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

Mourragui, S.M.C. (author), Loog, M. (author), van der Wiel, Mark A. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

Motivation: Cell lines and patient-derived xenografts (PDXs) have been used extensively to understand the molecular underpinnings of cancer. While core biological processes are typically conserved, these models also show important differences compared to human tumors, hampering the translation of findings from pre-clinical models to the human...

journal article 2019

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RUBIC identifies driver genes by detecting recurrent DNA copy number breaks

Van Dyk, H.O. (author), Hoogstraat, M (author), ten Hoeve, J (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

The frequent recurrence of copy number aberrations across tumour samples is a reliable hallmark of certain cancer driver genes. However, state-of-the-art algorithms for detecting recurrent aberrations fail to detect several known drivers. In this study, we propose RUBIC, an approach that detects recurrent copy number breaks, rather than...

journal article 2016

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Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors

Klijn, C. (author), Koudijs, M.J. (author), Kool, J. (author), Ten Hoeve, J. (author), Boer, M. (author), De Moes, J. (author), Akhtar, W. (author), Van Miltenburg, M. (author), Vendel-Zwaagstra, A. (author), Reinders, M.J.T. (author), Adams, D.J. (author), Van Lohuizen, M. (author), Hilkens, J. (author), Wessels, L.F.A. (author), Jonkers, J. (author)

Cancer develops through a multistep process in which normal cells progress to malignant tumors via the evolution of their genomes as a result of the acquisition of mutations in cancer driver genes. The number, identity and mode of action of cancer driver genes, and how they contribute to tumor evolution is largely unknown. This study deployed...

journal article 2013

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A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control

Van Dyk, E. (author), Reinders, M.J.T. (author), Wessels, L.F.A. (author)

Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including CMAR, STAC, GISTIC and KC SMART. GISTIC is widely used and...

journal article 2013

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Integration of Clinical and Gene Expression Data Has a Synergetic Effect on Predicting Breast Cancer Outcome

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

Breast cancer outcome can be predicted using models derived from gene expression data or clinical data. Only a few studies have created a single prediction model using both gene expression and clinical data. These studies often remain inconclusive regarding an obtained improvement in prediction performance. We rigorously compare three different...

journal article 2012

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KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data

De Ronde, J.J. (author), Klijn, C. (author), Velds, A. (author), Holstege, H. (author), Reinders, M.J.T. (author), Jonkers, J. (author), Wessels, L.F.A. (author)

Background: Most approaches used to find recurrent or differential DNA Copy Number Alterations (CNA) in array Comparative Genomic Hybridization (aCGH) data from groups of tumour samples depend on the discretization of the aCGH data to gain, loss or no-change states. This causes loss of valuable biological information in tumour samples, which are...

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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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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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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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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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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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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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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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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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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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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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