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
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VitisCyc: A metabolic pathway knowledgebase for grapevine (Vitis vinifera)
Frontiers in Plant Science, 2014 We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, ii) compare ...
Sushma eNaithani +6 more
doaj +1 more source
MetaboCraft: building a Minecraft plugin for metabolomics [PDF]
, 2018 Motivation: The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings. Results: We have developed
Burgess, Karl +2 more
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The Metabolic Phenotype of Prostate Cancer
Frontiers in Oncology, 2017 Prostate cancer is the most common non-cutaneous cancer in men in the United States. Cancer metabolism has emerged as a contemporary topic of great interest for improved mechanistic understanding of tumorigenesis.
Eric Eidelman +5 more
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On functional module detection in metabolic networks [PDF]
, 2013 Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided ...
Adleman +29 more
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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
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Exploring metabolic pathway disruption in the subchronic phencyclidine model of schizophrenia with the generalized singular value decomposition [PDF]
, 2011 The quantification of experimentally-induced alterations in biological pathways remains a major challenge in systems biology. One example of this is the quantitative characterization of alterations in defined, established metabolic pathways from complex ...
Dawson, Neil +6 more
core +4 more sources
Pathway identification by network pruning in the metabolic network of Escherichia coli [PDF]
Bioinformatics, 2009 Abstract Motivation: All metabolic networks contain metabolites, such as ATP and NAD, known as currency metabolites, which take part in many reactions. These are often removed in the study of these networks, but no consensus exists on what actually constitutes a currency metabolite, and it is also unclear how these highly connected nodes
Gerlee, Philip David Marcus +2 more
openaire +3 more sources
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis
BMC Bioinformatics, 2006 Background As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components.
Sun Shiwei +9 more
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Deciphering rice metabolic flux reprograming under salinity stress via in silico metabolic modeling
Computational and Structural Biotechnology Journal, 2020 Rice is one of the most economically important commodities globally. However, rice plants are salt susceptible species in which high salinity can significantly constrain its productivity. Several physiological parameters in adaptation to salt stress have
Kwanjeera Wanichthanarak +5 more
doaj +1 more source