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Eekhout, I. (author), van Buuren, S. (author), Visser, B. (author), Bink, M.C.A.M. (author), Huisman, A. (author)Intensive longitudinal data can be used to explore important associations and patterns between various types of inputs and outcomes. Nonlinear relations and irregular measurement occasions can pose problems to develop an accurate model for these kinds of data. This paper focuses on the development, fitting and evaluation of a prediction model...article 2023
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Balech, B. (author), Brennan, L. (author), Carrillo de Santa Pau, E. (author), Cavalieri, D. (author), Coort, S. (author), D’Elia, D. (author), Dragsted, L.O. (author), Eftimov, T. (author), Evelo, C.T. (author), Polonca Ferk, P. (author), Finglas, P. (author), Gori, G. (author), Hancock, J. (author), Kalaš, M. (author), Koroušić Seljak, B. (author), Lachat, C. (author), Leskošek, B. (author), Pasolli, E. (author), Pesole, G (author), Presser, K. (author), Sandionigi, A. (author), Santamaria, M. (author), Şener, D.D. (author), Traka, M. (author), Vergères, G. (author), Zimmermann, K.L. (author), Bouwman, J. (author)Non-communicable diseases are on the rise and are often related to food choices; nutrition affects infectious diseases too. Therefore, there is growing interest in research on public and personal health, as related to food, nutrition behaviour and well-being of consumers throughout the life cycle. These concepts and their relations are complex...article 2022
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Grinberg, M. (author), Stöber, R.M. (author), Edlund, K. (author), Rempel, E. (author), Godoy, P. (author), Reif, R. (author), Widera, A. (author), Madjar, K. (author), Schmidt-Heck, W. (author), Marchan, R. (author), Sachinidis, A. (author), Spitkovsky, D. (author), Hescheler, J. (author), Carmo, H. (author), Arbo, M.D. (author), van de Water, B. (author), Wink, S. (author), Vinken, M. (author), Rogiers, V. (author), Escher, S. (author), Hardy, B. (author), Mitic, D. (author), Myatt, G. (author), Waldmann, T. (author), Mardinoglu, A. (author), Damm, G. (author), Seehofer, D. (author), Nüssler, A. (author), Weiss, T.S. (author), Oberemm, A. (author), Lampen, A. (author), Schaap, M.M. (author), Luijten, M. (author), van Steeg, H. (author), Thasler, W.E. (author), Kleinjans, J.C.S. (author), Stierum, R.H. (author), Leist, M. (author), Rahnenführer, J. (author), Hengstler, J.G. (author)Correction to: Arch Toxicol (2014) 88:2261–2287 https://doi.org/10.1007/s00204-014-1400-x.article 2022
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Selberherr, E. (author), Grau, J.H. (author), Meixner, M. (author), Liere, K. (author), Ercolini, D. (author), de Filippo, C. (author), Caderni, G. (author), Brigidi, P. (author), Turroni, S. (author)The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining...article 2022
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Kuijpers, E. (author), van Wel, L. (author), Loh, M. (author), Galea, K.S. (author), Makris, K.C. (author), Stierum, R. (author), Fransman, W. (author), Pronk, A. (author)Introduction: Oil and gas workers have been shown to be at increased risk of chronic diseases including cancer, asthma, chronic obstructive pulmonary disease, and hearing loss, among others. Technological advances may be used to assess the external (e.g. personal sensors, smartphone apps and online platforms, exposure models) and internal...article 2021
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van Bilsen, J.H.M. (author), Verschuren, L. (author), Wagenaar, L. (author), Vonk, M.M. (author), van Esch, B.C.A.M. (author), Knippels, L.M.J. (author), Garssen, J. (author), Smit, J.J. (author), Pieters, R.H.H. (author), van den Broek, T.J. (author)Background: Oral immunotherapy (OIT) is a promising therapeutic approach to treat food allergic patients. However, concerns with regards to safety and long-term efficacy of OIT remain. There is a need to identify biomarkers that predict, monitor and/or evaluate the effects of OIT. Here we present a method to select candidate biomarkers for...article 2019
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Matualatupauw, J.C. (author), O'Grada, C. (author), Hughes, M.F. (author), Roche, H.M. (author), Afman, L.A. (author), Bouwman, J. (author)Scope: Several studies have examined the whole-genome gene expression response in blood cells to high-fat challenges with differing results. The study aims to identify consistently up- or downregulated genes and pathways in response to a high-fat challenge using several integration methods. Methods and results: Three studies measuring the gene...article 2019
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Remington, B. (author), Broekman, H.C.H. (author), Blom, W.M. (author), Capt, A. (author), Crevel, R.W.R. (author), Dimitrov, I. (author), Faeste, C.K. (author), Fernandez-Canton, R. (author), Giavi, S. (author), Houben, G.F. (author), Glenn, K.C. (author), Madsen, C.B. (author), Kruizinga, A.K. (author), Constable, A. (author)The development and introduction of new dietary protein sources has the potential to improve food supply sustainability. Understanding the potential allergenicity of these new or modified proteins is crucial to ensure protection of public health. Exposure to new proteins may result in de novo sensitization, with or without clinical allergy, or...article 2018
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- de Marchi, T. (author), Braakman, R.B.H. (author), Stingl, C. (author), van Duijn, M.M. (author), Smid, M. (author), Foekens, J.A. (author), Luider, T.M. (author), Martens, J.W.M. (author), Umar, A. (author) article 2016
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Grinberg, M. (author), Stöber, R.M. (author), Edlund, K. (author), Rempel, E. (author), Godoy, P. (author), Reif, R. (author), Widera, A. (author), Madjar, K. (author), Schmidt-Heck, W. (author), Marchan, R. (author), Sachinidis, A. (author), Spitkovsky, D. (author), Hescheler, J. (author), Carmo, H. (author), Arbo, M.D. (author), van de Water, B. (author), Wink, S. (author), Vinken, M. (author), Rogiers, V. (author), Escher, S. (author), Hardy, B. (author), Mitic, D. (author), Myatt, G. (author), Waldmann, T. (author), Mardinoglu, A. (author), Damm, G. (author), Seehofer, D. (author), Nüssler, A. (author), Weiss, T.S. (author), Oberemm, A. (author), Lampen, A. (author), Schaap, M.M. (author), Luijten, M. (author), van Steeg, H. (author), Thasler, W.E. (author), Kleinjans, J.C.S. (author), Stierum, R.H. (author), Leist, M. (author), Rahnenführer, J. (author), Hengstler, J.G. (author)A long-term goal of numerous research projects is to identify biomarkers for in vitro systems predicting toxicity in vivo. Often, transcriptomics data are used to identify candidates for further evaluation. However, a systematic directory summarizing key features of chemically influenced genes in human hepatocytes is not yet available. To bridge...article 2014
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Hettne, K.M. (author), Kleinjans, J. (author), Stierum, R.H. (author), Boorsma, A. (author), Kors, J.A. (author)This chapter concerns the application of bioinformatics methods to the analysis of toxicogenomics data. The chapter starts with an introduction covering how bioinformatics has been applied in toxicogenomics data analysis, and continues with a description of the foundations of a specific bioinformatics method called text-mining. Next, the...bookPart 2014
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Evelo, C.T. (author), van Bochove, K. (author), Saito, J.T. (author)The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A particularly urgent objective in coping with the data...article 2011
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TNO Kwaliteit van Leven (author), van Ommen, B. (author), Bouwman, J. (author), Dragsted, L.O. (author), Drevon, C.A. (author), Elliott, R. (author), de Groot, P. (author), Kaput, J. (author), Mathers, J.C. (author), Müller, M. (author), Pepping, F. (author), Saito, J. (author), Scalbert, A. (author), Radonjic, M. (author), Rocca-Serra, P. (author), Travis, A. (author), Wopereis, S. (author), Evelo, C.T. (author)The challenge of modern nutrition and health research is to identify food-based strategies promoting life-long optimal health and well-being. This research is complex because it exploits a multitude of bioactive compounds acting on an extensive network of interacting processes. Whereas nutrition research can profit enormously from the revolution...article 2010
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TNO Kwaliteit van Leven (author), van Ommen, B. (author), El-Sohemy, A. (author), Hesketh, J. (author), Kaput, J. (author), Fenech, M. (author), Evelo, C.T. (author), McArdle, H.J. (author), Bouwman, J. (author), Lietz, G. (author), Mathers, J.C. (author), Fairweather-Tait, S. (author), van Kranen, H. (author), Elliott, R. (author), Wopereis, S. (author), Ferguson, L.R. (author), Méplan, C. (author), Perozzi, G. (author), Allen, L. (author), Rivero, D. (author)Micronutrients influence multiple metabolic pathways including oxidative and inflammatory processes. Optimum micronutrient supply is important for the maintenance of homeostasis in metabolism and, ultimately, for maintaining good health. With advances in systems biology and genomics technologies, it is becoming feasible to assess the activity of...article 2010
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Smilde, A.K. (author), Kiers, H.A.L. (author), Bijlsma, S. (author), Rubingh, C.M. (author), van Erk, M.J. (author), TNO Kwaliteit van Leven (author)Motivation: Modern functional genomics generates high-dimensional datasets. It is often convenient to have a single simple number characterizing the relationship between pairs of such high-dimensional datasets in a comprehensive way. Matrix correlations are such numbers and are appealing since they can be interpreted in the same way as Pearson's...article 2009
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Nueda, M.J. (author), Conesa, A. (author), Westerhuis, J.A. (author), Hoefsloot, H.C.J. (author), Smilde, A.K. (author), Talón, M. (author), Ferrer, A. (author), TNO Kwaliteit van Leven (author)Motivation: Designed microarray experiments are used to investigate the effects that controlled experimental factors have on gene expression and learn about the transcriptional responses associated with external variables. In these datasets, signals of interest coexist with varying sources of unwanted noise in a framework of (co)relation among...article 2007
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Goodacre, R. (author), Broadhurst, D. (author), Smilde, A.K. (author), Kristal, B.S. (author), Baker, J.D. (author), Beger, R. (author), Bessant, C. (author), Connor, S. (author), Capuani, G. (author), Craig, A. (author), Ebbels, T. (author), Kell, D.B. (author), Manetti, C. (author), Newton, J. (author), Paternostro, G. (author), Somorjai, R. (author), Sjöström, M. (author), Trygg, J. (author), Wulfert, F. (author), TNO Kwaliteit van Leven (author)The goal of this group is to define the reporting requirements associated with the statistical analysis (including univariate, multivariate, informatics, machine learning etc.) of metabolite data with respect to other measured/collected experimental data (often called meta-data). These definitions will embrace as many aspects of a complete...article 2007
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van der Greef, J. (author), Adourian, A. (author), Muntendam, P. (author), McBurney, R.N. (author), TNO Kwaliteit van Leven (author)Too few drug discovery projects generate a marketed drug product, often because preclinical studies fail to predict the clinical experience with a drug candidate. Improving the success of preclinical-to-clinical translation is of paramount importance in optimizing the pharmaceutical value chain. Here, we advance the case for a molecular systems...article 2006
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Corthésy-Theulaz, I. (author), den Dunnen, J.T. (author), Ferré, P. (author), Geurts, J.M.W. (author), Müller, M. (author), van Belzen, N. (author), van Ommen, B. (author), TNO Kwaliteit van Leven (author)The interaction between the human body and nutrition is an extremely complex process involving multi-organ physiology with molecular mechanisms on all levels of regulation (genes, gene expression, proteins, metabolites). Only with the recent technology push have nutritional scientists been able to address this complexity. Both the challenges and...article 2005
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van der Greef, J. (author), McBurney, R.N. (author), TNO Kwaliteit van Leven (author)The pharmaceutical industry is currently beleaguered by close scrutiny from the financial community, regulators and the general public. Productivity, in terms of new drug approvals, has generally been falling for almost a decade and the safety of a number of highly successful drugs has recently been brought into question. Here, we discuss...article 2005
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