Wessel N. van Wieringen
VU University Amsterdam
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Publications 77
#1Iris BabionH-Index: 1
#2Viktorian MiokH-Index: 2
Last. Saskia M. WiltingH-Index: 20
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Next to a persistent infection with high-risk human papillomavirus (HPV), molecular changes are required for the development of cervical cancer. To identify which molecular alterations drive carcinogenesis, we performed a comprehensive and longitudinal molecular characterization of HPV-transformed keratinocyte cell lines. Comparative genomic hybridization, mRNA, and miRNA expression analysis of four HPV-containing keratinocyte cell lines at eight different time points was performed. Data was ana...
#1H. Ibrahim Korkmaz (VUMC: Vanderbilt University Medical Center)H-Index: 3
#1H Ibrahim Korkmaz (VUMC: Vanderbilt University Medical Center)
Last. Hans W. M. Niessen (VUMC: Vanderbilt University Medical Center)H-Index: 1
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AbstractThe ridge inverse covariance estimator is generalized to allow for entry-wise penalization. An efficient algorithm for its evaluation is proposed. Its computational accuracy is benchmarked ...
1 CitationsSource
#1Arjan Malekzadeh (UvA: University of Amsterdam)
#2Cyra E. Leurs (UvA: University of Amsterdam)H-Index: 7
Last. Charlotte E. Teunissen (UvA: University of Amsterdam)H-Index: 3
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BACKGROUND: The pathophysiology of multiple sclerosis disease progression remains undetermined. The aim of this study was to identify differences in plasma proteome during different stages of MS disease progression. METHODS: We used a multiplex aptamer proteomics platform (Somalogic) for sensitive detection of 1129 proteins in plasma. MS patients were selected and categorized based on baseline and a 4-year follow-up EDSS (delta EDSS) scores; relapse-onset (RO) slow progression (n = 31), RO with ...
#1Claire Bridel (VU: VU University Amsterdam)H-Index: 5
#2Wessel N. van Wieringen (VU: VU University Amsterdam)H-Index: 22
Last. Edward J. Wild (UCL Institute of Neurology)H-Index: 27
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textabstractImportance: Neurofilament light protein (NfL) is elevated in cerebrospinal fluid (CSF) of a number of neurological conditions compared with healthy controls (HC) and is a candidate biomarker for neuroaxonal damage. The influence of age and sex is largely unknown, and levels across neurological disorders have not been compared systematically to date. Objectives: To assess the associations of age, sex, and diagnosis with NfL in CSF (cNfL) and to evaluate its potential in discriminating...
9 CitationsSource
#1Carel F. W. Peeters (PHRI: Public Health Research Institute)H-Index: 1
#2Wiel van de MaH-Index: 28
Last. Wessel N. van WieringenH-Index: 22
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Many modern statistical applications ask for the estimation of a covariance (or precision) matrix in settings where the number of variables is larger than the number of observations. There exists a broad class of ridge-type estimators that employs regularization to cope with the subsequent singularity of the sample covariance matrix. These estimators depend on a penalty parameter and choosing its value can be hard, in terms of being computationally unfeasible or tenable only for a restricted set...
#1Amber van Broekhoven (VUMC: Vanderbilt University Medical Center)
#2Paul A. J. Krijnen (VUMC: Vanderbilt University Medical Center)
Last. Alexander B. A. Vonk (VUMC: Vanderbilt University Medical Center)H-Index: 1
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Background: Recently, it was shown that 12 weeks of lipopolysaccharide (LPS) administration to nonatherosclerotic mice induced thickening of the aortic heart valve (AV). Whether such effects may also occur even earlier is unknown. As most patients with AV stenosis also have atherosclerosis, we studied the short-term effect of LPS on the AVs in an atherosclerotic mouse model. Methods: ApoE*3Leiden mice, on an atherogenic diet, were injected intraperitoneally with either LPS or phosphate buffered ...
#1Viktorian Miok (VUmc: VU University Medical Center)H-Index: 2
#2Saskia M. Wilting (VUmc: VU University Medical Center)H-Index: 20
Last. Wessel N. van Wieringen (VU: VU University Amsterdam)H-Index: 22
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Time-course omics experiments enable the reconstruction of the dynamics of the cellular regulatory network. Here, we describe the means for this reconstruction and the downstream exploitation of the inferred network. It is assumed that one of the various vector-autoregressive models (VAR) models presented here serves as a reasonably accurate description of the time-course omics data. The models are estimated through ridge penalized likelihood maximization, accompanied by functionality for the de...
#1Gino B. KpogbezanH-Index: 2
#2Wiel van de MaH-Index: 28
Last. Aad van der VaartH-Index: 31
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We introduce a sparse high-dimensional regression approach that can incorporate prior information on the regression parameters and can borrow information across a set of similar datasets. Prior information may for instance come from previous studies or genomic databases, and information borrowed across a set of genes or genomic networks. The approach is based on prior modelling of the regression parameters using the horseshoe prior, with a prior on the sparsity index that depends on external inf...
Computational efficient evaluation of penalized estimators of multivariate exponential family distributions is sought. These distributions encompass amongst others Markov random fields with variates of mixed type (e.g. binary and continuous) as special case of interest. The model parameter is estimated by maximization of the pseudo-likelihood augmented with a convex penalty. The estimator is shown to be consistent. With a world of multi-core computers in mind, a computationally efficient paralle...