Metadag: a web tool to generate and analyse metabolic networks by Pere Palmer-Rodríguez, Ricardo Alberich, Mariana Reyes-Prieto, José A. Castro, Mercè Llabrés

Subjects: “…Metabolic networks construction…”
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In silico identification of switching nodes in metabolic networks by Mairet, Francis

“…The soundness of ISIS is shown with four case studies, using both core and genome-scale metabolic networks of Escherichia coli, Saccharomyces cerevisiae and the diatom Phaeodactylum tricornutum. …”
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Dynamic Metabolic Footprinting Reveals the Key Components of Metabolic Network in Yeast Saccharomyces cerevisiae by Pramote Chumnanpuen, Michael Adsetts Edberg Hansen, Jørn Smedsgaard, Jens Nielsen

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Machine learning methods for predicting essential metabolic genes from Plasmodium falciparum genome-scale metabolic network. by Itunuoluwa Isewon, Stephen Binaansim, Faith Adegoke, Jerry Emmanuel, Jelili Oyelade

“…Furthermore, this study enhanced the understanding of metabolic networks and their role in determining gene essentiality in Plasmodium falciparum. …”
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Analyzing sorbitol biosynthesis using a metabolic network flux model of a lichenized strain of the green microalga Diplosphaera chodatii by Hadi Nazem-Bokaee, Erik F. Y. Hom, Sarah Mathews, Cécile Gueidan

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Modeling the Differences in Biochemical Capabilities of Pseudomonas Species by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences? by Parizad Babaei, Tahereh Ghasemi-Kahrizsangi, Sayed-Amir Marashi

“…To date, several genome-scale metabolic networks have been reconstructed. These models cover a wide range of organisms, from bacteria to human. …”
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Genome-Wide Association Study of Metabolic Syndrome in Koreans by Seok Won Jeong, Myungguen Chung, Soo-Jung Park, Seong Beom Cho, Kyung-Won Hong

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Prediction and Analysis of metabolic mechanism for regional water system from the perspective of quantity-quality collaborative control——A case study of Zhejiang Province, China... by Siqi Li, Yang Zhang, Tianqi Liu, Jinbo Zhang, Huaicheng Guo, Xiao Pu, Lu Lu, Changbo Qin

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Effects of different types of ginseng on intercellular wireless communication networks and central carbon metabolism pathways by Yujiao Liu, Dingqiang Lu, Jiayi Qiang, Lianjie Xu, Ming Li, Xinqian Wang, Yixuan Liu, Yifei Zhang, Wei Xu, Chenyu Xu, Qingwei Song, Wenling Wu, Yimeng Bi, Ruijuan Ren, Guangchang Pang

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Mapping transcriptomic profiles of seminal vesiculitis and experimental verification by Chenkui Miao, Shaobo Zhang, Jiajin Wu, Meiling Bao, Zengjun Wang, Bianjiang Liu

“…We identified enriched Go Ontology terms, pathway maps, processes, toxicity, and metabolic networks of seminal vesiculitis. Results: Glutathione S-transferase activity is highly enriched, indicating its essential role in the disease's development. …”
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Research Progress on Genome-Scale Metabolic Models of Lactic Acid Bacteria and Their Application in the Food System by LIU Zihao, NI Haojie, LI Wenlu, WANG Fengzhong, WANG Yanbo, ZENG Hong

“…Genome-scale metabolic models (GSMMs) serve as essential tools for studying microbial metabolism, which simulate the metabolic networks of microorganisms and accurately describe the genotype-phenotype relationships. …”
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Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont by Shan Zhang, Weizhi Song, Geogios Marinos, Silvio Waschina, Johannes Zimmermann, Christoph Kaleta, Torsten Thomas

“…To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. …”
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Longitudinal network changes and phenoconversion risk in isolated REM sleep behavior disorder by Chris C. Tang, Yoshikazu Nakano, An Vo, Nha Nguyen, Katharina A. Schindlbeck, Paul J. Mattis, Kathleen L. Poston, Jean-François Gagnon, Ronald B. Postuma, Martin Niethammer, Yilong Ma, Shichun Peng, Vijay Dhawan, David Eidelberg

“…Using positron emission tomography, we assessed changes in Parkinson’s disease-related motor and cognitive metabolic networks and caudate/putamen dopaminergic input in a 4-year longitudinal imaging study of 13 male subjects with this disorder. …”
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Utilizing integrated bioinformatics and machine learning approaches to elucidate biomarkers linking sepsis to purine metabolism-associated genes by Fanqi Liang, Man Zheng, Jingjiu Lu, Peng Liu, Xinyu Chen

“…A pivotal element in the pathogenesis and progression of sepsis involves the significant disruption of oncological metabolic networks, where cells within the pathological milieu exhibit metabolic functions that diverge from their healthy counterparts. …”
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Insights of cellular and molecular changes in sugarcane response to oxidative signaling by Lucas Felipe Silva, Kellya F. M. Barreto, Helaine Cristiane Silva, Iara Dantas de Souza, Carlos H. S. G. Meneses, Adriana F. Uchôa, Katia C. Scortecci

“…The data suggest that sugarcane plants responded to oxidative signals by adjusting their metabolic networks, promoting sustained development and potential pathways for targeted plant breeding.…”
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Application of lipidomics in the study of traditional Chinese medicine by Yang Yang, Guangyi Yang, Wenpeng Zhang, Lingyi Xin, Jing Zhu, Hangtian Wang, Baodong Feng, Renyan Liu, Shuya Zhang, Yuanwu Cui, Qinhua Chen, Dean Guo

“…This field compares changes in diseases or drug impact, identifying biomarkers and molecular mechanisms present in lipid metabolic networks across different physiological or pathological states. …”
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Methionine-driven methylation modification overcomes plasmid-mediated high-level tigecycline resistance by Dan Fang, Tianqi Xu, Fulei Li, Yue Sun, Jingyi Sun, Yanqing Yin, Haijie Zhang, Zhiqiang Wang, Yuan Liu

“…Overall, this work highlights the therapeutic potential of Met in overcoming plasmid-mediated high-level tigecycline resistance, and provides a new paradigm to enhance antibiotic efficacy by harnessing cellular metabolic networks as well as epigenetic modifications.…”
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Metagenomic analysis revealing the metabolic role of microbial communities in the free amino acid biosynthesis of Monascus rice vinegar during fermentation by Hang Gao, Jian Zhang, Li Liu, Lijun Fu, Yan Zhao, Germán Mazza, Xin Zhang

“…FAA is one of the major metabolites produced by microorganisms; however, the microbial metabolic network on FAA biosynthesis remains unclear. …”
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The ability of pentose pathways to form all essential metabolites provides clues to the origins of metabolism. by Steffen N Lindner, Markus Ralser

“…The structure of the early metabolic network is unknown. Here, we report that when considered together, pentose utilization pathways form all life-essential precursors. …”
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