snijders, P.J.F., Steenbergen, R.D.M (2011), "Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infection", International Journal of Cancer, 131(4), E579-E585.
  33. Buffart, T.E., Carvalho, B., Van Grieken, N.C.T., Van Wieringen, W.N., Tijssen, M., Meershoek-Klein Kranenbarg, E., Verheul, H.M.W., Grabsch, H.I., Ylstra, B., Van de Velde, C.J.H., Meijer, G.A. (2012), "Losses of chromosome 5q and 14q are associated with favorable clinical outcome of patients with gastric cancer", The Oncologist, 17, 653-662.
  34. Van Wieringen, W.N., Unger, K., Leday, G.G.R., Krijgsman, O., De Menezes, R.X., Ylstra, B., Van de Wiel, M.A. (2012), "Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses", BMC Bioinformatics, 13:80.
  35. Bierkens, M., Wilting, S.M., Van Wieringen, W.N., Van de Wiel, M.A., Ylstra, B., Meijer, C.J.L.M., Snijders, P.J.F., Steenbergen, R.D.M (2012), "HPV type-related chromosomal profiles in highgrade cervical intraepithelial neoplasia", BMC Cancer, 12:36.
  36. Haan, J.C., Buffart, T.E., Eijk, P.P., Van de Wiel, M.A., Van Wieringen, W.N., Howdle, P.D., Mulder, C.J.J., Van de Velde, C.J., Quirke, P., Nagtegaal, I.D., Van Grieken, N.C.T., Grabsch, H., Meijer, G.A., Ylstra, B. (2011), "Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers", Annals of Oncology, 23, 367-374.
  37. Steenweg, M.E., Pouwels, P.J.W., Wolf, N.I., Van Wieringen, W.N., Barkhof, F., van der Knaap, M. S. (2011), "Leucoencephalopathy with brainstem and spinal cord involvement and high lactate: quantitative magnetic resonance imaging", Brain, 134(11), 3333-3341.
  38. Welvaart, W.N., Paul, M.A., Kuster, D.W.D., Van Wieringen, W.N., Rustenburg, F., Stienen, G.J.M., Vonk-Noordegraaf, A., Ottenheijm, C.A.C. (2011), "Gene expression profile in the diaphragm following contractile inactivity during thoracic surgery", International Journal of Physiology, Pathophysiology and Pharmacology, 3(3), 167-175.
  39. Smeets, S.J., Harjes, U., Van Wieringen, W.N., Sie, D., Brakenhoff, R.H., Meijer, G.A., Ylstra, B. (2011), "To DNA or not to DNA? That is the question, when it comes to molecular subtyping for the clinic!", Clinical Cancer Research, 17(15), 4959-4964.
  40. Van Wieringen, W.N., Van der Vaart, A.W. (2011), "Statistical analysis of the cancer cell's molecular entropy using high-throughput data", Bioinformatics, 27(4), 556-563.
  41. De Mast, J., Erdmann, T.P., Van Wieringen, W.N. (2011), "Measurement system analysis for binary inspection: continuous versus dichotomous measurands", Journal of Quality Technology, 43(2), 99-112.
  42. Van Wieringen, W.N., Van de Wiel, M.A. (2011), "Exploratory factor analysis of pathway copy number data with an application towards the integration with gene expression data", Journal of Computational Biology, 18(5), 729-741.
  43. Van de Wiel, M.A., Picard, F., Van Wieringen, W.N., Ylstra, B. (2011), "Preprocessing and downstream analysis of microarray DNA copy number profiles", Briefings in Bioinformatics, 12(1), 10-21.
  44. Steenweg, M.E., Vanderver, A., Blaser, S., Bizzi, A., De Koning, T.J., Mancini, G.M.S., Van Wieringen, W.N., Barkhof, F., Wolf, N.I., Van der Knaap, M.S. (2010), "Magnetic resonance imaging pattern recognition in hypomyelinating disorders", Brain, 133(10), 2971-2982.
  45. Van der Lei, H.D.W., Van Berkel, C.G.M., Van Wieringen, W.N. Brenner, C., Feigenbaum, A., Mercimek-Mahmutoglu, S., Philippart, M., Tatli, B., Wassmer, E., Scheper, G.C., Van der Knaap, M.S. (2010), "Genotype-phenotype correlation in vanishing white matter disease", Neurology, 75(17), 1555-1559.
  46. Van Boxtel, A.L., Pieterse, B., Cenijn, P., Harmen Kamstra, J., Brouwer, A., Van Wieringen, W.N., De Boer, J., Legler, J. (2010), "Dithiocarbamates Induce Craniofacial Abnormalities and Downregulate sox9a during Zebrafish Development", Toxicological Sciences, 117(1): 209-217.
  47. Liebman, B., Strating, R.P., Van Wieringen, W.N., Mulder, W., Oomen, J.L.T., Engel, A.F. (2010), "Risk modelling of outcome after general and trauma surgery (the IRIS score)", British Journal of Surgery, 97(1), 128-133.
  48. Van Wieringen, W.N., Berkhof, J., Van de Wiel, M.A. (2010), "A random coefficients model for regional co-expression associated with DNA copy number", Statistical Applications in Genetics and Molecular Biology, Volume 9, Issue1, Article 25, 1-28.
  49. De Mast, J., Van Wieringen, W.N. (2010), "Modeling and evaluating repeatability and reproducibility of ordinal classifications", Technometrics, 52(1), 94-106.
  50. Smeets, S.J., Brakenhoff, R.H., Ylstra, B., Van Wieringen, W.N., Van de Wiel, M.A., Leemans, C.R., Braakhuis, B.J.M. (2009), "Genetic classification of oral and oropharyngeal carcinomas identifies subgroups with a different prognosis", Cellular Oncology, 39, 291-300.
  51. Wilting, S.M., Smeets, S.J., Snijders, P.J.F., Van Wieringen, W.N., Van de Wiel, M.A., Meijer, G.A., Ylstra, B., Leemans, C.R., Meijer, C.J.L.M., Brakenhoff, R., Braakhuis, B.J.M., Steenbergen, R.D.M. (2009), "Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck", BMC Medical Genomics, 2:32, doi:10.1186/1755-8794-2-32.
  52. Wilting, S.M., Steenbergen, R.D.M., Tijssen, M., Van Wieringen, W.N., Helmerhorst, T.J.M., Van Kemenade, F.J., Bleeker, M.C.G., Van de Wiel, M.A., Carvalho, B., Meijer, G.A., Ylstra, B.,Meijer, C.J.L.M., Snijders, P.F. (2009), "Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas", Cancer Research, 69, 647-655.
  53. Oudejans, J.J., Van Wieringen, W.N., Smeets, S.J., Tijssen, M., Vosse, S.J., Meijer, C.J.L.M., Meijer, G.A., Van de Wiel, M.A., Ylstra, B. (2009), "Identification of genes putatively involved in the pathogenesis of diffuse large B-cell lymphomas by integrative genomics", Genes, Chromosomes & Cancer, 48, 250-260.
  54. Vekony, H., Roser, K., Loning, T., Ylstra, B., Meijer, G.A., Van Wieringen, W.N., Van de Wiel, M.A., Carvalho, B., Kok, K., Leemans, C.R., 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, 202-212.
  55. Van de Wiel, M.A., Berkhof, J., Van Wieringen, W.N. (2009), "Testing the error difference between two prediction procedures", Biostatistics, 10(3), 550-560.
  56. Van Wieringen, W.N., Van de Wiel, M.A. (2009), "Non-parametric testing for DNA copy number induced differential mRNA gene expression", Biometrics, 65(1), 19-29.
  57. Van Wieringen, W.N., Kun, D., Hampel, R., Boulesteix, A.-L. (2009), "Survival prediction using gene expression: a review and comparison", Computational Statistics & Data Analysis, 53(5), 1590-1603.
  58. Wilting, S.M., De Wilde, J., Meijer, C.J.L.M., Berkhof, J., Yajun Yi, Y., Van Wieringen, W.N., Braakhuis, B.J.M, Meijer, G.A., Ylstra, B., Snijders, P.J.F., Steenbergen, R.D.M. (2008), "Integrated genomic and transcriptional profiling identifies chromosomal loci with altered gene expression in cervical cancer", Genes, Chromosomes & Cancer, 47, 890-905.
  59. Levering, W.H.B.M., Van Wieringen, W.N., Kraan, J., Van Beers, W.A.M., Sintnicolaas, K., Van Rhenen, D.J., Gratama, J.W. (2008), "Flow cytometric lymphocyte subset enumeration: 10 years of external quality assessment in the Benelux countries", Cytometry Part B (Clinical Cytometry), 74, 79-90.
  60. Van Wieringen, W.N., Van de Wiel, M.A., Van der Vaart, A.W. (2008), "A test for partial differential expression", Journal of the American Statistical Association, 103(483), 1039-1049.
  61. Van Wieringen, W.N., De Mast, J. (2008), "Measurement system analysis for binary data", Technometrics, 50(4), 468-478.
  62. Van Wieringen, W.N., Van de Wiel, M.A., Ylstra, B. (2008), "Weighted clustering of called aCGH data", Biostatistics, 9(3), 484-500.
  63. Levering, W.B.H.M., Preyers, F.W.M.B., Van Wieringen, W.N., Kraan, J., Van Beers, W.A.M., Sintnicolaas, K., Van Rhenen, D.J., Gratama, J.W. (2007), "Flow cytometry CD34+ stem cell enumeration: lessons from nine years external quality assessment within the Benelux countries", Cytometry Part B (Clinical Cytometry), 72, 178--188.
  64. Van Wieringen, W.N., Van de Wiel, M.A., Ylstra, B. (2007), "Normalized, segmented or called aCGH data?", Cancer Informatics, 3, 331-337.
  65. Van de Wiel, M.A., Kim, K.I., Vosse, S.J., Van Wieringen, W.N., Wilting, S.M. , Ylstra, B. (2007), "CGHcall: an algorithm for calling aberrations for multiple array CGH tumor profiles", Bioinformatics, 23, 892-894.
  66. Van de Wiel, M.A., Van Wieringen, W.N. (2007), "CGHregions: dimension reduction for array CGH data with minimal information loss", Cancer Informatics, 2, 55-63.
  67. De Mast, J., Van Wieringen, W.N. (2007), "Measurement system analysis for categorical measurements:agreement and kappa type indices", Journal of Quality Technology, 39, 191-202.
  68. Fatehi, D. Van der Zee, J., Van der Wal, E., Van Wieringen, W.N., Van Rhoon, G.C. (2006), "Temperature data analysis for 22 patients with advanced cervical carcinoma treated in Rotterdam using radiotherapy, hyperthermia and chemotherapy: A reference point is needed", International Journal of Hyperthermia, 22, 353-363.
  69. Fatehi, D., Van der Zee, J., Wielheesen, D.H.M., Van Wieringen, W.N., Van Rhoon, G.C. (2006), "Intra-luminal thermometry: Is tissue type ssignment a necessity for thermal analysis?", International Journal of Hyperthermia, 22, 463-473.
  70. De Mast, J., Van Wieringen, W.N. (2006), "The Iota coefficient as an index of repeatability and reproducibility of ordinal measurements", Technical Report, University of Amsterdam.
  71. Van Wieringen, W.N., Belien, J.A.M., Vosse, S.J., Achame, E.M., Ylstra, B. (2006), "ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data", Bioinformatics, 22(15), 1919-1920.
  72. Verdonck, L.F., Van Imhoff, G.W., Raemakers, J.M.M., Verhoef, G., Kramer, M.H.H., Ossenkoppele, G.J., Doorduijn, J.K., Meulendijks, I.A.M.H., Van Wieringen, W.N., Sonneveld, P. (2005), "Six courses of intensified CHOP plus G-CSF compared to eight courses of standard CHOP in patients with intermediate-risk aggressive non-Hodgkin lymphoma results of a prospective randomized HOVON trial", Blood, 106, Abstract 14.
  73. Wu, K.L., Van Wieringen, W.N., Vellenga, E., Zweegman, S., Smit, W.M., Lokhorst, H.M., Sonneveld, P. (2005), "Analysis of the efficacy and toxicity of bortezomib for treatment of relapsed or refractory multiple myeloma: beyond the context of a clinical trial", Haematologica, 90, 996-997.
  74. Van Wieringen, W.N. (2005), "On the identification of certain latent class models", Statistics and Probability Letters, 75, 211-218.
  75. Van Wieringen, W.N., Van den Heuvel, E.R. (2005), "A comparison of methods for the evaluation of binary measurement systems", Quality Engineering, 17, 495-507.
  76. De Mast, J., Van Wieringen, W.N. (2004), "Measurement system analysis for bounded ordinal data", Quality and Reliability Engineering International, 20, 383-395.
  77. Van Wieringen, W.N., Statistical models for the precision of categorical measurements systems, Ph.D. Thesis, University of Amsterdam, 2003.

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