13 Result(s)
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Huub C.J. Hoefsloot
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Article
Open AccessGlobal testing of shifts in metabolic phenotype
Current metabolomics approaches to unravel impact of diet- or lifestyle induced phenotype variation and shifts predominantly deploy univariate or multivariate approaches, with a posteriori interpretation at pa...
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Open AccessDynamic elementary mode modelling of non-steady state flux data
A novel framework is proposed to analyse metabolic fluxes in non-steady state conditions, based on the new concept of dynamic elementary mode (dynEM): an elementary mode activated partially depending on the ti...
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Open AccessGenome-wide map** of transcriptional enhancer candidates using DNA and chromatin features in maize
While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part,...
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Open AccessScaling in ANOVA-simultaneous component analysis
In omics research often high-dimensional data is collected according to an experimental design. Typically, the manipulations involved yield differential effects on subsets of variables. An effective approach t...
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Open AccessQuantitative proteomics analysis of an ethanol- and a lactate-producing mutant strain of Synechocystis sp. PCC6803
This study aimed at exploring the molecular physiological consequences of a major redirection of carbon flow in so-called cyanobacterial cell factories: quantitative whole-cell proteomics analyses were carried...
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Open AccessValidation and selection of ODE based systems biology models: how to arrive at more reliable decisions
Most ordinary differential equation (ODE) based modeling studies in systems biology involve a hold-out validation step for model validation. In this framework a pre-determined part of the data is used as valid...
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Reflections on univariate and multivariate analysis of metabolomics data
Metabolomics experiments usually result in a large quantity of data. Univariate and multivariate analysis techniques are routinely used to extract relevant information from the data with the aim of providing b...
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Open AccessA critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass
Less than 25% of patients with a pelvic mass who are presented to a gynecologist will eventually be diagnosed with epithelial ovarian cancer. Since there is no reliable test to differentiate between different ...
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Open AccessBetween Metabolite Relationships: an essential aspect of metabolic change
Not only the levels of individual metabolites, but also the relations between the levels of different metabolites may indicate (experimentally induced) changes in a biological system. Component analysis method...
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Open AccessIndividual differences in metabolomics: individualised responses and between-metabolite relationships
Many metabolomics studies aim to find ‘biomarkers’: sets of molecules that are consistently elevated or decreased upon experimental manipulation. Biological effects, however, often manifest themselves along a ...
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Article
Open AccessMultivariate paired data analysis: multilevel PLSDA versus OPLSDA
Metabolomics data obtained from (human) nutritional intervention studies can have a rather complex structure that depends on the underlying experimental design. In this paper we discuss the complex structure i...
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Open AccessDiscriminant Q2 (DQ2) for improved discrimination in PLSDA models
In this paper we introduce discriminant Q2 (DQ2) as an improvement for the Q2 value used in the validation of PLSDA models. DQ2 does not penalize class predictions beyond the class label value. With rigorous Mont...
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Open AccessAssessment of PLSDA cross validation
Classifying groups of individuals based on their metabolic profile is one of the main topics in metabolomics research. Due to the low number of individuals compared to the large number of variables, this is no...
