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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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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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Hulsman, M. (author), Mentink, A. (author), Van Someren, E.P. (author), Dechering, K.J. (author), De Boer, J. (author), Reinders, M.J.T. (author)Background: Oligonucleotide arrays have become one of the most widely used high-throughput tools in biology. Due to their sensitivity to experimental conditions, normalization is a crucial step when comparing measurements from these arrays. Normalization is, however, far from a solved problem. Frequently, we encounter datasets with significant...journal article 2010
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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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- van den Berg, B.A. (author), Reinders, M.J.T. (author), Bellomo, Domenico (author) poster 2009
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Sontrop, H.M.J. (author), Moerland, P.D. (author), Van den Ham, R. (author), Reinders, M.J.T. (author), Verhaegh, W.F.J. (author)Background: Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement...journal article 2009
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De Groot, M.J.L. (author), Van Berlo, R.J.P. (author), Van Winden, W.A. (author), Verheijen, P.J.T. (author), Reinders, M.J.T. (author), De Ridder, D. (author)Motivation: Many enzymes are not absolutely specific, or even promiscuous: they can catalyze transformations of more compounds than the traditional ones as listed in e.g. KEGG. This information is currently only available in databases, such as the BRENDA enzyme activity database. In this paper, we propose to model enzyme aspecificity by...journal article 2009
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- 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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- Van Vliet, M.H. (author), Wessels, L.F.A. (author), Reinders, M.J.T. (author) journal article 2009
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Ten Holt, G.A. (author), Arendsen, J. (author), De Ridder, H. (author), Van Doorn, A.J. (author), Reinders, M.J.T. (author), Hendriks, E.A. (author)Current automatic sign language recognition (ASLR) seldom uses perceptual knowledge about the recognition of sign language. Using such knowledge can improve ASLR because it can give an indication which elements or phases of a sign are important for its meaning. Also, the current generation of data-driven ASLR methods has shortcomings which may...conference paper 2009
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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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Van Nes, P. (author), Bellomo, D. (author), Reinders, M.J.T. (author), De Ridder, D. (author)In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we extend a previously proposed method by...journal article 2009
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De Ridder, D. (author), Li, Y. (author), De Groot, M.J.L. (author), Reinders, M.J.T. (author)Comparative analysis of metabolic networks in multiple species yields important information on their evolution, and has great practical value in metabolic engineering, human disease analysis, drug design etc. In this work, we aim to systematically search for conserved pathways in two species, quantify their similarities, and focus on the...journal article 2008
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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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Hendriks, E.A. (author), Reinders, M.J.T. (author)Methods commonly used for speech and sign language recognition often rely on outputs of Hidden Markov Models (HMM) or Dynamic TimeWarping (DTW) for classification, which aremerely factorized observation likelihoods. Instead, we propose to use Statistical DTW (SDTW) only for warping, while classifying the synchronized features with either of two...conference paper 2008
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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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Wang, J. (author), Robertson, S. (author), De Vries, A.P. (author), Reinders, M.J.T. (author)Collaborative filtering is concerned with making recommendations about items to users. Most formulations of the problem are specifically designed for predicting user ratings, assuming past data of explicit user ratings is available. However, in practice we may only have implicit evidence of user preference; and furthermore, a better view of the...journal article 2008
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Lichtenauer, J.F. (author), Hendriks, E.A (author), Reinders, M.J.T. (author)To recognize speech, handwriting, or sign language, many hybrid approaches have been proposed that combine Dynamic Time Warping (DTW) or Hidden Markov Models (HMMs) with discriminative classifiers. However, all methods rely directly on the likelihood models of DTW/HMM. We hypothesize that time warping and classification should be separated...journal article 2008
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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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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