Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/33130

TitleAlgorithms to infer metabolic flux ratios from fluxomics data
Author(s)Carreira, Rafael
Rocha, Miguel
Villas-Bôas, S. G.
Rocha, I.
KeywordsBiochemistry
Biology computing
Cellular biophysics
Genomics
13C labeling distribution
Carbon atom transition maps
Constraint-based methods
Flux balance analysis
Fluxomics data
Genome-scale metabolic models
in silico cell simulation
Metabolic flux ratios
Metabolic network
Metabolite fragments
Reaction reversibility
Atomic measurements
Biochemistry
Bioinformatics
Carbon
Equations
Labeling
Vectors
Issue dateDec-2013
PublisherIEEE
CitationCarreira, R.; Rocha, Miguel; Villas-Boas, S. G.; Rocha, I., Algorithms to infer metabolic flux ratios from fluxomics data. BIBM 2013 - IEEE International Conference on Bioinformatics and Biomedicine. Shanghai, China, 18-21 Dec., 205-2092013.
Abstract(s)In silico cell simulation approaches based in the use of genome-scale metabolic models (GSMMs) and constraint-based methods such as Flux Balance Analysis are gaining importance, but methods to integrate these approaches with omics data are still greatly needed. In this work, the focus relies on fluxomics data that provide valuable information on the intracellular fluxes, although in many cases in an indirect, incomplete and noisy way. The proposed framework enables the integration of fluxomics data, in the form of 13C labeling distribution for metabolite fragments, with GSMMs enriched with carbon atom transition maps. The algorithms implemented allow to infer labeling distributions for fragments/metabolites not measured and to build expressions for the relevant flux ratios that can be then used to enrich constraint-based methods for flux determination. This approach does not require any assumptions on the metabolic network and reaction reversibility, allowing to compute ratios originating from coupled joint points of the network. Also, when enough data do not exist, the system tries to infer ratio bounds from the measurements.
TypeConference paper
URIhttp://hdl.handle.net/1822/33130
DOI10.1109/BIBM.2013.6732490
Peer-Reviewedyes
AccessOpen access
Appears in Collections:CEB - Artigos em Livros de Atas / Papers in Proceedings

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