20052019
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Research Output 2005 2019

2019

Genome-wide microRNA analysis of HPV-positive self-samples yields novel triage markers for early detection of cervical cancer

Snoek, B. C., Verlaat, W., Babion, I., Novianti, P. W., van de Wiel, M. A., Wilting, S. M., van Trommel, N. E., Bleeker, M. C. G., Massuger, L. F. A. G., Melchers, W. J. G., Sie, D., Heideman, D. A. M., Snijders, P. J. F., Meijer, C. J. L. M. & Steenbergen, R. D. M., 15 Jan 2019, In : International Journal of Cancer. 144, 2, p. 372-379 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

High amyloid burden is associated with fewer specific words during spontaneous speech in individuals with subjective cognitive decline

Verfaillie, S. C. J., Witteman, J., Slot, R. E. R., Pruis, I. J., Vermaat, L. E. W., Prins, N. D., Schiller, N. O., van de Wiel, M., Scheltens, P., van Berckel, B. N. M., van der Flier, W. M. & Sikkes, S. A. M., 2019, In : Neuropsychologia. 131, p. 184-192

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Learning from a lot: Empirical Bayes for high-dimensional model-based prediction

van de Wiel, M. A., te Beest, D. E. & Münch, M. M., 2019, In : Scandinavian Journal of Statistics. 46, 1, p. 2-25

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting

GoNL Consortium, 24 Jun 2019, In : Biology. 17, 1, p. 50

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2018

Combination of a six microRNA expression profile with four clinicopathological factors for response prediction of systemic treatment in patients with advanced colorectal cancer

Neerincx, M., Poel, D., Sie, D. L. S., van Grieken, N. C. T., Shankaraiah, R. C., van der Wolf-de Lijster, F. S. W., van Waesberghe, J-H. T. M., Burggraaf, J-D., Eijk, P. P., Verhoef, C., Ylstra, B., Meijer, G. A., van de Wiel, M. A., Buffart, T. E. & Verheul, H. M. W., 2018, In : PLoS ONE. 13, 8, p. e0201809

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Comprehensive molecular characterisation of HPV-induced transformation by longitudinal statistical modelling

Miok, V., 2018, 176 p.

Research output: ThesisResearch VU University Amsterdam, graduation VU University AmsterdamAcademic

Identification and validation of a 3-gene methylation classifier for HPV-based cervical screening on self-samples

Verlaat, W., Snoek, B. C., Heideman, D. A. M., Wilting, S. M., Snijders, P. J. F., Novianti, P. W., van Splunter, A. P., Peeters, C. F. W., van Trommel, N. E., Massuger, L. F. A. G., Bekkers, R. L. M., Melchers, W. JG., van Kemenade, F. J., Berkhof, J., van de Wiel, M. A., Meijer, C. J. L. M. & Steenbergen, R. D. M., 9 Apr 2018, In : Clinical Cancer Research. p. clincanres.3615.2017

Research output: Contribution to journalArticleAcademicpeer-review

2017

An empirical Bayes approach to network recovery using external knowledge

Kpogbezan, G. B., van der Vaart, A. W., van Wieringen, W. N., Leday, G. G. R. & van de Wiel, M. A., 1 Sep 2017, In : Biometrical Journal. 59, 5, p. 932-947 16 p.

Research output: Contribution to journalArticleAcademicpeer-review

35 Downloads (Pure)

Better diagnostic signatures from RNAseq data through use of auxiliary co-data

Novianti, P. W., Snoek, B. C., Wilting, S. M. & Van De Wiel, M. A., 15 May 2017, In : Bioinformatics. 33, 10, p. 1572-1574 3 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
File

Bioinformatic solutions for chromosomal copy number analysis in cancer

Scheinin, I., 2017, 130 p.

Research output: ThesisResearch VU University Amsterdam, graduation VU University AmsterdamAcademic

Open Access

Blood-based metabolic signatures in Alzheimer's disease

de Leeuw, F. A., Peeters, C. F. W., Kester, M. I., Harms, A. C., Struys, E. A., Hankemeier, T., van Vlijmen, H. W. T., van der Lee, S. J., van Duijn, C. M., Scheltens, P., Demirkan, A., van de Wiel, M. A., van der Flier, W. M. & Teunissen, C. E., 2017, In : Alzheimer's and Dementia: Diagnosis, Assessment and Disease Monitoring. 8, p. 196-207 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

GeneBreak: Detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes

Fijneman, R. J. A., van den Broek, E., van Lieshout, S., Rausch, C., Ylstra, B., van de Wiel, M. A., Meijer, G. A. & Abeln, S., 1 Jan 2017, In : F1000Research. 5

Research output: Contribution to journalArticleAcademicpeer-review

Gene network reconstruction using global-local shrinkage priors

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., 1 Mar 2017, In : Annals of Applied Statistics. 11, 1, p. 41-68 28 p.

Research output: Contribution to journalArticleAcademicpeer-review

Improved high-dimensional prediction with Random Forests by the use of co-data

te Beest, D. E., Mes, S. W., Wilting, S. M., Brakenhoff, R. H. & van de Wiel, M. A., 28 Dec 2017, In : BMC Bioinformatics. 18, 1, 584.

Research output: Contribution to journalArticleAcademicpeer-review

Profiling peripheral metabolic dysregulation in Alzheimer’s disease: The added value of multiple signatures. Alzheimer’s & Dementia

de Leeuw, F. A., Peeters, C. F. W., Kester, M. I., Harms, A. C., Hankemeier, T., Struys, E. A., Demirkan, A., Scheltens, P., van Vlijmen, H. W. T., van de Wiel, M. A., van Duijn, C. M., van der Flier, W. M. & Teunissen, C. E., Jun 2017, In : Alzheimers & Dementia. 13, 7, p. P1024-P1025

Research output: Contribution to journalMeeting AbstractAcademic

Prognostic modeling of oral cancer by gene profiles and clinicopathological co-variables

Mes, S. W., te Beest, D., Poli, T., Rossi, S., Scheckenbach, K., van Wieringen, W. N., Brink, A., Bertani, N., Lanfranco, D., Silini, E. M., van Diest, P. J., Bloemena, E., René Leemans, C., van de Wiel, M. A. & Brakenhoff, R. H., 2017, In : Oncotarget. 8, 35, p. 59312-59323 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

2016

A prognostic classifier for patients with colorectal cancer liver metastasis, based on AURKA, PTGS2 and MMP9

Goos, J. A. C. M., Coupe, V. M. H., van de Wiel, M. A., Diosdado, B., Delis-Van Diemen, P. M., Hiemstra, A. C., de Cuba, E. M. V., Belien, J. A. M., Geldof, A. A., Meijer, G. A., Hoekstra, O. S., Fijneman, R. J. A. & Menke, C. W., 12 Jan 2016, In : Oncotarget. 7, 2, p. 2123-2134

Research output: Contribution to journalArticleAcademicpeer-review

Better prediction by use of co-data: adaptive group-regularized ridge regression

van de Wiel, M. A., Lien, T. G., Verlaat, W., van Wieringen, W. N. & Wilting, S. M., 10 Feb 2016, In : Statistics in Medicine. 35, 3, p. 368-381

Research output: Contribution to journalArticleAcademicpeer-review

Genomic profiling of stage II and III colon cancers reveals APC mutations to be associated with survival in stage III colon cancer patients

van den Broek, E., Krijgsman, O., Sie, D., Tijssen, M., Mongera, S., van de Wiel, M. A., Belt, E. J. T., den Uil, S. H., Bril, H., Stockmann, H. B. A. C., Ylstra, B., Carvalho, B., Meijer, G. A. & Fijneman, R. J. A., 8 Nov 2016, In : Oncotarget. 7, 45, p. 73876-73887

Research output: Contribution to journalArticleAcademicpeer-review

MiR expression profiles can predict response to systemic treatment in patients with advanced colorectal cancer

Poel, D., Neerincx, M., Sie, D. L. S., van Grieken, N. C. T., Shankaraiah, R., van der Wolf, F. S. W., van Waesberghe, J. H. T. M., Burggraaf, J. D., Eijk, P. P., Ylstra, B., Verhoef, C., van de Wiel, M. A., Verheul, H. M. W. & Buffart, T. E., Jul 2016, In : Cancer Research. 76

Research output: Contribution to journalArticleAcademicpeer-review

Molecular imaging of aurora kinase A (AURKA) expression: Synthesis and preclinical evaluation of radiolabeled alisertib (MLN8237)

Goos, J. A. C. M., Verbeek, J., Geldof, A. A., van de Wiel, M. A., Adamzek, K. A., Delis-Van Diemen, P. M., Stroud, S. G., Bradley, D. P., Meijer, G. A., Hoekstra, O. S., Fijneman, R. J. A., Windhorst, A. D. & Hiemstra, AC., Jan 2016, In : Nuclear Medicine and Biology. 43, 1, p. 63-72

Research output: Contribution to journalArticleAcademicpeer-review

Reduced genomic tumor heterogeneity after neoadjuvant chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma

Obulkasim, A., Ylstra, B., van Essen, H. F., Benner, C., Stenning, S., Langley, R., Allum, W., Cunningham, D., Inam, I., Hewitt, L. C., West, N. P., Meijer, G. A., van de Wiel, M. A. & Grabsch, H. I., 12 Jul 2016, In : Oncotarget. 7, 28, p. 44084-44095

Research output: Contribution to journalArticleAcademicpeer-review

Testing for association between RNA-Seq and high-dimensional data

Rauschenberger, A., Jonker, M. A., van de Wiel, M. A. & Menezes, R. X., 8 Mar 2016, In : BMC Bioinformatics. 17, 118.

Research output: Contribution to journalArticleAcademicpeer-review

2015

High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer

van den Broek, E., Dijkstra, M. J. J., Krijgsman, O., Sie, D. L. S., Haan, J. C., Traets, J. J. H., van de Wiel, M. A., Nagtegaal, I. D., Punt, C. J. A., Carvalho, B., Ylstra, B., Abeln, S., Meijer, G. A. & Fijneman, R. J. A., 2015, In : PLoS ONE. 10, 9, e0138141.

Research output: Contribution to journalArticleAcademicpeer-review

19 Downloads (Pure)

Integrative Classification and Clustering Using Cancer Genomics Data

Obulkasim, A., 2015

Research output: ThesisResearch VU University Amsterdam, graduation VU University AmsterdamAcademic

File

M-CSF Priming of Osteoclast Precursors Can Cause Osteoclastogenesis-Insensitivity, Which Can be Prevented and Overcome on Bone

de Vries, T. J., Schoenmaker, T., Aerts, D., Grevers, L. C., Souza, P. P. C., Nazmi, K., van de Wiel, M. A., Ylstra, B., van Lent, P. L., Leenen, P. J. M. & Everts, V., 2015, In : Journal of Cellular Physiology. 230, 1, p. 210-225

Research output: Contribution to journalArticleAcademicpeer-review

MiR expression profiles of paired primary colorectal cancer and metastases by next-generation sequencing

Neerincx, M., Sie, D. L. S., van de Wiel, M. A., van Grieken, N. C. T., Burggraaf, J. D., Dekker, H., Eijk, P. P., Ylstra, B., Verhoef, C., Meijer, G. A., Buffart, T. E. & Verheul, H. M. W., 2015, In : Oncogenesis. 4, e170.

Research output: Contribution to journalArticleAcademicpeer-review

Semi-supervised adaptive-height snipping of the hierarchical clustering tree

Obulkasim, A., Meijer, G. A. & van de Wiel, M. A., 2015, In : BMC Bioinformatics. 16, 15.

Research output: Contribution to journalArticleAcademicpeer-review

2014

Analysis of Next Generation Sequencing Data Using Integrated Nested Laplace Approximation (INLA)

Riebler, A., Robinson, M. D. & van de Wiel, M. A., 2014, Statistical Analysis of Next Generation Sequencing Data. Switzerland: Springer International Publishing, p. 75-91

Research output: Chapter in Book/Report/Conference proceedingChapterAcademic

DNA copy number aberrations in endobronchial lesions: a validated predictor for cancer

van Boerdonk, R. A. A., Daniels, J. M. A., Snijders, P. J. F., Grünberg, K., Thunnissen, F. B. J. M., van de Wiel, M., Ylstra, B., Postmus, P. E., Meijer, C. J. L. M., Meijer, G. A., Smit, E. F., Sutedja, T. G. & Heideman, D. A. M., 2014, In : Thorax. 69, 5, p. 451-457

Research output: Contribution to journalArticleAcademicpeer-review

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

Scheinin, I., Sie, D. L. S., Bengtsson, H., van de Wiel, M. A., Olshen, A. B., van Thuijl, H. F., van Essen, H. F., Eijk, P. P., Rustenburg, F., Meijer, G. A., Reijneveld, J. C., Wesseling, P., Pinkel, D., Albertson, DG. & Ylstra, B., 2014, In : Genome Research. 24, 12, p. 2022-2032

Research output: Contribution to journalArticleAcademicpeer-review

FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations

Krijgsman, O., Benner, C., Meijer, G. A., van de Wiel, M. A. & Ylstra, B., 2014, In : Cancer Informatics. 13, p. 153-156

Research output: Contribution to journalArticleAcademicpeer-review

Genomic landscape of metastatic colorectal cancer

Haan, J. C., Labots, M., Rausch, C., Koopman, M., de Nooy-van Tol, J., Mekenkamp, L. J. M., van de Wiel, M. A., Israeli, D., van Essen, H. F., van Grieken, N. C. T., Voorham, Q. J. M., Bosch, L. J. W., Qu, X., Kabbarah, O., Verheul, H. M. W., Nagtegaal, I. D., Punt, C. J. A., Ylstra, B. & Meijer, G. A., 2014, In : Nature Communications. 5, 5457.

Research output: Contribution to journalArticleAcademicpeer-review

Het zit in de genen, toch?

van de Wiel, M. A., 2014, Amsterdam: Vrije Universiteit.

Research output: Book/ReportInaugural speechOther research output

Penalized differential pathway analysis of integrative oncogenomics studies

van Wieringen, W. N. & van de Wiel, M. A., 2014, In : Statistical Applications in Genetics and Molecular Biology. 13, 2, p. 141-158

Research output: Contribution to journalArticleAcademicpeer-review

RNA Sequencing of Creatine Transporter (SLC6A8) Deficient Fibroblasts Reveals Impairment of the Extracellular Matrix

Nota, B., Ndika, J. D. T., van de Kamp, J. M., Kanhai, W. A., van Dooren, S. J. M., van de Wiel, M. A., Pals, G. & Salomons, G. S., 2014, In : Human Mutation. 35, 9, p. 1128-1135

Research output: Contribution to journalArticleAcademicpeer-review

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

van Thuijl, H. F., Scheinin, I., Sie, D. L. S., Alentorn, A., van Essen, H. F., Cordes, M., Fleischeuer, R., Beute, G., van den Brink, W. A., Meijer, G. A., Havenith, M., Idbaih, A., Hoang-Xuan, K., Mokhtari, K., Verhaak, R. G. W., van der Valk, P., van de Wiel, M. A., Heimans, J. J., Aronica, E., Reijneveld, J. C. & 2 othersWesseling, P. & Ylstra, B., 2014, In : Genome Biology. 15, 9, 471.

Research output: Contribution to journalArticleAcademicpeer-review

StepwiseCM: An R Package for Stepwise Classification of Cancer Samples Using Multiple Heterogeneous Data Sets

Obulkasim, A. & van de Wiel, M. A., 2014, In : Cancer Informatics. 13, p. 1-11

Research output: Contribution to journalArticleAcademicpeer-review

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

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, In : BMC Bioinformatics. 15, p. 327 327.

Research output: Contribution to journalArticleAcademicpeer-review

2013

Altered microRNA expression associated with chromosomal changes contributes to cervical carcinogenesis

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. & Steenbergen, R. D. M., 2013, In : Oncogene. 32, p. 106-116

Research output: Contribution to journalArticleAcademicpeer-review

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors

van de Wiel, M. A., Leday, G. G. R., Pardo, L. M., Rue, H., van der Vaart, A. W. & van Wieringen, W. N., 2013, In : Biostatistics. 14, 1, p. 113-128

Research output: Contribution to journalArticleAcademicpeer-review

DNA copy number profiling reveals extensive genomic loss in hereditary BRCA1 and BRCA2 ovarian carcinomas

Kamieniak, M. M., Munoz-Repeto, I., Rico, D., Osorio, A., Urioste, M., Garcia-Donas, J., Hernando, S., Robles-Diaz, L., Ramon, Y. C., Cazorla, A., Saez, R., Garcia-Bueno, J. M., Domingo, S., Borrego, S., Palacios, J., van de Wiel, M., Ylstra, B., Benitez, J. & Garcia, M. J., 2013, In : British Journal of Cancer. 108, 8, p. 1732-1742

Research output: Contribution to journalArticleAcademicpeer-review

General power and sample size calculations for high-dimensional genomic data

van Iterson, M., van de Wiel, M., Boer, J. M. & Menezes, R., 2013, In : Statistical Applications in Genetics and Molecular Biology. 12, 4, p. 449-467

Research output: Contribution to journalArticleAcademicpeer-review

Methotrexate Normalizes Up-Regulated Folate Pathway Genes in Rheumatoid Arthritis

Blits, M., Jansen, G., Assaraf, Y. G., van de Wiel, M., Lems, W. F., Nurmohamed, M. T., van Schaardenburg, D., Voskuyl, A. E., Wolbink, G. J., Vosslamber, S. & Verweij, C. L., 2013, In : Arthritis & Rheumatism. 65, 11, p. 2791-2802

Research output: Contribution to journalArticleAcademicpeer-review

Modeling Association Between Dna Copy Number and Gene Expression with Constrained Piecewise Linear Regression Splines

Leday, G. G. R., van der Vaart, A. W., van Wieringen, W. N. & van de Wiel, M., 2013, In : The Annals of Applied Statistics. 7, 2, p. 823-845

Research output: Contribution to journalArticleAcademicpeer-review