Mark A Wiel

Mark A van de Wiel

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Mark A Wiel

Mark A van de Wiel

Publications by authors named "Mark A van de Wiel"

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1PubMed Central Citations

Molecular Characterization of Locally Relapsed Head and Neck Cancer after Concomitant Chemoradiotherapy.

Clin Cancer Res 2019 Aug 22. Epub 2019 Aug 22.

Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head & Neck Surgery, Cancer Center Amsterdam, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1158/1078-0432.CCR-19-0628DOI Listing
August 2019

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors.

Bioinformatics 2019 Jul;35(14):i510-i519

Computational Cancer Biology, Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, Amsterdam CX, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btz372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612899PMC
July 2019

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

Scand Stat Theory Appl 2019 Mar 1;46(1):2-25. Epub 2018 Jun 1.

Department of Epidemiology and Biostatistics, Amsterdam Public Health Research Institute VU University Medical Center Amsterdam The Netherlands.

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http://dx.doi.org/10.1111/sjos.12335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472625PMC
March 2019

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

BMC Bioinformatics 2017 12 28;18(1):584. Epub 2017 Dec 28.

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, 1007 MB, The Netherlands.

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http://dx.doi.org/10.1186/s12859-017-1993-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745983PMC
December 2017

An empirical Bayes approach to network recovery using external knowledge.

Biom J 2017 Sep 10;59(5):932-947. Epub 2017 Apr 10.

Department of Mathematics, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081, HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/bimj.201600090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510725PMC
September 2017

A Strategy to Find Suitable Reference Genes for miRNA Quantitative PCR Analysis and Its Application to Cervical Specimens.

J Mol Diagn 2017 09;19(5):625-637

Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15251578173006
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http://dx.doi.org/10.1016/j.jmoldx.2017.04.010DOI Listing
September 2017

Blood-based metabolic signatures in Alzheimer's disease.

Alzheimers Dement (Amst) 2017 6;8:196-207. Epub 2017 Sep 6.

Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.dadm.2017.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607205PMC
September 2017

Methods for significance testing of categorical covariates in logistic regression models after multiple imputation: power and applicability analysis.

BMC Med Res Methodol 2017 Aug 22;17(1):129. Epub 2017 Aug 22.

Department of Epidemiology & Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s12874-017-0404-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568368PMC
August 2017

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

Bioinformatics 2017 May;33(10):1572-1574

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btw837DOI Listing
May 2017

Gene Network Reconstruction using Global-Local Shrinkage Priors.

Ann Appl Stat 2017 Mar;11(1):41-68

Vrije Universiteit Amsterdam, Department of Mathematics, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388190PMC
March 2017

Erratum to: Assessment of predictive performance in incomplete data by combining internal validation and multiple imputation.

BMC Med Res Methodol 2016 12 5;16(1):170. Epub 2016 Dec 5.

Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007, Amsterdam, MB, The Netherlands.

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http://bmcmedresmethodol.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/s12874-016-0271-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5139144PMC
December 2016

Assessment of predictive performance in incomplete data by combining internal validation and multiple imputation.

BMC Med Res Methodol 2016 10 26;16(1):144. Epub 2016 Oct 26.

Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, Amsterdam, 1007, MB, The Netherlands.

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http://dx.doi.org/10.1186/s12874-016-0239-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080703PMC
October 2016

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

BMC Bioinformatics 2016 Mar 8;17:118. Epub 2016 Mar 8.

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands.

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http://dx.doi.org/10.1186/s12859-016-0961-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4782413PMC
March 2016

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

Stat Med 2016 Feb 13;35(3):368-81. Epub 2015 Sep 13.

Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/sim.6732DOI Listing
February 2016

HCsnip: An R Package for Semi-supervised Snipping of the Hierarchical Clustering Tree.

Cancer Inform 2015 22;14:1-19. Epub 2015 Mar 22.

Department of Epidemiology and Biostatistics, Vrije Universiteit Medical Center, Amsterdam, The Netherlands. ; Department of Mathematics, Vrije Universiteit, Amsterdam, The Netherlands.

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http://dx.doi.org/10.4137/CIN.S22080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372030PMC
April 2015

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

BMC Bioinformatics 2015 Jan 16;16:15. Epub 2015 Jan 16.

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s12859-014-0448-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302100PMC
January 2015

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

Cancer Inform 2014 1;13:153-6. Epub 2014 Dec 1.

Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.

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http://journals.sagepub.com/doi/10.4137/CIN.S19519
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http://dx.doi.org/10.4137/CIN.S19519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4251178PMC
December 2014

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

BMC Bioinformatics 2014 Oct 2;15:327. Epub 2014 Oct 2.

Department of Epidemiology and Biostatistics, VU University Medical Center, P,O, Box 7057, 1007 MB, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-15-327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288633PMC
October 2014

RNA sequencing of creatine transporter (SLC6A8) deficient fibroblasts reveals impairment of the extracellular matrix.

Hum Mutat 2014 Sep 15;35(9):1128-35. Epub 2014 Jul 15.

Metabolic Unit, Department of Clinical Chemistry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands; Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/humu.22609DOI Listing
September 2014

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

Cancer Inform 2014 2;13:1-11. Epub 2014 Jan 2.

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands. ; Department of Mathematics, VU University, Amsterdam, The Netherlands.

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http://dx.doi.org/10.4137/CIN.S13075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885337PMC
June 2014

Penalized differential pathway analysis of integrative oncogenomics studies.

Stat Appl Genet Mol Biol 2014 Apr;13(2):141-58

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http://dx.doi.org/10.1515/sagmb-2013-0020DOI Listing
April 2014

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs.

BMC Bioinformatics 2014 Apr 26;15:116. Epub 2014 Apr 26.

Department of Epidemiology and Biostatistics, VU University medical center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-15-116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098777PMC
April 2014

Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening.

BMC Med Genomics 2013 7;6 Suppl 2:S1. Epub 2013 May 7.

Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, the Netherlands.

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http://dx.doi.org/10.1186/1755-8794-6-S2-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654870PMC
October 2013

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

Stat Appl Genet Mol Biol 2013 Aug;12(4):449-67

Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1515/sagmb-2012-0046DOI Listing
August 2013

Regional differences in gene expression and promoter usage in aged human brains.

Neurobiol Aging 2013 Jul 19;34(7):1825-36. Epub 2013 Feb 19.

Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.neurobiolaging.2013.01.005DOI Listing
July 2013

PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data.

Bioinformatics 2013 Apr 17;29(8):1081-2. Epub 2013 Feb 17.

Department of Mathematics, VU University, De Boelelaan 1081a, Amsterdam, The Netherlands.

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http://bioinformatics.oxfordjournals.org/content/early/2013/
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http://bioinformatics.oxfordjournals.org/content/early/2013/
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btt082DOI Listing
April 2013

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.

Biostatistics 2013 Jan 17;14(1):113-28. Epub 2012 Sep 17.

Department of Epidemiology and Biostatistics, VU University (Medical Center), PO Box 7057, 1007 MB Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/biostatistics/kxs031DOI Listing
January 2013

TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progression.

Gut 2012 Nov 29;61(11):1568-75. Epub 2011 Dec 29.

VU University Medical Center, Department of Pathology, De Boelelaan 1117, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1136/gutjnl-2011-301153DOI Listing
November 2012

Chromosome 5q loss in colorectal flat adenomas.

Clin Cancer Res 2012 Sep 3;18(17):4560-9. Epub 2012 Jul 3.

Departments of Pathology, Epidemiology and Biostatistics, Gynaecology, and Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1158/1078-0432.CCR-11-2385DOI Listing
September 2012

An 82-year-old woman with small-cell lung cancer: relapse after 9 years or a new primary?

J Thorac Oncol 2012 Aug;7(8):e3-5

Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1097/JTO.0b013e31825bceadDOI Listing
August 2012

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses.

BMC Bioinformatics 2012 May 4;13:80. Epub 2012 May 4.

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-13-80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475006PMC
May 2012

HPV type-related chromosomal profiles in high-grade cervical intraepithelial neoplasia.

BMC Cancer 2012 Jan 24;12:36. Epub 2012 Jan 24.

Department of Pathology, Unit of Molecular Pathology, VU University Medical Center, PO box 7057, 1007 MB Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2407-12-36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305644PMC
January 2012

Stepwise classification of cancer samples using clinical and molecular data.

BMC Bioinformatics 2011 Oct 28;12:422. Epub 2011 Oct 28.

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3221726PMC
October 2011

Exploratory factor analysis of pathway copy number data with an application towards the integration with gene expression data.

J Comput Biol 2011 May;18(5):729-41

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://www.liebertpub.com/doi/10.1089/cmb.2009.0209
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http://dx.doi.org/10.1089/cmb.2009.0209DOI Listing
May 2011

Spatial clustering of array CGH features in combination with hierarchical multiple testing.

Stat Appl Genet Mol Biol 2010 16;9:Article40. Epub 2010 Nov 16.

National Cancer Institute, USA.

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http://dx.doi.org/10.2202/1544-6115.1532DOI Listing
March 2011

Confidence scores for prediction models.

Biom J 2011 Mar 17;53(2):259-74. Epub 2011 Feb 17.

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http://dx.doi.org/10.1002/bimj.201000157DOI Listing
March 2011

Preprocessing and downstream analysis of microarray DNA copy number profiles.

Brief Bioinform 2011 Jan 19;12(1):10-21. Epub 2010 Feb 19.

Department of Epidemiology & Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bib/bbq004DOI Listing
January 2011

A random coefficients model for regional co-expression associated with DNA copy number.

Stat Appl Genet Mol Biol 2010 22;9:Article25. Epub 2010 Jun 22.

VU University Medical Center, & VU University Amsterdam.

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http://dx.doi.org/10.2202/1544-6115.1531DOI Listing
October 2010

Analysis of multiple candidate genes in association with phenotypes of multiple sclerosis.

Mult Scler 2010 Jun 8;16(6):652-9. Epub 2010 Apr 8.

Department of Neurology, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1177/1352458510364633DOI Listing
June 2010

CGHpower: exploring sample size calculations for chromosomal copy number experiments.

BMC Bioinformatics 2010 Jun 17;11:331. Epub 2010 Jun 17.

Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-11-331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911457PMC
June 2010

Identification of key genes for carcinogenic pathways associated with colorectal adenoma-to-carcinoma progression.

Tumour Biol 2010 Apr 21;31(2):89-96. Epub 2010 Jan 21.

Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s13277-009-0012-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848338PMC
April 2010

Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility.

BMC Genomics 2010 Feb 17;11:112. Epub 2010 Feb 17.

Neuroregeneration Laboratory, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA Amsterdam, the Netherlands.

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http://dx.doi.org/10.1186/1471-2164-11-112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838842PMC
February 2010

Genetic classification of oral and oropharyngeal carcinomas identifies subgroups with a different prognosis.

Cell Oncol 2009 ;31(4):291-300

Section Tumor Biology, Department of Otolaryngology/Head-Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.3233/CLO-2009-0471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618915PMC
September 2009

Testing the prediction error difference between 2 predictors.

Biostatistics 2009 Jul 20;10(3):550-60. Epub 2009 Apr 20.

Department of Epidemiology and Biostatistics, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/biostatistics/kxp011DOI Listing
July 2009

Smoothing waves in array CGH tumor profiles.

Bioinformatics 2009 May 10;25(9):1099-104. Epub 2009 Mar 10.

Department of Epidemiology & Biostatistics, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btp132DOI Listing
May 2009

Nonparametric testing for DNA copy number induced differential mRNA gene expression.

Biometrics 2009 Mar 13;65(1):19-29. Epub 2008 May 13.

Department of Mathematics, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1111/j.1541-0420.2008.01052.xDOI Listing
March 2009

Identification of genes putatively involved in the pathogenesis of diffuse large B-cell lymphomas by integrative genomics.

Genes Chromosomes Cancer 2009 Mar;48(3):250-60

Department of Pathology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/gcc.20632DOI Listing
March 2009

Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomas.

Genes Chromosomes Cancer 2009 Feb;48(2):202-12

Department of Oral and Maxillofacial Surgery/Oral Pathology, Academic Centre for Dentistry (ACTA), VU University Medical Center, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/gcc.20631DOI Listing
February 2009

Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas.

Cancer Res 2009 Jan;69(2):647-55

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.

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http://dx.doi.org/10.1158/0008-5472.CAN-08-2478DOI Listing
January 2009

MLPAnalyzer: data analysis tool for reliable automated normalization of MLPA fragment data.

Cell Oncol 2008 ;30(4):323-35

Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619037PMC
October 2008

Weighted clustering of called array CGH data.

Biostatistics 2008 Jul 22;9(3):484-500. Epub 2007 Dec 22.

Department of Mathematics, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/biostatistics/kxm048DOI Listing
July 2008

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

Genome Biol 2007 ;8(10):R215

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.

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http://dx.doi.org/10.1186/gb-2007-8-10-r215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246289PMC
May 2008

Validation of oligoarrays for quantitative exploration of the transcriptome.

BMC Genomics 2008 May 30;9:258. Epub 2008 May 30.

Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, Oslo, Norway.

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http://dx.doi.org/10.1186/1471-2164-9-258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430212PMC
May 2008

Support vector machine approach to separate control and breast cancer serum samples.

Stat Appl Genet Mol Biol 2008 21;7(2):Article11. Epub 2008 Feb 21.

Vrije Universiteit Medical Center.

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http://dx.doi.org/10.2202/1544-6115.1355DOI Listing
April 2008

Effects of dependence in high-dimensional multiple testing problems.

BMC Bioinformatics 2008 Feb 25;9:114. Epub 2008 Feb 25.

Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-9-114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375137PMC
February 2008

Normalized, segmented or called aCGH data?

Cancer Inform 2007 Sep 17;3:321-7. Epub 2007 Sep 17.

Department of Mathematics, Vrije Universiteit De Boelelaan 1081a, Amsterdam, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675832PMC
September 2007

Estimating the false discovery rate using nonparametric deconvolution.

Biometrics 2007 Sep;63(3):806-15

Department of Mathematics, Vrije Universiteit, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1111/j.1541-0420.2006.00736.xDOI Listing
September 2007

Some comments on false discovery rate.

J Bioinform Comput Biol 2007 Aug;5(4):987-90

Institut National d'Agronomie, 16 rue Claude Bernard, 75005 Paris, France.

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August 2007

DNA copy number gains at loci of growth factors and their receptors in salivary gland adenoid cystic carcinoma.

Clin Cancer Res 2007 Jun;13(11):3133-9

Department of Oral and Maxillofacial Surgery/Oral Pathology, Academic Centre for Dentistry Amsterdam, the Netherlands.

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http://dx.doi.org/10.1158/1078-0432.CCR-06-2555DOI Listing
June 2007

CGHcall: calling aberrations for array CGH tumor profiles.

Bioinformatics 2007 Apr 31;23(7):892-4. Epub 2007 Jan 31.

Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btm030DOI Listing
April 2007

CGHregions: dimension reduction for array CGH data with minimal information loss.

Cancer Inform 2007 Feb 8;3:55-63. Epub 2007 Feb 8.

Department of Pathology and Department of Biostatistics (KEB), VU University Medical Center, Amsterdam, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675846PMC
February 2007

Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

Nucleic Acids Res 2005 Oct 4;33(17):e143. Epub 2005 Oct 4.

Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Norway.

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http://dx.doi.org/10.1093/nar/gni141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1243803PMC
October 2005

CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data.

Bioinformatics 2005 Jul 6;21(14):3193-4. Epub 2005 May 6.

Department of Mathematics and Computer Science, Technische Universiteit Eindhoven PO Box 513, 5600 MB, Eindhoven, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bti489DOI Listing
July 2005

Microarray data analysis: from hypotheses to conclusions using gene expression data.

Cell Oncol 2004 ;26(5-6):279-90

Department of Mathematics, Vrije Universiteit, Amsterdam, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612267PMC
June 2005

Mortality and progression to AIDS after starting highly active antiretroviral therapy.

AIDS 2003 Oct;17(15):2227-36

HIV Monitoring Foundation, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1097/00002030-200310170-00011DOI Listing
October 2003