99 research outputs found
Unravelling the Yeast Cell Cycle Using the TriGen Algorithm
Analyzing microarray data represents a computational challenge
due to the characteristics of these data. Clustering techniques are
widely applied to create groups of genes that exhibit a similar behavior
under the conditions tested. Biclustering emerges as an improvement of
classical clustering since it relaxes the constraints for grouping allowing
genes to be evaluated only under a subset of the conditions and not under
all of them. However, this technique is not appropriate for the analysis of
temporal microarray data in which the genes are evaluated under certain
conditions at several time points. In this paper, we present the results of
applying the TriGen algorithm, a genetic algorithm that finds triclusters
that take into account the experimental conditions and the time points,
to the yeast cell cycle problem, where the goal is to identify all genes
whose expression levels are regulated by the cell cycle
Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson’s disease: a comparison of 33 human and animal studies
Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23
Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research
Mass spectrometry (MS) techniques, because of their sensitivity and selectivity, have become methods of choice to characterize the human metabolome and MS-based metabolomics is increasingly used to characterize the complex metabolic effects of nutrients or foods. However progress is still hampered by many unsolved problems and most notably the lack of well established and standardized methods or procedures, and the difficulties still met in the identification of the metabolites influenced by a given nutritional intervention. The purpose of this paper is to review the main obstacles limiting progress and to make recommendations to overcome them. Propositions are made to improve the mode of collection and preparation of biological samples, the coverage and quality of mass spectrometry analyses, the extraction and exploitation of the raw data, the identification of the metabolites and the biological interpretation of the results
The small RNA diversity from Medicago truncatularoots under biotic interactions evidences the environmental plasticity of the miRNAome
Mining the key regulatory genes of chicken inosine 5′-monophosphate metabolism based on time series microarray data
Solid-phase arsenic speciation in aquifer sediments: A micro-X-ray absorption spectroscopy approach for quantifying trace-level speciation
Arsenic (As) is a geogenic contaminant affecting groundwater in geologically diverse systems globally. Arsenic release from aquifer sediments to groundwater is favored when biogeochemical conditions, especially oxidation-reduction (redox) potential, in aquifers fluctuate. The specific objective of this research is to identify the solid-phase sources and geochemical mechanisms of release of As in aquifers of the Des Moines Lobe glacial advance. The overarching concept is that conditions present at the aquifer-aquitard interfaces promote a suite of geochemical reactions leading to mineral alteration and release of As to groundwater. A microprobe X-ray absorption spectroscopy (μXAS) approach is developed and applied to rotosonic drill core samples to identify the solid-phase speciation of As in aquifer, aquitard, and aquifer-aquitard interface sediments. This approach addresses the low solid-phase As concentrations, as well as the fine-scale physical and chemical heterogeneity of the sediments. The spectroscopy data are analyzed using novel cosine-distance and correlation-distance hierarchical clustering for Fe 1s and As 1s μXAS datasets. The solid-phase Fe and As speciation is then interpreted using sediment and well-water chemical data to propose solid-phase As reservoirs and release mechanisms. The results confirm that in two of the three locations studied, the glacial sediment forming the aquitard is the source of As to the aquifer sediments. The results are consistent with three different As release mechanisms: (1) desorption from Fe (oxyhydr)oxides, (2) reductive dissolution of Fe (oxyhydr)oxides, and (3) oxidative dissolution of Fe sulfides. The findings confirm that glacial sediments at the interface between aquifer and aquitard are geochemically active zones for As. The diversity of As release mechanisms is consistent with the geographic heterogeneity observed in the distribution of elevated-As wells
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