Metabolome Analyses:: Strategies for Systems Biology

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  • Introduction;
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Nucleic Acids Research, 43 , D Cho, K. Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling. Journal of Proteome Research, 7 , — Cottret, L. MetExplore: A web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Research, 38 , W—W Crown, S. Parallel labeling experiments and metabolic flux analysis: Past, present and future methodologies. Metabolic Engineering, 16 , 21— Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions.

BMC Systems Biology, 5 , Dhanasekaran, A. Metabolome searcher: A high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction. BMC Bioinformatics, 16 , DiLeo, M. Dong, W. Review of metabolic pathways activated in cancer cells as determined through isotopic labeling and network analysis.

Metabolic Engineering , 43, — Doniger, S. Genome Biology, 4 , R7—R7. Eden, E. GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics, 10 , Fabregat, A. The reactome pathway knowledgebase. Faith, J. Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology, 5 , e8. Fan, T. Stable isotope-resolved metabolomics and applications for drug development.

Fiehn, O. Metabolomics—the link between genotypes and phenotypes. Plant molecular biology, 48 , — Fouladiha, H. Biomedical applications of cell- and tissue-specific metabolic network models. Journal of Biomedical Informatics, 68 , 35— Frainay, C.

Metabolome Analyses: - Strategies for Systems Biology | Seetharaman Vaidyanathan | Springer

Computational methods to identify metabolic sub-networks based on metabolomic profiles. Briefings in bioinformatics, 18 , 43— Fukushima, A. Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach.

BMC System Biology. Google Scholar. Gao, J. Metscape: A Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. Paintomics: A web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics, 27 , — Ghini, V.

Metabolome Analyses:

Allostasis and resilience of the human individual metabolic phenotype. Journal of Proteome Research, 14 , — Gipson, G. Assignment of MS-based metabolomic datasets via compound interaction pair mapping. Metabolomics, 4 , 94— Gloaguen, Y. PubMedCentral Google Scholar. Goeman, J. A global test for groups of genes: Testing association with a clinical outcome.

Bioinformatics, 20 , 93— Goodacre, R. Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics, 3 , — Griffin, J.

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The Cinderella story of metabolic profiling: Does metabolomics get to go to the functional genomics ball? He, L. WUFlux: An open-source platform for 13 C metabolic flux analysis of bacterial metabolism. BMC Bioinformatics, 17 , Hendrickx, D.

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Network inference from time-resolved metabolomics data. Amsterdam: University of Amsterdam. Reverse engineering of metabolic networks, a critical assessment. Molecular BioSystems, 7 , — Global test for metabolic pathway differences between conditions. Analytica Chimica Acta, , 8— Higashi, R. Raftery Ed. Holmes, E.

Supporting Information

Human metabolic phenotype diversity and its association with diet and blood pressure. Nature, , — Horning, E. Clinical Chemistry, 17 , — PubMed Google Scholar. Hu, T.

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Metabolomics differential correlation network analysis of osteoarthritis biocomputing In Pacific symposium on biocomputing pp. World Scientific, Singapore. Hulsegge, I. In BMC proceedings Vol. Hummel, M. Bioinformatics, 24 , 78— Jeong, H. Lethality and centrality in protein networks. Nature, , 41— Jiang, J. Development of novel tools for the in vitro investigation of drug-induced liver injury. Jourdan, F.

Strategies for Systems Biology

MetaNetter: Inference and visualization of high-resolution metabolomic networks. Bioinformatics, 24 , — Kanehisa, M. KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Research, 45 , D—D KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research, 40 , D—D KEGG as a reference resource for gene and protein annotation.

Mukesh Verma - USA - Metabolomics & Systems Biology 2015 - Conferenceseries LLC

Nucleic Acids Research , 44 , D—D Kankainen, M. MPEA—metabolite pathway enrichment analysis. Karnovsky, A.