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A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets

Lai, C. (author), Reinders, M.J. (author), Van 't Veer, L.J. (author), Wessels, L.F. (author)

journal article 2006

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A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets

Lai, C. (author), Reinders, M.J.T. (author), Van't Veer, L.J. (author), Wessels, L.F.A. (author)

journal article 2006

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Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens

De Ridder, J. (author), Uren, A. (author), Kool, J. (author), Reinders, M. (author), Wessels, L. (author)

Retroviral insertional mutagenesis screens, which identify genes involved in tumor development in mice, have yielded a substantial number of retroviral integration sites, and this number is expected to grow substantially due to the introduction of high-throughput screening techniques. The data of various retroviral insertional mutagenesis...

journal article 2006

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Exploiting combinatorial cultivation conditions to infer transcriptional regulation

Knijnenburg, T.A. (author), De Winde, J.H. (author), Daran, J.M. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

journal article 2007

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SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets

Lai, C. (author), Horlings, H.M. (author), Van De Vijver, M.J. (author), Van Beers, E.H. (author), Nederlof, P.M. (author), Wessels, L.F.A. (author), Reinders, M.J.T. (author)

journal article 2007

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Exploiting combinatorial cultivation conditions to infer transcriptional regulation

Knijnenburg, T.A. (author), De Winde, J.H. (author), Daran, J.M. (author), Daran-Lapujade, P. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

journal article 2007

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Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes

De Ridder, J. (author), Kool, J. (author), Uren, A. (author), Bot, J. (author), Wessels, L. (author), Reinders, M. (author)

Motivation: Cancers are caused by an accumulation of multiple independent mutations that collectively deregulate cellular pathways, e.g. such as those regulating cell division and cell-death. The publicly available Retroviral Tagged Cancer Gene Database (RTCGD) contains the data of many insertional mutagenesis screens, in which the virally...

journal article 2007

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Module-Based Outcome Prediction Using Breast Cancer Compendia

Van Vliet, M.H. (author), Klijn, C.N. (author), Wessels, L.F. (author), Reinders, M.J.T. (author)

Background. The availability of large collections of microarray datasets (compendia), or knowledge about grouping of genes into pathways (gene sets), is typically not exploited when training predictors of disease outcome. These can be useful since a compendium increases the number of samples, while gene sets reduce the size of the feature space....

journal article 2007

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Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Meuleman, W. (author), Engwegen, J.Y.M.N. (author), Gast, M.C.W. (author), Beijnen, J.H. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

OA Fund TU Delft

journal article 2008

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A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer

Reyal, F. (author), Van Vliet, M.H. (author), Armstrong, N.J. (author), Horlings, H.M. (author), De Visser, K.E. (author), Kok, M. (author), Teschendorff, A.E. (author), Mook, S. (author), Van 't Veer, L. (author), Caldas, C. (author), Salmon, R.J. (author), Vijver, M.J. (author), Wessels, L.F.A. (author)

journal article 2008

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Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability

Van Vliet, M.H. (author), Reyal, F. (author), Horlings, H.M. (author), Van De Vijver, M.J. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

OA fund TU Delft

journal article 2008

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Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data

Klijn, C.N. (author), Holstege, H. (author), De Ridder, J. (author), Liu, X. (author), Reinders, M. (author), Jonkers, J. (author), Wessels, L. (author)

Tumor formation is in part driven by DNA copy number alterations (CNAs), which can be measured using microarray-based Comparative Genomic Hybridization (aCGH). Multiexperiment analysis of aCGH data from tumors allows discovery of recurrent CNAs that are potentially causal to cancer development. Until now, multiexperiment aCGH data analysis has...

journal article 2008

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Combinatorial influence of environmental parameters on transcription factor activity

Knijnenburg, T.A. (author), Wessels, L.F.A. (author), Reinders, M.J.T. (author)

Motivation: Cells receive a wide variety of environmental signals, which are often processed combinatorially to generate specific genetic responses. Changes in transcript levels, as observed across different environmental conditions, can, to a large extent, be attributed to changes in the activity of transcription factors (TFs). However, in...

journal article 2008

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Biclustering Sparse Binary Genomic Data

Van Uitert, M. (author), Meuleman, W. (author), Wessels, L.F.A. (author)

Genomic datasets often consist of large, binary, sparse data matrices. In such a dataset, one is often interested in finding contiguous blocks that (mostly) contain ones. This is a biclustering problem, and while many algorithms have been proposed to deal with gene expression data, only two algorithms have been proposed that specifically deal...

journal article 2008

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Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data

Knijnenburg, T.A. (author), Daran, J.M.G. (author), Van den Broek, M.A. (author), Daran-Lapujade, P.A.S. (author), De Winde, J.H. (author), Pronk, J.T. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

OA Fund TU delft Background: Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on...

journal article 2009

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Analysis of mass spectrometry data using sub-spectra

Meuleman, W. (author), Engwegen, J.Y.M.N. (author), Gast, M.C.W. (author), Wessels, L.F.A. (author), Reinders, M.J.T. (author)

journal article 2009

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Knowledge driven decomposition of tumor expression profiles

Van Vliet, M.H. (author), Wessels, L.F.A. (author), Reinders, M.J.T. (author)

journal article 2009

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Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach

Klijn, C. (author), Bot, J. (author), Adams, D.J. (author), Reinders, M. (author), Wessels, L. (author), Jonkers, J. (author)

Tumorigenesis is a multi-step process in which normal cells transform into malignant tumors following the accumulation of genetic mutations that enable them to evade the growth control checkpoints that would normally suppress their growth or result in apoptosis. It is therefore important to identify those combinations of mutations that...

journal article 2010

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Inferring combinatorial association logic networks in multimodal genome-wide screens

De Ridder, J. (author), Gerrits, A. (author), Bot, J. (author), De Haan, G. (author), Reinders, M. (author), Wessels, L. (author)

We propose an efficient method to infer combinatorial association logic networks from multiple genome-wide measurements from the same sample. We demonstrate our method on a genetical genomics dataset, in which we search for Boolean combinations of multiple genetic loci that associate with transcript levels. Our method provably finds the global...

journal article 2010

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Cross-species comparison of aCGH data from mouse and human BRCA1- and BRCA2-mutated breast cancers

Holstege, H. (author), Van Beers, E. (author), Velds, A. (author), Liu, X. (author), Joosse, S.A. (author), Klarenbeek, S. (author), Schut, E. (author), Kerkhoven, R. (author), Klijn, C.N. (author), Wessels, L.F.A. (author), Nederlof, P.M. (author), Jonkers, J. (author)

Background: Genomic gains and losses are a result of genomic instability in many types of cancers. BRCA1- and BRCA2-mutated breast cancers are associated with increased amounts of chromosomal aberrations, presumably due their functions in genome repair. Some of these genomic aberrations may harbor genes whose absence or overexpression may give...

journal article 2010