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Lago Garcia, J. (author), De Ridder, Fjo (author), Mazairac, Wiet (author), De Schutter, B.H.K. (author)
To mitigate the effects of the intermittent generation of renewable energy sources, reliable and efficient energy storage is critical. Since nearly 80% of households energy consumption is destined to water and space heating, thermal energy storage is particularly important. In this context, we propose and validate a new model for one of the...
journal article 2019
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Lago Garcia, J. (author), De Ridder, Fjo (author), Vrancx, Peter (author), De Schutter, B.H.K. (author)
Motivated by the increasing integration among electricity markets, in this paper we propose two different methods to incorporate market integration in electricity price forecasting and to improve the predictive performance. First, we propose a deep neural network that considers features from connected markets to improve the predictive...
journal article 2018
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Lago Garcia, J. (author), De Brabandere, Karel (author), De Ridder, Fjo (author), De Schutter, B.H.K. (author)
Due to the increasing integration of solar power into the electrical grid, forecasting short-term solar irradiance has become key for many applications, e.g. operational planning, power purchases, reserve activation, etc. In this context, as solar generators are geographically dispersed and ground measurements are not always easy to obtain,...
journal article 2018
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Lago Garcia, J. (author), De Ridder, Fjo (author), De Schutter, B.H.K. (author)
In this paper, a novel modeling framework for forecasting electricity prices is proposed. While many predictive models have been already proposed to perform this task, the area of deep learning algorithms remains yet unexplored. To fill this scientific gap, we propose four different deep learning models for predicting electricity prices and...
journal article 2018
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Heringa, Jaap (author), Reinders, M.J.T. (author), Abeln, Sanne (author), De Ridder, Jeroen (author)
contribution to periodical 2016
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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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Allahyar, A. (author), De Ridder, J. (author)
Motivation: Breast cancer outcome prediction based on gene expression profiles is an important strategy for personalize patient care. To improve performance and consistency of discovered markers of the initial molecular classifiers, network-based outcome prediction methods (NOPs) have been proposed. In spite of the initial claims, recent studies...
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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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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Rijlaarsdam, M.A. (author), Tax, D.M.J. (author), Gillis, A.J.M. (author), Dorssers, L.C.J. (author), Koestler, D.C. (author), De Ridder, J. (author), Looijenga, L.H.J. (author)
The cell of origin of the five subtypes (I-V) of germ cell tumors (GCTs) are assumed to be germ cells from different maturation stages. This is (potentially) reflected in their methylation status as fetal maturing primordial germ cells are globally demethylated during migration from the yolk sac to the gonad. Imprinted regions are erased in the...
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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Li, J. (author), Vermeeren, A.P.O.S. (author), De Ridder, H. (author)
In this article, we present examples of using designerly ways to explore “crowd” phenomenon in a cross-disciplinary project named EWiDS. The phrase ‘designerly ways’ refers to visual communication methods such as drawings and videos, which are widely acknowledged as effective approaches to crossdisciplinary collaboration. This study started with...
journal article 2014
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De Ridder, J. (author), Meysman, P. (author), Oluwagbemi, O. (author), Abeel, T. (author)
Contributing to a student organization, such as the International Society for Computational Biology Student Council (ISCB-SC) and its Regional Student Group (RSG) program, takes time and energy. Both are scarce commodities, especially when you are trying to find your place in the world of computational biology as a graduate student. It comes as...
journal article 2014
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Hulsman, M. (author), Dimitrakopoulos, C. (author), De Ridder, J. (author)
MOTIVATION: The network architecture of physical protein interactions is an important determinant for the molecular functions that are carried out within each cell. To study this relation, the network architecture can be characterized by graph topological characteristics such as shortest paths and network hubs. These characteristics have an...
journal article 2014
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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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De Jong, J. (author), Akhtar, W. (author), Badhai, J. (author), Rust, A.G. (author), Rad, R. (author), Hilkens, J. (author), Berns, A. (author), Van Lohuizen, M. (author), Wessels, L.F.A. (author), De Ridder, J. (author)
The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of to unselected...
journal article 2014
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