- document
-
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
- document
-
Thissen, U. (author), Coulier, L. (author), Overkamp, K.M. (author), Jetten, J. (author), van de Werff, B.J.C. (author), van de Ven, T. (author), van der Werf, M.J. (author)In agricultural and food products, typical quality parameters are sensory properties, shelf-life, safety, health, nutritional value, crop yield per area and disease resistance. It is known that these parameters are importantly determined by the metabolites in the crops and food products. Metabolomics is the state-of-the-art routine technique...article 2011
- document
-
Braaksma, M. (author), Bijlsma, S. (author), Coulier, L. (author), Punt, P.J. (author), van der Werf, M.J. (author)For the optimization of microbial production processes, the choice of the quantitative phenotype to be optimized is crucial. For instance, for the optimization of product formation, either product concentration or productivity can be pursued, potentially resulting in different targets for strain improvement. The choice of a quantitative...article 2011
- document
-
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
- document
- van Tol, E.A.F. (author), Russell, W.M. (author), Herz, U. (author), Renz, H. (author), Garn, H. (author), Braaksma, M. (author), van der Werf, M.J. (author), Overkamp, K.M. (author) patent 2011
- document
-
Rumbold, K. (author), van Buijsen, H.J.J. (author), Gray, V.M. (author), van Groenestijn, J.W. (author), Overkamp, K.M. (author), Slomp, R.S. (author), van der Werf, M.J. (author), Punt, P.J. (author), TNO Kwaliteit van Leven (author)Increasingly lignocellulosic biomass hydrolysates are used as the feedstock for industrial fermentations. These biomass hydrolysates consist of complex mixtures of different fermentable sugars, but also contain inhibitors and salts that affect the performance of the productgenerating microbes. The performance of six industrially relevant...article 2010
- document
-
van den Berg, R.A. (author), Braaksma, M. (author), van der Veen, D. (author), van der Werf, M.J. (author), Punt, P.J. (author), van der Oost, J. (author), de Graaff, L.H. (author), TNO Kwaliteit van Leven (author)The fungus Aspergillus niger has been studied in considerable detail with respect to various industrial applications. Although its central metabolic pathways are established relatively well, the mechanisms that control the adaptation of its metabolism are understood rather poorly. In this study, clustering of co-expressed genes has been...article 2010
- document
- Braaksma, M. (author), van den Berg, R.A. (author), van der Werf, M.J. (author), Punt, P.J. (author), TNO Kwaliteit van Leven (author) bookPart 2010
- document
-
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
- document
-
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
- document
-
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
- document
-
Smilde, A.K. (author), van der Werf, M.J. (author), Schaller, J.-P. (author), Kistemaker, C. (author), TNO Kwaliteit van Leven (author)In conventional analytical chemistry it is customary to report figures of merit - such as precision, analysis time, limit of detection - for the chemical analysis performed. Usually, such figures of merit are reported for each analyte separately, generating a list of figures of merit. In metabolomics such a listing is not informative, since very...article 2009
- document
-
Verouden, M.P.H. (author), Notebaart, R.A. (author), Westerhuis, J.A. (author), van der Werf, M.J. (author), Teusink, B. (author), Smilde, A.K. (author), TNO Kwaliteit van Leven (author)With the availability of genome sequences of many organisms and information about gene-protein-reaction (GPR) associations with respect to these organisms genome-scale metabolic networks can be reconstructed. In cellular systems biology these networks are used to model the behavior of metabolism in context of cell growth in terms of fluxes ...article 2009
- document
-
Braaksma, M. (author), Smilde, A.K. (author), van der Werf, M.J. (author), Punt, P.J. (author), TNO Kwaliteit van Leven (author)Proteolytic degradation by host proteases is one of the key issues in the application of filamentous fungi for non-fungal protein production. In this study the influence of several environmental factors on the production of extracellular proteases of Aspergillus niger was investigated systematically in controlled batch cultures. Of all factors...article 2009
- document
-
Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sourcesvan der Werf, M.J. (author), Overkamp, K.M. (author), Muilwijk, B. (author), Koek, M.M. (author), van der Werff van der - Vat, B.J.C. (author), Jellema, R.H. (author), Coulier, L. (author), Hankemeier, T. (author), TNO Kwaliteit van Leven (author)Metabolomics is an emerging, powerful, functional genomics technology that involves the comparative non-targeted analysis of the complete set of metabolites in an organism. We have set-up a robust quantitative metabolomics platform that allows the analysis of 'snapshot' metabolomes. In this study, we have applied this platform for the...article 2008
- document
-
TNO Kwaliteit van Leven (author), Hageman, J.A. (author), Hendriks, M.M.W.B. (author), Westerhuis, J.A. (author), van der Werf, M.J. (author), Berger, R. (author), Smilde, A.K. (author)One of the new expanding areas in functional genomics is metabolomics: measuring the metabolome of an organism. Data being generated in metabolomics studies are very diverse in nature depending on the design underlying the experiment. Traditionally, variation in measurements is conceptually broken down in systematic variation and noise where the...article 2008
- document
-
TNO Kwaliteit van Leven (author), Hageman, J.A. (author), van den Berg, R.A. (author), Westerhuis, J.A. (author), van der Werf, M.J. (author), Smilde, A.K. (author)Metabolomics and other omics tools are generally characterized by large data sets with many variables obtained under different environmental conditions. Clustering methods and more specifically two-mode clustering methods are excellent tools for analyzing this type of data. Two-mode clustering methods allow for analysis of the behavior of...article 2008
- document
-
van der Werf, M.J. (author), Takors, R. (author), Smedsgaard, J. (author), Nielsen, J. (author), Ferenci, T. (author), Portais, J.C. (author), Wittmann, C. (author), Hooks, M. (author), Tomassini, A. (author), Oldiges, M. (author), Fostel, J. (author), Sauer, U. (author), TNO Kwaliteit van Leven (author)With the increasing use of metabolomics as a means to study a large number of different biological research questions, there is a need for a minimal set of reporting standards that allow the scientific community to evaluate, understand, repeat, compare and re-investigate metabolomics studies. Here we propose, a first draft of minimal...article 2007
- document
-
Pieterse, B. (author), Jellema, R.H. (author), van der Werf, M.J. (author), TNO Kwaliteit van Leven (author)Messenger RNA levels change on a minutes scale due to both degradation and de novo transcription. Consequently, alterations in the transcript profiles that are not representative for the condition of interest are easily introduced during sample harvesting and work-up. In order to avoid these unwanted changes we have validated a - 45°C methanol...article 2006
- document
-
van der Werf, M.J. (author), Pieterse, B. (author), van Luijk, N. (author), Schuren, F. (author), van der Werff van der - Vat, B. (author), Overkamp, K. (author), Jellema, R.H. (author), TNO Kwaliteit van Leven (author)The value of the multivariate data analysis tools principal component analysis (PCA) and principal component discriminant analysis (PCDA) for prioritizing leads generated by microarrays was evaluated. To this end, Pseudomonas putida S12 was grown in independent triplicate fermentations on four different carbon sources, i.e. fructose, glucose,...article 2006