Inferring qualitative relations in genetic networks and metabolic pathways [PDF]
Bioinformatics, 2000 Abstract Motivation: Inferring genetic network architecture from time series data of gene expression patterns is an important topic in bioinformatics. Although inference algorithms based on the Boolean network were proposed, the Boolean network was not sufficient as a model of a genetic network.
Satoru Kuhara +2 more
semanticscholar +6 more sources
A Toolbox Model of Evolution of Metabolic Pathways on Networks of Arbitrary Topology [PDF]
PLoS Computational Biology, 2011 34 pages, 9 figures, 2 ...
Tin Yau Pang +2 more
doaj +8 more sources
SS-mPMG and SS-GA: tools for finding pathways and dynamic simulation of metabolic networks. [PDF]
Plant and Cell Physiology, 2013 Metabolomics analysis tools can provide quantitative information on the concentration of metabolites in an organism. In this paper, we propose the minimum pathway model generator tool for simulating the dynamics of metabolite concentrations (SS-mPMG) and
Tetsuo Katsuragi +13 more
semanticscholar +2 more sources
The large-scale organization of metabolic networks [PDF]
Nature, 2000 In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the key role these
Albert, R. +4 more
core +5 more sources
Enumerating all possible biosynthetic pathways in metabolic networks [PDF]
Scientific Reports, 2018 AbstractExhaustive identification of all possible alternate pathways that exist in metabolic networks can provide valuable insights into cellular metabolism. With the growing number of metabolic reconstructions, there is a need for an efficient method to enumerate pathways, which can also scale well to large metabolic networks, such as those ...
Aarthi Ravikrishnan +4 more
openaire +4 more sources
Analysis on relationship between extreme pathways and correlated reaction sets [PDF]
BMC Bioinformatics, 2009 Background: Constraint-based modeling of reconstructed genome-scale metabolic networks has been successfully applied on several microorganisms. In constraint-based modeling, in order to characterize all allowable phenotypes, network-based pathways, such ...
Cao, Ming +4 more
core +4 more sources
Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis [PDF]
BMC Microbiology, 2021 Background Graph-based analysis (GBA) of genome-scale metabolic networks has revealed system-level structures such as the bow-tie connectivity that describes the overall mass flow in a network.
Yajie Gao +4 more
doaj +2 more sources
Reconstruction of phyletic trees by global alignment of multiple metabolic networks [PDF]
BMC Bioinformatics, 2013 Background: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective.
Berger, Bonnie +5 more
core +2 more sources
An improved multi-parametric programming algorithm for flux balance analysis of metabolic networks [PDF]
Journal of Optimization Theory and Applications, 2018 Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to mass-balance ...
Akbari, Amir, Barton, Paul I.
core +2 more sources
Inferring branching pathways in genome-scale metabolic networks [PDF]
BMC Systems Biology, 2009 A central problem in computational metabolic modelling is how to find biochemically plausible pathways between metabolites in a metabolic network. Two general, complementary frameworks have been utilized to find metabolic pathways: constraint-based modelling and graph-theoretical path finding approaches.
Paula Jouhten, Esa Pitkänen, Juho Rousu
openaire +4 more sources