Clustering analysis of tumor metabolic networks
BMC Bioinformatics, 2020 Background Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene regulatory, and metabolic pathways ...
Ichcha Manipur +3 more
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MetNet: A two-level approach to reconstructing and comparing metabolic networks.
PLoS ONE, 2021 Metabolic pathway comparison and interaction between different species can detect important information for drug engineering and medical science. In the literature, proposals for reconstructing and comparing metabolic networks present two main problems ...
Nicoletta Cocco +3 more
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The large-scale organization of metabolic networks [PDF]
, 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
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The link between ferroptosis and airway inflammatory diseases: A novel target for treatment
Frontiers in Molecular Biosciences, 2022 Ferroptosis is an iron-dependent mode of cell death characterized by intracellular lipid peroxide accumulation and a redox reaction imbalance. Compared with other modes of cell death, ferroptosis has specific biological and morphological features.
Zhiwei Lin +5 more
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Extreme Pathway Lengths and Reaction Participation in Genome-Scale Metabolic Networks [PDF]
Genome Research, 2002 Extreme pathways are a unique and minimal set of vectors that completely characterize the steady-state capabilities of genome-scale metabolic networks. A framework is provided to mathematically characterize extreme pathway length and to study how individual reactions participate in the extreme pathway structure of a network.
Jason A, Papin +2 more
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Benchmarking procedures for high-throughput context specific reconstruction algorithms
Frontiers in Physiology, 2016 Recent progress in high-throughput data acquisition has shifted the focus from data generation to processing and understanding of how to integrate collected information.
Maria ePires Pacheco +2 more
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Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows [PDF]
, 2017 We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and hyperedges to ...
Andersen, Jakob L. +3 more
core +2 more sources
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.
Mithani, A, Preston, G, Hein, J
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What do we learn from correlations of local and global network properties? [PDF]
, 2006 In complex networks a common task is to identify the most important or "central" nodes. There are several definitions, often called centrality measures, which often lead to different results.
Albert +42 more
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Metabolic Reprogramming in Triple-Negative Breast Cancer
Frontiers in Oncology, 2020 Metabolic reprogramming is an emerging hallmark of cancer cells, in which cancer cells exhibit distinct metabolic phenotypes to fuel their proliferation and progression.
Xiangyu Sun +9 more
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