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Taskesen, E. (author), Babaei, S. (author), Reinders, M.J.M. (author), De Ridder, J. (author)Background Acute Myeloid Leukemia (AML) is characterized by various cytogenetic and molecular abnormalities. Detection of these abnormalities is important in the risk-classification of patients but requires laborious experimentation. Various studies showed that gene expression profiles (GEP), and the gene signatures derived from GEP, can be used...journal article 2015
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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 Delftjournal article 2008
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Taskesen, E. (author), Hoogeboezem, R. (author), Delwel, R. (author), Reinders, M.J.T. (author)Probing protein-deoxyribonucleic acid (DNA) is gaining popularity as it sheds light on molecular mechanisms that regulate the expression of genes. Currently, tiling-arrays and next-generation sequencing technology can be used to measure these interactions. Both methods generate a signal over the genome in which contiguous regions of peaks on the...journal article 2013
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Nijkamp, J.F. (author), Winterbach, W. (author), Van den Broek, M. (author), Daran, J.M. (author), Reinders, M.J.T. (author), De Ridder, D. (author)De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for...journal article 2010
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Taskesen, E. (author), Beekman, R. (author), De Ridder, J. (author), Wouters, B.J. (author), Peeters, J.K. (author), Touw, I.P. (author), Reinders, M.J.T. (author), Delwel, R. (author)Background: Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased), the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., contiguous probes with...journal article 2010
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Sontrop, H.M.J. (author), Verhaegh, W.F.J. (author), Reinders, M.J.T. (author), Moerland, P.D. (author)In recent years increasing evidence appeared that breast cancer may not constitute a single disease at the molecular level, but comprises a heterogeneous set of subtypes. This suggests that instead of building a single monolithic predictor, better predictors might be constructed that solely target samples of a designated subtype, which are...journal article 2011
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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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Gehrmann, T. (author), Reinders, M.J.T. (author)Background: With more and more genomes being sequenced, detecting synteny between genomes becomes more and more important. However, for microorganisms the genomic divergence quickly becomes large, resulting in different codon usage and shuffling of gene order and gene elements such as exons. Results: We present Proteny, a methodology to detect...journal article 2015
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- 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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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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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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Abbott, D.A. (author), Knijnenburg, T.A. (author), De Poorter, L.M. (author), Reinders, M.J. (author), Pronk, J.T. (author), Van Maris, A.J. (author)Transcriptional responses to four weak organic acids (benzoate, sorbate, acetate and propionate) were investigated in anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. To enable quantitative comparison of the responses to the acids, their concentrations were chosen such that they caused a 50% decrease of the biomass...journal article 2007
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Hulsman, M. (author), Reinders, M.J.T. (author), De Ridder, D. (author)In recent years, more and more high-throughput data sources useful for protein complex prediction have become available (e.g., gene sequence, mRNA expression, and interactions). The integration of these different data sources can be challenging. Recently, it has been recognized that kernel-based classifiers are well suited for this task. However...journal article 2008
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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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- 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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Wang, J. (author), Pouwelse, J. (author), Fokker, J. (author), De Vries, A.P. (author), Reinders, M.J.T. (author)We introduce personalization on Tribler, a peer-to-peer (P2P) television system. Personalization allows users to browse programs much more efficiently according to their taste. It also enables to build social networks that can improve the performance of current P2P systems considerably, by increasing content availability, trust and the...journal article 2007
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- Veenman, C.J. (author), Reinders, M.J.T. (author), Backer, E. (author) journal article 2003
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Winterbach, W. (author), Van Mieghem, P. (author), Reinders, M. (author), Wang, H. (author), De Ridder, D. (author)Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that...journal article 2013
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Van den Berg, B.A. (author), Reinders, M.J. (author), Roubos, J.A. (author), De Ridder, D. (author)Background Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software tools are available for both feature extraction and classifier construction, their application is not straightforward,...journal article 2014
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Van den Akker, E.B. (author), Passtoors, W.M. (author), Jansen, R. (author), Van Zwet, E.W. (author), Goeman, J.J. (author), Hulsman, M. (author), Emilsson, V. (author), Perola, M. (author), Willemsen, G. (author), Penninx, B.W.J.H. (author), Heijmans, B.T. (author), Maier, A.B. (author), Boomsma, D.I. (author), Kok, J.N. (author), Slagboom, P.E. (author), Reinders, M.J.T. (author), Beekman, M. (author)The bodily decline that occurs with advancing age strongly impacts on the prospects for future health and life expectancy. Despite the profound role of age in disease etiology, knowledge about the molecular mechanisms driving the process of aging in humans is limited. Here, we used an integrative network-based approach for combining multiple...journal article 2013