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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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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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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Predicting metabolic pathways from metabolic networks with limited biological knowledge [PDF]
2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), 2010 Understanding the metabolism of new species (e.g. endophytic fungi that produce fuel) have tremendous impact on human lives. Based on predicted proteins and existing reaction databases, one can construct the metabolic network for the species. Next is to identify critical metabolic pathways from the network.
Henry C M Leung +2 more
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The global integrative network: integration of signaling and metabolic pathways
ABIOTECH, 2022 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. However, current databases use distinct structures to present signaling and metabolic pathways,
Xiao Chang, Xiaoquan Qi, Xu Chi
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Enumerating all possible biosynthetic pathways in metabolic networks [PDF]
Scientific Reports, 2018 Abstract Exhaustive 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 ...
Aarthi Ravikrishnan +2 more
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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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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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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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