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Altered microRNA expression associated with chromosomal changes contributes to cervical carcinogenesis
Little is known about the alterations in microRNA (miRNA) expression patterns during the consecutive stages of cervical cancer development and their association with chromosomal instability. In this… Expand
Survival prediction using gene expression data: A review and comparison
- W. N. Wieringen, David Kun, Regina Hampel, A. Boulesteix
- Biology, Computer Science
- Comput. Stat. Data Anal.
- 1 March 2009
We give an inventory of methods that have been used to model survival using gene expression is given. Expand
CGHcall: calling aberrations for array CGH tumor profiles
- M. A. V. D. Wiel, K. I. Kim, S. Vosse, W. N. Wieringen, S. Wilting, B. Ylstra
- Computer Science, Medicine
- 1 April 2007
CGHcall achieves high calling accuracy for array CGH data by effective use of breakpoint information from segmentation and by inclusion of several biological concepts that are ignored by existing algorithms. Expand
Ridge estimation of inverse covariance matrices from high-dimensional data
The ridge estimation of the precision matrix is investigated in the setting where the number of variables is large relative to the sample size. Expand
CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss
An algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. Expand
Lecture notes on ridge regression
- W. N. Wieringen
- 30 September 2015
The linear regression model cannot be fitted to high-dimensional data, as the high-dimensionality brings about empirical non-identifiability. Penalized regression overcomes this non-identifiability… Expand
Preprocessing and downstream analysis of microarray DNA copy number profiles
- M. A. V. D. Wiel, F. Picard, W. N. Wieringen, B. Ylstra
- Computer Science, Medicine
- Briefings Bioinform.
We discuss the typical characteristics of DNA copy number data, as measured by microarray technology and review the extensive literature on preprocessing methods such as segmentation and calling. Expand
Nonparametric testing for DNA copy number induced differential mRNA gene expression.
The central dogma of molecular biology relates DNA with mRNA. Array CGH measures DNA copy number and gene expression microarrays measure the amount of mRNA. Methods that integrate data from these two… Expand
Targeted Fused Ridge Estimation of Inverse Covariance Matrices from Multiple High-Dimensional Data Classes
- A. E. Bilgrau, C. F. Peeters, P. S. Eriksen, M. Bøgsted, W. N. Wieringen
- Mathematics, Biology
- J. Mach. Learn. Res.
- 26 September 2015
We consider the problem of jointly estimating multiple inverse covariance matrices from high-dimensional data consisting of distinct classes. Expand
Measurement system analysis for categorical measurements: Agreement and kappa-type indices
The standard method for the assessment of the precision of measurement systems that measure on a metric scale is the gauge R&R method, but this method is not applicable for measurement systems that… Expand