Searched for: author:"De Ridder, D."
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Groß, C. (author), Derks, Martijn (author), Megens, Hendrik Jan (author), Bosse, Mirte (author), Groenen, Martien A.M. (author), Reinders, M.J.T. (author), de Ridder, D. (author)
Background: In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by...
journal article 2020
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Groß, C. (author), de Ridder, D. (author), Reinders, M.J.T. (author)
Background: Predicting the deleteriousness of observed genomic variants has taken a step forward with the introduction of the Combined Annotation Dependent Depletion (CADD) approach, which trains a classifier on the wealth of available human genomic information. This raises the question whether it can be done with less data for non-human...
journal article 2018
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Derks, Martijn F.L. (author), Megens, Hendrik-Jan (author), Bosse, Mirte (author), Visscher, Jeroen (author), Peeters, Katrijn (author), Bink, Marco C.A.M. (author), Vereijken, Addie (author), Groß, C. (author), de Ridder, D. (author), Reinders, M.J.T. (author), Groenen, Martien A.M. (author)
Background: Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genetic variation can impact population fitness substantially. In this study, we examined the genome of commercial purebred chicken...
journal article 2018
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Gritsenko, A. (author), Weingarten-Gabbay, Shira (author), Elias-Kirma, Shani (author), Nir, Ronit (author), de Ridder, D. (author), Segal, Eran (author)
Translation of mRNAs through Internal Ribosome Entry Sites (IRESs) has emerged as a prominent mechanism of cellular and viral initiation. It supports cap-independent translation of select cellular genes under normal conditions, and in conditions when cap-dependent translation is inhibited. IRES structure and sequence are believed to be...
journal article 2017
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Brand, H.K. (author), Ahout, I.M.L. (author), De Ridder, D. (author), Diepen, A. (author), Li, Y. (author), Zaalberg, M. (author), Andeweg, A. (author), Roeleveld, N. (author), De Groot, R. (author), Warris, A. (author), Hermans, P.W.M. (author), Ferwerda, G. (author), Staal, F.J.T. (author)
Background Respiratory viral infections follow an unpredictable clinical course in young children ranging from a common cold to respiratory failure. The transition from mild to severe disease occurs rapidly and is difficult to predict. The pathophysiology underlying disease severity has remained elusive. There is an urgent need to better...
journal article 2015
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Yao, Y. (author), Docter, M. (author), De Ridder, D. (author), Joo, C. (author)
Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we...
journal article 2015
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Van den Broek, M. (author), Bolat, I. (author), Nijkamp, J.F. (author), Ramos, E. (author), Luttik, M.A.H. (author), Koopman, F. (author), Geertman, J.M. (author), De Ridder, D. (author), Pronk, J.T. (author), Daran, J.M. (author)
Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers...
journal article 2015
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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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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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Hebly, M. (author), De Ridder, D. (author), De Hulster, E.A. (author), De la Torre Cortes, P. (author), Pronk, J.T. (author), Daran-Lapujade, P.A.S. (author)
Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures...
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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Oud, B. (author), Guadalupe-Medina, V. (author), Nijkamp, J.F. (author), De Ridder, D. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author), Daran, J.G. (author)
Laboratory evolution of the yeast Saccharomyces cerevisiae in bioreactor batch cultures yielded variants that grow as multicellular, fast-sedimenting clusters. Knowledge of the molecular basis of this phenomenon may contribute to the understanding of natural evolution of multicellularity and to manipulating cell sedimentation in laboratory and...
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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Van Dongen, M.N. (author), Serdijn, W.A. (author), De Ridder, D. (author)
Tissue- or neurostimulator, comprising a power supply (Vdd) and an implantable pulse generator (IPG) powered by said power supply (Vdd) to which an electrode or electrodes are connected or connectable for delivery of pulses from the pulse generator to a patient's region of interest or tissue so as to provide said region of interest or tissue...
patent 2013
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van den Berg, B.A. (author), Thornton, JM (author), Reinders, M.J.T. (author), de Ridder, D. (author), Beer, TAP (author)
Our aim is to prioritize human missense mutations by their probability of being disease causing. Such a computational method could be used to obtain a reduced set of mutations with a relatively large fraction of disease related mutations, thereby aiding in the search for this type of mutation within a large mutation set.<br/><br/>Whereas a range...
poster 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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Winterbach, W. (author), De Ridder, D. (author), Wang, H.J. (author), Reinders, M. (author), Van Mieghem, P. (author)
conference paper 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
Searched for: author:"De Ridder, D."
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