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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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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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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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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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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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