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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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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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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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- Veenman, C.J. (author), Reinders, M.J.T. (author) journal article 2005
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- Veenman, C.J. (author), Reinders, M.J.T. (author), Backer, E. (author) journal article 2001
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- 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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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.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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- 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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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. (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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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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De Ridder, J. (author), Uren, A. (author), Kool, J. (author), Reinders, M. (author), Wessels, L. (author)Retroviral insertional mutagenesis screens, which identify genes involved in tumor development in mice, have yielded a substantial number of retroviral integration sites, and this number is expected to grow substantially due to the introduction of high-throughput screening techniques. The data of various retroviral insertional mutagenesis...journal article 2006
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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 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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Mahfouz, A. (author), Ziats, M.N. (author), Rennert, O.M. (author), Lelieveldt, B.P.F. (author), Reinders, M.J.T. (author)Autism spectrum disorder (ASD) is a neurodevelopmental syndrome known to have a significant but complex genetic etiology. Hundreds of diverse genes have been implicated in ASD; yet understanding how many genes, each with disparate function, can all be linked to a single clinical phenotype remains unclear. We hypothesized that understanding...journal article 2015
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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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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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- Rares, A. (author), Reinders, M.J.T. (author), Biemond, J. (author) journal article 2005
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Apostolou, G. (author), Reinders, A.H.M.E. (author), Verwaal, M. (author)This article presents a simple comparative model which has been developed for the estimation of the performance of photovoltaic (PV) products' cells in indoor environments. The model predicts the performance of PV solar cells, as a function of the distance from a spectrum of artificial (fluorescent light, halogen light, and light-emitting diodes...journal article 2016