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Taskesen, E. (author), Staal, F.J.T. (author), Reinders, M.J.T. (author)Background The wingless-Int (WNT) pathway has an essential role in cell regulation of hematopoietic stem cells (HSC). For Acute Myeloid Leukemia (AML), the malignant counterpart of HSC, currently only a selective number of genes of the WNT pathway are analyzed by using either gene expression or DNA-methylation profiles for the identification of...journal article 2015
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Mahfouz, A.M.E.T.A. (author), Van de Giessen, M. (author), Van der Maaten, L.J.P. (author), Huisman, S.M.H. (author), Reinders, M.J.T. (author), Hawrylycz, M.J. (author), Lelieveldt, B.P.F. (author)The Allen Brain Atlases enable the study of spatially resolved, genome-wide gene expression patterns across the mammalian brain. Several explorative studies have applied linear dimensionality reduction methods such as Principal Component Analysis (PCA) and classical Multi-Dimensional Scaling (cMDS) to gain insight into the spatial organization...journal article 2014
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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
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Straver, R. (author), Sistermans, E.A. (author), Holstege, H. (author), Visser, A. (author), Oudejans, C.B.M. (author), Reinders, M.J.T. (author)Genetic disorders can be detected by prenatal diagnosis using Chorionic Villus Sampling, but the 1:100 chance to result in miscarriage restricts the use to fetuses that are suspected to have an aberration. Detection of trisomy 21 cases noninvasively is now possible owing to the upswing of next-generation sequencing (NGS) because a small...journal article 2013
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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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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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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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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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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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Entrop, A.G. (author), Reinders, A.H.M.E. (author)Er is een experiment uitgevoerd met vier betonnen vloeren in een semiadiabatische omgeving. Twee vloeren bevatten PCMs en, ter referentie, twee vloeren geen PCMs. De opstelling moest op schaal een woning voorstellen met een raam op het zuiden. De omgevingscondities en de temperatuurontwikkelingen in de vloeren en boxen werden gemonitord. Het...journal article 2012
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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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Alves, H. (author), Van Ginkel, J. (author), Groen, N. (author), Hulsman, N. (author), Mentink, A. (author), Reinders, M.J.T. (author), Van Blitterswijk, C. (author), De Boer, J. (author)Human aging is associated with loss of function and regenerative capacity. Human bone marrow derived mesenchymal stromal cells (hMSCs) are involved in tissue regeneration, evidenced by their capacity to differentiate into several lineages and therefore are considered the golden standard for cell-based regeneration therapy. Tissue maintenance and...journal article 2012
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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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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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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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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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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