Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study by M. A. Kulyashov, R. Hamilton, Y. Afshin, S. K. Kolmykov, T. S. Sokolova, T. M. Khlebodarova, M. G. Kalyuzhnaya, I. R. Akberdin

“…We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. …”
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Spatial metabolomics in mental disorders and traditional Chinese medicine: a review by Chaofang Lei, Jiaxu Chen, Zhigang Chen, Chongyang Ma, Xudong Chen, Xiongxing Sun, Xukun Tang, Jun Deng, Shiliang Wang, Junlin Jiang, Dahua Wu, Le Xie

“…Spatial metabolomics precisely reflects the characteristics of metabolic network changes in metabolites within entire tissues or specific micro-regions. …”
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Mental Health Across the Metabolic Spectrum by Vrinda Saxena, Isaac Marin-Valencia

“…This shortcoming is attributable to the complex and multilayered nature of both the metabolic network and mental processes, as well as the lack of robust quantitative methods to analyze the workings of the mind. …”
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Tumor metabolic regulators: key drivers of metabolic reprogramming and the promising targets in cancer therapy by Kun Huang, Ying Han, Yihong Chen, Hong Shen, Shan Zeng, Changjing Cai

“…Research indicates that various metabolic regulators form a metabolic network in the TME and interact with immune cells, coordinating the tumor immune response. …”
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Analysis of fermentation characteristics in fermented grains across seven rounds of sauce-flavored Baijiu: Microbial communities structure, physicochemical parameters, volatile and... by Xiaomin Liu, Yingchun Mu, Xiangxiang Lv, Nuo Chen, Lei Chen, Tangzheng Wen, Wei Su

“…Correlation analysis revealed Issatchenkia, Kroppenstedtia, Monascus, Virgibacillus, and Pichia significantly contributed to flavor compound. Finally, a metabolic network was constructed to predict microbial and flavor compound metabolic pathways. …”
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The formation pathway of flavor compounds in steamed Antarctic krill (Euphausia superba) based on untargeted metabolomics by Tingting Yang, Yang Liu, Jing Bai, Yan Fan, Ye Chen, Ping Dong, Xia Yang, Hu Hou

“…Hierarchical clustering and volcano plot showed metabolic shifts between raw and steamed krill, with differential metabolites like hydroquinone and gamma-aminobutyric acid emerging as key contributors to flavor changes. Furthermore, metabolic network further linked these shifts to reactions involving amino acids, nucleotide and other compounds during steaming, impacting the overall taste.…”
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Ecological Network Analysis for a Low-Carbon and High-Tech Industrial Park by Yi Lu, Meirong Su, Gengyuan Liu, Bin Chen, Shiyi Zhou, Meiming Jiang

“…In order to reveal the processes of carbon metabolism in a low-carbon high-tech industrial park, we selected Beijing Development Area (BDA) International Business Park in Beijing, China as case study, establishing a seven-compartment- model low-carbon metabolic network based on the methodology of Ecological Network Analysis (ENA). …”
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Genome-wide transcriptomics revealed carbon source-mediated gamma-aminobutyric acid (GABA) production in a probiotic, Lactiplantibacillus pentosus 9D3 by Nachon Raethong, Pitakthai Chamtim, Roypim Thananusak, Kanyawee Whanmek, Chalat Santivarangkna

“…The integration of transcriptome data with a genome-scale metabolic network (GSMN) revealed that L. pentosus 9D3 displays adaptability by synthesizing GABA as an alternative acid-tolerant mechanism when lactose is used as a carbon source rather than depending on the fatty acid synthesis and the arginine catabolic pathway. …”
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Glyoxylate, a New Marker Metabolite of Type 2 Diabetes by Victoria J. Nikiforova, Pieter Giesbertz, Jan Wiemer, Bianca Bethan, Ralf Looser, Volker Liebenberg, Patricia Ruiz Noppinger, Hannelore Daniel, Dietrich Rein

“…Glyoxylate in its metabolic network may serve as an early marker in diabetes diagnosis with predictive qualities for associated complications and as potential to guide the development of new antidiabetic therapies.…”
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A Novel Metabolic Connectome Method to Predict Progression to Mild Cognitive Impairment by Min Wang, Zhuangzhi Yan, Shu-yun Xiao, Chuantao Zuo, Jiehui Jiang

“…In this study, we acquired fluorodeoxyglucose PET images and clinical assessments from 420 MCI patients with 36 months follow-up. Individual metabolic network based on connectome analysis was constructed, and the metabolic connectivity in this network was extracted as predictive features. …”
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The perspectives of metabolomics studies of potato plants by R. K. Puzanskiy, V. V. Yemelyanov, T. A. Gavrilenko, M. F. Shishova

“…The sum of metabolites, which is produced as a result of metabolic network activity, is defined as metabolome. Complex studies of metabolic diversity with the use of modern state-of-the-art chromatography approaches and highly precise detection of individual compounds revealed specificity of metabolic spectra from subcellular to organism levels and its amazing plasticity under the influence of a variety of internal and external stimuli. …”
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The Analysis of Estrogen-Degrading and Functional Metabolism Genes in Rhodococcus equi DSSKP-R-001 by Kejian Tian, Fanxing Meng, Qi Meng, Yan Gao, Lili Zhang, Le Wang, Yuqing Wang, Xue Li, Hongliang Huo

“…In summary, the biodegradation of estrogens is coordinated by a metabolic network of estrogen-degrading enzymes, transporters, metabolic enzymes, and other coenzymes. …”
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Metabolic Profiling by UPLC–Orbitrap–MS/MS of Liver from C57BL/6 Mice with DSS-Induced Inflammatory Bowel Disease by Zhongquan Xin, Zhenya Zhai, Hongrong Long, Fan Zhang, Xiaojun Ni, Jinping Deng, Lunzhao Yi, Baichuan Deng

“…Notably, 133 metabolites were identified by an integrated database. Metabolism network and pathway analyses demonstrated that the metabolic disturbance of the liver in IBD mice was mainly enriched in bile acid metabolism, arachidonic acid metabolism, amino acid metabolism, and steroid hormone biosynthesis, while those disturbances were regulated or reversed through cecropin A and antibiotic treatment. …”
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Coupling genome-wide continuous perturbation with biosensor screening reveals the potential targets in yeast isopentanol synthesis network by Qi Xiao, Jingjing Shi, Lixian Wang, Guoping Zhao, Yanfei Zhang

“…Additionally, functional analysis of the co-DEGs revealed that MAL33 is associated with the synthesis of branched-chain higher alcohols, expanding the intracellular metabolic network and offering new possibilities for green, cost-effective biofuel production.…”
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Molybdenum Can Regulate the Expression of Molybdase Genes, Affect Molybdase Activity and Metabolites, and Promote the Cell Wall Bio-Synthesis of Tobacco Leaves by Yuan Zhao, Yu Zhang, Kai Zhang, Jiashu Tian, Huanyu Teng, Zicheng Xu, Jiayang Xu, Huifang Shao, Wei Jia

“…Furthermore, the cell walls thickened, increasing the ability of the plant to withstand disturbances. The metabolic network diagrams indicate that Mo regulated galactose metabolism, and arginine and proline acid biosynthesis. …”
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