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Summer, G. (author), Kelder, T. (author), Radonjic, M. (author), van Bilsen, M. (author), Wopereis, S. (author), Heymans, S. (author)
Motivation: Much of the biological knowledge accumulated over the last decades is stored in different databases governed by various organizations and institutes. Integrating and connecting these vast knowledge repositories is an extremely useful method to support life sciences research and help formulate novel hypotheses. Results: We developed...
article 2016
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Summer, G. (author), Kelder, T. (author), Ono, K. (author), Radonjic, M. (author), Heymans, S. (author), Demchak, B. (author)
We developed cyNeo4j, a Cytoscape App to link Cytoscape and Neo4j databases to utilize the performance and storage capacities Neo4j offers. We implemented a Neo4j NetworkAnalyzer, ForceAtlas2 layout and Cypher component to demonstrate the possibilities a distributed setup of Cytoscape and Neo4j have. © The Author 2015. Published by Oxford...
article 2015
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Vlemmix, T. (author), Eskes, H.J. (author), Piters, A.J.M. (author), Schaap, M. (author), Sauter, F.J. (author), Kelder, H. (author), Levelt, P.F. (author)
A 14-month data set of MAX-DOAS (Multi-Axis Differential Optical Absorption Spectroscopy) tropospheric NO2 column observations in De Bilt, the Netherlands, has been compared with the regional air quality model Lotos-Euros. The model was run on a 7×7 km2 grid, the same resolution as the emission inventory used. A study was performed to assess the...
article 2015
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Goelela, V.S. (author), Kelder, T. (author), Adriaens, M.E. (author), Evelo, C.T. (author), Radonijc, M. (author)
Background Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and...
article 2015
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Derous, D. (author), Kelder, T. (author), van Schothorst, E.M. (author), van Erk, M. (author), Voigt, A. (author), Klaus, S. (author), Keijer, J. (author), Radonjic, M. (author)
Health is influenced by interplay of molecular, physiological and environmental factors. To effectively maintain health and prevent disease, health-relevant relations need to be understood at multiple levels of biological complexity. Network-based methods provide a powerful platform for integration and mining of data and knowledge characterizing...
article 2015
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Kelder, T. (author), Verschuren, L. (author), van Ommen, B. (author), van Gool, A.J. (author), Radonjic, M. (author)
Background: Multifactorial diseases such as type 2 diabetes mellitus (T2DM), are driven by a complex network of interconnected mechanisms that translate to a diverse range of complications at the physiological level. To optimally treat T2DM, pharmacological interventions should, ideally, target key nodes in this network that act as determinants...
article 2014
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Kelder, T. (author), Stroeve, J.H.M. (author), Bijlsma, S. (author), Radonjic, M. (author), Roeselers, G. (author)
BACKGROUND: Recent evidence suggests that the gut microbiota plays an important role in human metabolism and energy homeostasis and is therefore a relevant factor in the assessment of metabolic health and flexibility. Understanding of these host–microbiome interactions aids the design of nutritional strategies that act via modulation of the...
article 2014
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Verschuren, L. (author), Wielinga, P.Y. (author), Kelder, T. (author), Radonjic, M. (author), Salic, K. (author), Kleemann, R. (author), van Ommen, B. (author), Kooistra, T. (author)
Background : Cardiac pathological hypertrophy is associated with a significantly increased risk of coronary heart disease and has been observed in diabetic patients treated with rosiglitazone whereas most published studies do not suggest a similar increase in risk of cardiovascular events in pioglitazone-treated diabetic subjects. This study...
article 2014
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Radonjic, M. (author), Wielinga, P.Y. (author), Wopereis, S. (author), Kelder, T. (author), Goelela, V.S. (author), Verschuren, L. (author), Toet, K. (author), van Duyvenvoorde, W. (author), van der Werff van der Vat, B. (author), Stroeve, J.H.M. (author), Cnubben, N. (author), Kooistra, T. (author), van Ommen, B. (author), Kleemann, R. (author)
Excess caloric intake leads to metabolic overload and is associated with development of type 2 diabetes (T2DM). Current disease management concentrates on risk factors of the disease such as blood glucose, however with limited success. We hypothesize that normalizing blood glucose levels by itself is insufficient to reduce the development of...
article 2013
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Sugimoto-Kawabata, K. (author), Shimada, H. (author), Sakai, K. (author), Suzuki, K. (author), Kelder, T. (author), Pieterman, E.J. (author), Cohen, L.H. (author), Havekes, L.M. (author), Princen, H.M. (author), van den Hoek, A.M. (author)
Bile acid sequestrants (BASs) are cholesterollowering drugs that also affect hyperglycemia. The mechanism by which BASs exert these and other metabolic effects beyond cholesterol lowering remains poorly understood. The present study aimed to investigate the effects of a BAS, colestilan, on body weight, energy expenditure, and glucose and lipid...
article 2013
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Liang, W. (author), Tonini, G. (author), Mulder, P. (author), Kelder, T. (author), van Erk, M. (author), van den Hoek, A.M. (author), Mariman, R. (author), Wielinga, P.Y. (author), Baccini, M. (author), Kooistra, T. (author), Biggeri, A. (author), Kleemann, R. (author)
Background:Chronic metabolic overload results in lipid accumulation and subsequent inflammation in white adipose tissue (WAT), often accompanied by non-alcoholic fatty liver disease (NAFLD). In response to metabolic overload, the expression of genes involved in lipid metabolism and inflammatory processes is adapted. However, it still remains...
article 2013
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Kutmon, M. (author), Kelder, T. (author), Mandaviya, P. (author), Evelo, C.T.A. (author), Coort, S.L. (author)
Introduction: The high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the cellular machinery. By deciphering the role of important players, including transcription factors, microRNAs, or small molecules, a better understanding of key regulatory...
article 2013
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Verschuren, L. (author), Radonjic, M. (author), Wielinga, P.Y. (author), Kelder, T. (author), Kooistra, T. (author), van Ommen, B. (author), Kleemann, R. (author)
AIMS: Combination-drug therapy takes advantage of the complementary action of their individual components, thereby potentiating its therapeutic effect. Potential disadvantages include side effects that are not foreseen on basis of the data available from drug monotherapy. Here, we used a systems biology approach to understand both the efficacy...
article 2012
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Bachmair, E.-M. (author), Bots, M.L. (author), Mennen, L.I. (author), Kelder, T. (author), Evelo, C.T. (author), Horgan, G.W. (author), Ford, I. (author), de Roos, B. (author)
Scope: The dietary fatty acid cis9,trans11 conjugated linoleic acid (cis9,trans11 CLA) has been shown to modify the function of endothelial cells, monocytes, and platelets, all of which are involved in the development of atherosclerosis. Potential mechanisms for the platelet effects have not been assessed previously. In this study, we assessed...
article 2012
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Kelder, T. (author), van Iersel, M.P. (author), Hanspers, K. (author), Kutmon, M. (author), Conklin, B.R. (author), Evelo, C.T. (author), Pico, A.R. (author)
Here, we describe the development of WikiPathways http://www.wikipathways.org, a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to...
article 2012
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Rodríguez-Gutiérrez, G. (author), Duthie, G.G. (author), Wood, S. (author), Morrice, P. (author), Nicol, F. (author), Reid, M. (author), Cantlay, L.L. (author), Kelder, T. (author), Horgan, G.W. (author), Fernández-Bolaños Guzmán, J. (author), de Roos, B. (author)
Scope: Olive products are rich in phenolic compounds, which are natural antioxidants in vitro. We tested the in vivo effects of alperujo, an olive production by-product, as well as hydroxytyrosol and 3,4-dihydroxyphenylglycol (DHPG) isolated from alperujo, on indices and pathways of oxidative and metabolic stress in a vitamin E-deficient rat...
article 2012
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Kelder, T. (author), Eijssen, L. (author), Kleemann, R. (author), van Erk, M. (author), Kooistra, T. (author), Evelo, C. (author)
Background: Complex phenotypes such as insulin resistance involve different biological pathways that may interact and influence each other. Interpretation of related experimental data would be facilitated by identifying relevant pathway interactions in the context of the dataset.Results: We developed an analysis approach to study interactions...
article 2011
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TNO Kwaliteit van Leven (author), Kleemann, R. (author), van Erk, M. (author), Verschuren, L. (author), van den Hoek, A.M. (author), Koek, M. (author), Wielinga, P.Y. (author), Jie, A. (author), Pellis, L. (author), Bobeldijk-Pastorova, I. (author), Kelder, T. (author), Toet, K. (author), Wopereis, S. (author), Cnubben, N. (author), Evelo, C. (author), van Ommen, B. (author), Kooistra, T. (author)
BACKGROUND: The sequence of events leading to the development of insulin resistance (IR) as well as the underlying pathophysiological mechanisms are incompletely understood. As reductionist approaches have been largely unsuccessful in providing an understanding of the pathogenesis of IR, there is a need for an integrative, time-resolved approach...
article 2010
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TNO Kwaliteit van Leven (author), Caesar, R. (author), Manieri, M. (author), Kelder, T. (author), Boekschoten, M. (author), Evelo, C. (author), Müller, M. (author), Kooistra, T. (author), Cinti, S. (author), Kleemann, R. (author), Drevon, C.A. (author)
Depot-dependent differences in adipose tissue physiology may reflect specialized functions and local interactions between adipocytes and surrounding tissues. We combined time-resolved microarray analyses of mesenteric- (MWAT), subcutaneous- (SWAT) and epididymal adipose tissue (EWAT) during high-fat feeding of male transgenic ApoE3Leiden mice...
article 2010
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TNO Kwaliteit van Leven (author), Baccini, M. (author), Bachmaier, E.M. (author), Biggeri, A. (author), Boekschoten, M.V. (author), Bouwman, F.G. (author), Brennan, L. (author), Caesar, R. (author), Cinti, S. (author), Coort, S.L. (author), Crosley, K. (author), Daniel, H. (author), Drevon, C.A. (author), Duthie, S. (author), Eijssen, L. (author), Elliott, R.M. (author), van Erk, M. (author), Evelo, C. (author), Gibney, M. (author), Heim, C. (author), Horgan, G.W. (author), Johnson, I.T. (author), Kelder, T. (author), Kleemann, R. (author), Kooistra, T. (author), van Iersel, M.P. (author), Mariman, E.C. (author), Mayer, C. (author), McLoughlin, G. (author), Müller, M. (author), Mulholland, F. (author), van Ommen, B. (author), Polley, A.C. (author), Pujos-Guillot, E. (author), Rubio-Aliaga, I. (author), Roche, H.M. (author), de Roos, B. (author), Sailer, M. (author), Tonini, G. (author), Williams, L.M. (author), de Wit, N. (author)
article 2008
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