Searched for: author:"Smilde, A.K."
(1 - 20 of 62)

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Stroeve, J.H.M. (author), Saccenti, E. (author), Bouwman, J. (author), Dane, A. (author), Strassburg, K. (author), Vervoort, J. (author), Hankemeier, T. (author), Astrup, A. (author), Smilde, A.K. (author), van Ommen, B. (author), Saris, W.H.M. (author)
Objective: Aim is to predict successful weight loss by metabolic signatures at baseline and to identify which differences in metabolic status may underlie variations in weight loss success. Methods: In DiOGenes, a randomized, controlled trial, weight loss was induced using a low calorie diet (800 kcal) for 8-weeks. Men (N5236) and women (N5431)...
article 2016
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Vis, D.J. (author), Westerhuis, J.A. (author), Hoefsloot, H.C.J. (author), Roelfsema, F. (author), van der Greef, J. (author), Hendriks, M.M.W.B. (author), Smilde, A.K. (author)
Relations among hormone serum concentrations are complex and depend on various factors, including gender, age, body mass index, diurnal rhythms and secretion stochastics. Therefore, endocrine deviations from healthy homeostasis are not easily detected or understood. A generic method is presented for detecting regulatory relations between...
article 2014
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Kaduk, M. (author), Hoefsloot, H.C.J. (author), Vis, D.J. (author), Reijmers, T. (author), van der Greef, J. (author), Smilde, A.K. (author), Hendriks, M.M.W.B. (author)
Modern chromatography-based metabolomics measurements generate large amounts of data in the form of abundances of metabolites. An increasingly popular way of representing and analyzing such data is by means of association networks. Ideally, such a network can be interpreted in terms of the underlying biology. A property of chromatography-based...
article 2014
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Zha, Y. (author), Westerhuis, J.A. (author), Muilwijk, B. (author), Overkamp, K.M. (author), Nijmeijer, B.M. (author), Coulier, L. (author), Smilde, A.K. (author), Punt, P.J. (author)
Background: Inhibitors are formed that reduce the fermentation performance of fermenting yeast during the pretreatment process of lignocellulosic biomass. An exometabolomics approach was applied to systematically identify inhibitors in lignocellulosic biomass hydrolysates.Results: We studied the composition and fermentability of 24 different...
article 2014
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Saccenti, E. (author), Tenori, L. (author), Verbruggen, P. (author), Timmerman, M.E. (author), Bouwman, J. (author), van der Greef, J. (author), Luchinat, C. (author), Smilde, A.K. (author)
Background: Metabolomics has attracted the interest of the medical community for its potential in predicting early derangements from a healthy to a diseased metabolic phenotype. One key issue is the diversity observed in metabolic profiles of different healthy individuals, commonly attributed to the variation of intrinsic (such as (epi)genetic...
article 2014
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Vis, D.J. (author), Westerhuis, J.A. (author), Jacobs, D.M. (author), van Duynhoven, J.P.M. (author), Wopereis, S. (author), van Ommen, B. (author), Hendriks, M.M.W.B. (author), Smilde, A.K. (author)
Challenge tests are used to assess the resilience of human beings to perturbations by analyzing responses to detect functional abnormalities. Well known examples are allergy tests and glucose tolerance tests. Increasingly, metabolomics analysis of blood or serum samples is used to analyze the biological response of the individual to these...
article 2014
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Rubingh, C.M. (author), Martens, H. (author), van der Voet, H. (author), Smilde, A.K. (author)
Each data-driven action in data modelling consumes degrees of freedom, whether it concerns estimation of parameters, estimation of meta-parameters or selecting variables. By using a double cross validation approach for degrees of freedom calculation the costs for meta-parameter estimation and variable selection can be determined explicitly. The...
article 2013
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van Deun, K. (author), van Mechelen, I. (author), Thorrez, L. (author), Schouteden, M. (author), de Moor, B. (author), van der Werf, M.J. (author), de Lathauwer, L. (author), Smilde, A.K. (author), Kiers, H.A.L. (author)
Background: In systems biology it is common to obtain for the same set of biological entities information from multiple sources. Examples include expression data for the same set of orthologous genes screened in different organisms and data on the same set of culture samples obtained with different high-throughput techniques. A major challenge...
article 2012
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SzymaƄska, E. (author), Bouwman, J. (author), Strassburg, K. (author), Vervoort, J. (author), Kangas, A.J. (author), Soininen, P. (author), Ala-Korpela, M. (author), Westerhuis, J. (author), van Duynhoven, J.P.M. (author), Mela, D.J. (author), MacDonald, I.A. (author), Vreeken, R.J. (author), Smilde, A.K. (author), Jacobs, D.M. (author)
Obesity is a risk factor for cardiovascular diseases and type 2 diabetes especially when the fat is accumulated to central depots. Novel biomarkers are crucial to develop diagnostics for obesity and related metabolic disorders. We evaluated the associations between metabolite profiles (136 lipid components, 12 lipoprotein subclasses, 17 low...
article 2012
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van Batenburg, M.F. (author), Coulier, L. (author), van Eeuwijk, F. (author), Smilde, A.K. (author), Westerhuis, J.A. (author)
In the field of metabolomics, hundreds of metabolites are measured simultaneously by analytical platforms such as gas chromatography/mass spectrometry (GC/MS), liquid chromatography/mass spectrometry (LC/MS) and NMR to obtain their concentration levels in a reliable way. Analytical repeatability (intrabatch precision) is a common figure of merit...
article 2011
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Rubingh, C.M. (author), van Erk, M.J. (author), Wopereis, S. (author), van Vliet, T. (author), Verheij, E.R. (author), Cnubben, N.H.P. (author), van Ommen, B. (author), van der Greef, J. (author), Hendriks, H.F.J. (author), Smilde, A.K. (author)
Many benefits can be gained if multi-factorial diseases with a high incidence and prevalence are better understood. Sophisticated approaches like multilevel analyses are needed to discover subtle differences between healthy people and people at the onset of disease in these types of studies. Multilevel analysis generates different sub-models for...
article 2011
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Saccenti, E. (author), Westerhuis, J.A. (author), Smilde, A.K. (author), van der Werf, M.J. (author), Hageman, J.A. (author), Hendriks, M.M.W.B. (author)
One of the first steps in analyzing high-dimensional functional genomics data is an exploratory analysis of such data. Cluster Analysis and Principal Component Analysis are then usually the method of choice. Despite their versatility they also have a severe drawback: they do not always generate simple and interpretable solutions. On the basis of...
article 2011
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Smilde, A.K. (author), Westerhuis, J.A. (author), Hoefsloot, H.C.J. (author), Bijlsma, S. (author), Rubingh, C.M. (author), Vis, D.J. (author), Jellema, R.H. (author), Pijl, H. (author), Roelfsema, F. (author), van der Greef, J. (author), TNO Kwaliteit van Leven (author)
In metabolomics, time-resolved, dynamic or temporal data is more and more collected. The number of methods to analyze such data, however, is very limited and in most cases the dynamic nature of the data is not even taken into account. This paper reviews current methods in use for analyzing dynamic metabolomic data. Moreover, some methods from...
article 2010
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van Erk, M.J. (author), Wopereis, S. (author), Rubingh, C. (author), van Vliet, T. (author), Verheij, E. (author), Cnubben, N.H. (author), Pedersen, T.L. (author), Newman, J.W. (author), Smilde, A.K. (author), Greef, J.V.D. (author), Hendriks, H.F. (author), van Ommen, B. (author), TNO Kwaliteit van Leven (author)
Background. Chronic systemic low-grade inflammation in obese subjects is associated with health complications including cardiovascular diseases, insulin resistance and diabetes. Reducing inflammatory responses may reduce these risks. However, available markers of inflammatory status inadequately describe the complexity of metabolic responses to...
article 2010
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Vis, D.J. (author), Westerhuis, J.A. (author), Hoefsloot, H.C.J. (author), Pijl, H. (author), Roelfsema, F. (author), van der Greef, J. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)
The detection of hormone secretion episodes is important for understanding normal and abnormal endocrine functioning, but pulse identification from hormones measured with short interval sampling is challenging. Furthermore, to obtain useable results, the model underlying hormone secretion and clearance must be augmented with restrictions based...
article 2010
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Verouden, M.P.H. (author), Westerhuis, J.A. (author), van der Werf, M.J. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)
In metabolomics research a large number of metabolites are measured that reflect the cellular state under the experimental conditions studied. In many occasions the experiments are performed according to an experimental design to make sure that sufficient variation is induced in the metabolite concentrations. However, as metabolomics is a...
article 2009
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van den Berg, R.A. (author), Rubingh, C.M. (author), Westerhuis, J.A. (author), van der Werf, M.J. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)
In metabolomics research, it is often important to focus the data analysis to specific areas of interest within the metabolome. In this paper, we describe the application of consensus principal component analysis (CPCA) and canonical correlation analysis (CCA) as a means to explore the relation between metabolome data and (i) biochemically...
article 2009
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Wopereis, S. (author), de Rubingh, C.M. (author), van Erk, M.J. (author), Verheij, E.R. (author), van Vliet, T. (author), Cnubben, N.H. (author), Smilde, A.K. (author), van der Greef, J. (author), van Ommen, B. (author), Hendriks, H.F. (author), TNO Kwaliteit van Leven (author)
BACKGROUND: The prevalence of overweight is increasing globally and has become a serious health problem. Low-grade chronic inflammation in overweight subjects is thought to play an important role in disease development. Novel tools to understand these processes are needed. Metabolic profiling is one such tool that can provide novel insights into...
article 2009
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Rubingh, C.M. (author), Bijlsma, S. (author), Jellema, R.H. (author), Overkamp, K.M. (author), van der Werf, M.J. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)
A longitudinal experimental design in combination with metabolomics and multiway data analysis is a powerful approach in the identification of metabolites whose correlation with bioproduct formation shows a shift in time. In this paper, a strategy is presented for the analysis of longitudinal microbial metabolomics data, which was performed in...
article 2009
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Thissen, U. (author), Wopereis, S. (author), van den Berg, S.A.A. (author), Bobeldijk, I. (author), Kleemann, R. (author), Kooistra, T. (author), van Dijk, K.W. (author), van Ommen, B. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)
Background: In the fields of life sciences, so-called designed studies are used for studying complex biological systems. The data derived from these studies comply with a study design aimed at generating relevant information while diminishing unwanted variation (noise). Knowledge about the study design can be used to decompose the total data...
article 2009
Searched for: author:"Smilde, A.K."
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