The global integrative network: integration of signaling and metabolic pathways [PDF]
aBIOTECH, 2022 Abstract The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis.
Yuying Lin +4 more
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Metabolic pathways variability and sequence/networks comparisons [PDF]
BMC Bioinformatics, 2006 Background In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees ...
Palumbo Maria +3 more
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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. Most studies have focused on the classification of organisms based on structural
Ma Cheng-Yu +5 more
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Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison [PDF]
Bioinformatics, 2009 Abstract Summary:We present a tool called Rahnuma for prediction and analysis of metabolic pathways and comparison of metabolic networks. Rahnuma represents metabolic networks as hypergraphs and computes all possible pathways between two or more metabolites.
Aziz Mithani +2 more
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Metabolic network visualization eliminating node redundance and preserving metabolic pathways [PDF]
BMC Systems Biology, 2007 AbstractBackgroundThe tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two ...
Romain Bourqui +6 more
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Linking Metabolic QTLs with Network and cis-eQTLs Controlling Biosynthetic Pathways [PDF]
PLoS Genetics, 2007 Phenotypic variation between individuals of a species is often under quantitative genetic control. Genomic analysis of gene expression polymorphisms between individuals is rapidly gaining popularity as a way to query the underlying mechanistic causes of variation between individuals.
Adam M. Wentzell +5 more
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Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models. [PDF]
PLoS ONE, 2017 Over 100 genome-scale metabolic networks (GSMNs) have been published in recent years and widely used for phenotype prediction and pathway design.
Qianqian Yuan +9 more
doaj +3 more sources
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.
Tatsuya Akutsu +2 more
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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
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps [PDF]
Bioinformatics, 2003 Abstract Motivation: The analysis of structure, pathways and flux distributions in metabolic networks has become an important approach for understanding the functionality of metabolic systems. The need of a user-friendly platform for stoichiometric modeling of metabolic networks in silico is evident.
Steffen Klamt +3 more
openalex +5 more sources