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Making sense of Omics

Statistics for Omics

Welcome to the site of the Statistics for Omics unit! Our aim is to link omics to clinical response by novel, problem-specific statistical methods.

As part of the Department of Epidemiology and Biostatistics of the VU University Medical Center, our unit is involved in consultancy, research and teaching. More information about who we are, our work and how to reach us can be found in these pages.

Statistics for Omics

Statistics

Networks                                                                                                                                                                              Our research generates methods to learn molecular network from omics data. In particular, identifying (parts of these) networks to be differential between disease stages is a first step towards network medicine.

Integrated analysis of omics datasets 
Our research also involves methods to unravel associations between different types of molecular profiles. These make use of many molecular features at the same time, and are ideal to be used in genome-wide studies.

Clinical prediction using co-data 
Omics data is 2 x Big data: a) number of features ánd b) sources of auxiliary data: co-data. We develop methods that jointly use co-data and the main data, rendering better predictions and markers for several applications.

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Omics

Omics data refers to the high-throughput quantification of some pool of molecular molecules. Often, these data have more features than observations. Our group provides statistical support for the processing and analysis of a wide variety of omics data, such as genomicmetabolomic, and microbiomic data. Our expertise ranges from microarrays to next-generation sequencing platforms for genomics, and includes various platforms for metabolomics and microbiomics.

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Software & Support

Research Support
Omics data analysis support is core business for our group. We supply tailored solutions for a variety of omics data analysis questions in the VUmc, covering study design, preprocessing and downstream analysis. Our focus is cancer genomics, but our support extends towards others diseases, like Alzheimer.

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Software
Software is the tool for disseminating our research. We have contributed >15 R packages (>30,000 downloads per year) to well-known public repositories like CRAN, Bioconductor and Github.

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Latest News

New software available: gren

30-07-2018

Adaptive group-regularized elastic net regression (gren) method is implemented in an R package and it is now available on CRAN.

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Publication: Testing for pathway (in)activation using Gaussian graphical models

17-04-2018

Our paper on a two-sample test for the detection of a systematic difference between Gaussian graphical models appeared online in the Journal of the Royal Statistical Society - Series C.

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Two articles accepted

23-03-2018

March 2018: Two articles accepted!
1. van Wieringen WN, Peeters CFW, De Menezes RX, van de Wiel MA (2018). Testing for pathway (in)activation using Gaussian graphical models. To appear in JRSS-C.
2. van de Wiel MA, te Beest DE, Münch M (2018). Learning from a lot: Empirical Bayes in high-dimensional model-based prediction settings. To appear in Scand J Stat.
 

 

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