Polyamines in the Context of Metabolic Networks.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7398-9_1
Abstract: Polyamines (PAs) are essential biomolecules that are known to be involved in the regulation of many plant developmental and growth processes as well as their response to different environmental stimuli. Maintaining the cellular pools of… read more here.
Keywords: pas; plant; context metabolic; polyamines context ... See more keywords
Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Molecular Evolution"
DOI: 10.1007/s00239-021-10018-0
Abstract: Uncovering the general principles that govern the structure of metabolic networks is key to understanding the emergence and evolution of living systems. Artificial chemistries can help illuminate this problem by enabling the exploration of chemical… read more here.
Keywords: network; stoichiometric modeling; string chemistries; chemistry ... See more keywords
Thermodynamic Constraints Improve Metabolic Networks.
Sign Up to like & getrecommendations! Published in 2017 at "Biophysical journal"
DOI: 10.1016/j.bpj.2017.06.018
Abstract: In pursuit of establishing a realistic metabolic phenotypic space, the reversibility of reactions is thermodynamically constrained in modern metabolic networks. The reversibility constraints follow from heuristic thermodynamic poise approximations that take anticipated cellular metabolite concentration… read more here.
Keywords: reversibility constraints; reversibility; network; reconciliation ... See more keywords
Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks.
Sign Up to like & getrecommendations! Published in 2017 at "Metabolic engineering"
DOI: 10.1016/j.ymben.2016.11.006
Abstract: The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state… read more here.
Keywords: thermodynamics; analysis; sensitivity analysis; thermodynamics based ... See more keywords
Discovering missing reactions of metabolic networks by using gene co-expression data
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DOI: 10.1038/srep41774
Abstract: Flux coupling analysis is a computational method which is able to explain co-expression of metabolic genes by analyzing the topological structure of a metabolic network. It has been suggested that if genes in two seemingly… read more here.
Keywords: gap; expression data; gene expression; expression ... See more keywords
Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach
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DOI: 10.1093/bioinformatics/btaa280
Abstract: Abstract Motivation Elementary flux modes (EFMs) are a key tool for analyzing genome-scale metabolic networks, and several methods have been proposed to compute them. Among them, those based on solving linear programming (LP) problems are… read more here.
Keywords: flux modes; genome scale; elementary flux; linear programming ... See more keywords
MinReact: a systematic approach for identifying minimal metabolic networks
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa497
Abstract: MOTIVATION Genome-scale metabolic models are widely constructed and studied for understanding various design principles underlying metabolism, predominantly redundancy. Metabolic networks are highly redundant and it is possible to minimise the metabolic networks into smaller networks… read more here.
Keywords: minimal reactomes; minimal metabolic; multiple minimal; metabolic networks ... See more keywords
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate–product pairs
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DOI: 10.1093/bioinformatics/btab368
Abstract: Abstract Motivation Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in… read more here.
Keywords: biochemical networks; metabolic pathways; product; metabolic networks ... See more keywords
Sequential computation of elementary modes and minimal cut sets in genome‐scale metabolic networks using alternate integer linear programming
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DOI: 10.1093/bioinformatics/btx171
Abstract: Motivation: Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome‐scale networks remains challenging due to combinatorial… read more here.
Keywords: integer linear; genome scale; computation; integer ... See more keywords
MetExplore: collaborative edition and exploration of metabolic networks
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DOI: 10.1093/nar/gky301
Abstract: Abstract Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate… read more here.
Keywords: network; exploration; metexplore collaborative; omics data ... See more keywords
A study on multi-omic oscillations in Escherichia coli metabolic networks
Sign Up to like & getrecommendations! Published in 2018 at "BMC Bioinformatics"
DOI: 10.1186/s12859-018-2175-5
Abstract: BackgroundTwo important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They are are actually coupled beause the integration… read more here.
Keywords: coli metabolic; information; multi omics; multi omic ... See more keywords