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Gritsenko, A.A. (author), Hulsman, M. (author), Reinders, M.J.T. (author), De Ridder, D. (author)Translation of RNA to protein is a core process for any living organism. While for some steps of this process the effect on protein production is understood, a holistic understanding of translation still remains elusive. In silico modelling is a promising approach for elucidating the process of protein synthesis. Although a number of...journal article 2015
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Babaei, S. (author), Mahfouz, A.M.E.T.A. (author), Hulsman, M. (author), Lelieveldt, B.P.F. (author), De Ridder, J. (author), Reinders, M.J.T. (author)The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains...journal article 2015
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Van den Berg, B.A. (author), Reinders, M.J.T. (author), De Ridder, D. (author), De Beer, T.A.P. (author)A variety of methods that predict human nonsynonymous single nucleotide polymorphisms (SNPs) to be neutral or disease-associated have been developed over the last decade. These methods are used for pinpointing disease-associated variants in the many variants obtained with next-generation sequencing technologies. The high performances of current...journal article 2015
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Babaei, S. (author), Akhtar, W. (author), De Jong, J. (author), Reinders, M.J.T. (author), De Ridder, J. (author)Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D...journal article 2015
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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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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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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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Babaei, S. (author), Hulsman, M. (author), Reinders, M.J.T. (author), De Ridder, J. (author)Background Delineating the molecular drivers of cancer, i.e. determining cancer genes and the pathways which they deregulate, is an important challenge in cancer research. In this study, we aim to identify pathways of frequently mutated genes by exploiting their network neighborhood encoded in the protein-protein interaction network. To this end...journal article 2013
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Van den Berg, B.A. (author), Reinders, M.J.T. (author), Hulsman, M. (author), Wu, L. (author), Pel, H.J. (author), Roubos, J.A. (author), De Ridder, D. (author)Protein sequence features are explored in relation to the production of over-expressed extracellular proteins by fungi. Knowledge on features influencing protein production and secretion could be employed to improve enzyme production levels in industrial bioprocesses via protein engineering. A large set, over 600 homologous and nearly 2,000...journal article 2012
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Nikerel, I.E. (author), Berkhout, J. (author), Hu, F. (author), Teusink, B. (author), Reinders, M.J.T. (author), De Ridder, D. (author)Understanding cellular regulation of metabolism is a major challenge in systems biology. Thus far, the main assumption was that enzyme levels are key regulators in metabolic networks. However, regulation analysis recently showed that metabolism is rarely controlled via enzyme levels only, but through non-obvious combinations of hierarchical ...journal article 2012
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Gritsenko, A.A. (author), Nijkamp, J.F. (author), Reinders, M.J.T. (author), De Ridder, D. (author)Motivation: The increasing availability of second-generation highthroughput sequencing (HTS) technologies has sparked a growing interest in de novo genome sequencing. This in turn has fueled the need for reliable means of obtaining high-quality draft genomes from short-read sequencing data. The millions of reads usually involved in HTS...journal article 2012
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Nijkamp, J.F. (author), Van den Broek, M.A. (author), Datema, E. (author), De Kok, S. (author), Bosman, L. (author), Luttik, M.A.H. (author), Daran-Lapujade, P.A.S. (author), Vongsangnak, W. (author), Nielsen, J. (author), Heijne, W.H.M. (author), Klaassen, P. (author), Paddon, C.J. (author), Platt, D. (author), Kötter, P. (author), Van Ham, R.C. (author), Reinders, M.J.T. (author), Pronk, J.T. (author), De Ridder, D. (author), Daran, J.M. (author)Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae...journal article 2012
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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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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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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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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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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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