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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A toolbox model of evolution of metabolic pathways on networks of arbitrary topology. [PDF]
PLoS Computational Biology, 2011 In prokaryotic genomes the number of transcriptional regulators is known to be proportional to the square of the total number of protein-coding genes.
Tin Yau Pang, Sergei Maslov
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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 ...
Wang Weirong +4 more
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Pathway Preserving Representation of Metabolic Networks [PDF]
Computer Graphics Forum, 2011 AbstractImprovements in biological data acquisition and genomes sequencing now allow to reconstruct entire metabolic networks of many living organisms. The size and complexity of these networks prohibit manual drawing and thereby urge the need of dedicated visualization techniques.
Lambert, Antoine +2 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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Network structure of metabolic pathways [PDF]
Journal of Biological Physics and Chemistry, 2001 networks (or graphs) consist of nodes and links between them. The number of links per node, which we call the class of the node, may vary between nodes, but in a homogeneous network the statistical distribution of links will be the same from region to region across the network.
Vic Norris, Upres A Cnrs, Derek Raine
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Serum and urine metabolomic biomarkers for predicting prognosis in patients with immunoglobulin A nephropathy [PDF]
Kidney Research and Clinical Practice, 2023 Background Immunoglobulin A nephropathy (IgAN) is the most prevalent form of glomerulonephritis worldwide. Prediction of disease progression in IgAN can help to provide individualized treatment based on accurate risk stratification.
You Hyun Jeon +7 more
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Metabolomic approaches applied to the study of cervical cancer: a systematic review
Brazilian Journal of Oncology, 2022 Background: Cervical cancer (CC) is the fourth leading cause of cancer among women in the world. Metabolomics can provide a deeper understanding of the underlying metabolic alterations associated with its pathophysiology ...
Natalia Damasceno Almeida +3 more
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Integrated RNA-sequencing and network analysis approach to identify the Hub genes and vital pathways associated with gastric cancer [PDF]
Journal of Pharmacy & Pharmacognosy Research, 2023 Context: Gastric cancer is one of the most prevalent types of cancer in developing countries and ranks fourth in terms of death causes. Helicobacter pylori infection is a significant contributor to the emergence of gastric cancer. Lack of early diagnosis
Karthick Vasudevan +12 more
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Finding branched pathways in metabolic network via atom group tracking.
PLoS Computational Biology, 2021 Finding non-standard or new metabolic pathways has important applications in metabolic engineering, synthetic biology and the analysis and reconstruction of metabolic networks.
Yiran Huang +3 more
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