Systems Biology of Metabolism

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

Vander Heiden, M. G., Cantley, L. C., & Thompson, C. B. (2009) · Science · doi:10.1126/science.1160809 · Cited by 16,197

Tissue-based map of the human proteome

Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624

Diet rapidly and reproducibly alters the human gut microbiome

David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100

A metagenome-wide association study of gut microbiota in type 2 diabetes

Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762

Exploring the metabolic and genetic control of gene expression on a genomic scale.

Derisi, J., Iyer, V., & Brown, P. (1997) · Science · doi:10.1126/science.278.5338.680 · Cited by 4,832

Functional interactions between the gut microbiota and host metabolism

Tremaroli, V., & Bäckhed, F. (2012) · Nature · doi:10.1038/nature11552 · Cited by 4,387

Resveratrol improves health and survival of mice on a high-calorie diet

Baur, J. A., Pearson, K. J., Price, N. L., Jamieson, H. A., Lerin, C., Kalra, A., Prabhu, V. V., Allard, J. S., Lopez-Lluch, G., Lewis, K., et al. (2006) · Nature · doi:10.1038/nature05354 · Cited by 4,290

Systems biology: a brief overview

Kitano, H. (2002) · Science · doi:10.1126/science.1069492 · Cited by 4,265

Amino acid and nucleotide metabolism shape the selection of trophic levels in animalsPreprint

Yu, R., Wang, H., & Nielsen, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.01.450789 · Cited by 1

Isotopologue Profiling of Infectious Disease

Steiner, T. M., & Eisenreich, W. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-818731-9.00149-x · Cited by 1

The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import by enhancing assembly of the TOM complexPreprint

Rödl, S., den Brave, F., Räschle, M., Lenhard, S., Groh, C., Becker, H., Zimmermann, J., Morgan, B., Richling, E., Becker, T., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.26.489513 · Cited by 1

An enzyme activation network provides evidence for extensive regulatory crosstalk between metabolic pathwaysPreprint

Zubaidi, S. M. A., Nasar, M. I., Ralser, M., Notebaart, R. A., & Alam, M. T. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.16.567372 · Cited by 1

TRANSCRIPTOMIC ANALYSES AND COMPUTATIONAL MODELING REVEAL THAT FATTY ACID TRANSPORT PROTEIN 2 (FATP2) IMPACTS THE TRANSCRIPTIONAL ACTIVITY OF PPARα THUS ALTERING THE LIPID METABOLIC LANDSCAPE

Perez, V. M. (2019) · Lincoln (University of Nebraska)

Uncovering oomycete metabolism using systems biology

Rodenburg, S. Y. A. (2020) · doi:10.18174/528798

Population-based Optimization for Kinetic Parameter Identification in Glycolytic Pathway in Saccharomyces cerevisiaePreprint

Węglarz‐Tomczak, E., Tomczak, J. M., Eiben, A. E., & Brul, S. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2010.06456

Racing-red chassis : Advancing Rhodobacter sphaeroides as platform for isoprenoid production

Orsi, E. (2020) · doi:10.18174/514533

Maternal and Fetal Metabonomic Alterations in Maternal Lipopolysaccharide Exposure-induced Male Offspring Glucose Metabolism DisordersPreprint

Qing, Q., Huang, L., & Zhao, M. (2020) · Research Square · doi:10.21203/rs.3.rs-133666/v1

Rapid hazard characterization of environmental chemicals using a compendium of human cell lines from different organs_suppl

Chen, Z. (2020) · ALTEX · doi:10.14573/altex.2002291s

Construction of an inter-organ transomic network for whole-body metabolism

Kokaji, T., & Kuroda, S. (2022) · Current Opinion in Endocrine and Metabolic Research · doi:10.1016/j.coemr.2022.100361

Salmonella typhimurium induces intestinal inflammatory response through activation of Cav- 1/Akt/IKKα/NF-κB signaling pathwayPreprint

Li, H., Shang, Z., Wei, Z., Wang, Y., Liu, X., & Qiao, J. (2022) · Research Square · doi:10.21203/rs.3.rs-2194918/v1

A systems level approach to study metabolic networks in prokaryotes with the aromatic amino acid biosynthesis pathway

K, P. V., & Sinha, S. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2022.1084727

Fluxomics as a methodological tool for designing drugs

Ponamarev, V. S. (2023) · Legal regulation in veterinary medicine · doi:10.52419/issn2782-6252.2023.1.72

Métodos numéricos para modelos de redes metabólicas.

de Oliveira, R. D. (2022) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.3.2022.tde-05072023-111915

Learning metabolic dynamics from irregular observations by Bidirectional Time-Series State Transfer Network

Xu, S., Xu, T., Yang, Y., & Chen, X. (2024) · mSystems · doi:10.1128/msystems.00697-24

Auxotrophy-based curation improves the consensus genome-scale metabolic model of yeast

Han, S., Wu, K., Wang, Y., Li, F., & Chen, Y. (2024) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2024.07.006

Evaluating the Mechanism of a Traditional Herbal Syrup for Anemia Treatment Using Liver Metabolomics

Dai, W., Zhang, D., Li, J., & Han, L. (2024) · Journal of Visualized Experiments · doi:10.3791/67225

Metabolic makeover: how to gain weight fast on a formate diet : Exploring and engineering synthetic metabolism in E. coli for optimal growth on formate

Yilmaz, S. (2024) · doi:10.18174/662566

Organic acid disorders

Seashore, M. R., & Pascual, J. M. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-19041-4.00081-9

Systems biology at a glance

Hassan, M. S., Nasrin, T., Vishwakarma, A., Hoque, M., & Ali, S. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-22326-6.00001-8

Model-Driven Elucidation of Lactose and Galactose Metabolism via Oxidoreductive Pathway in Sungouiella intermedia for Cell Factory ApplicationsPreprint

Peri, K. V. R., Domenzain, I., Alalam, H., Rascón, A. V., Nielsen, J., & Geijer, C. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.19.624258

Metabolic implications for dual substrate growth in “ Candidatus Accumulibacter”Preprint

Páez-Watson, T., Jansens, C., van Loosdrecht, M. C. M., & Roy, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.13.628880

Systems biology methods to study the epigenome and metabolic-epigenetic interactions

Manjunatha, P. B., Bhowmick, R., & Chandrasekaran, S. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26759-8.00006-0

Progress in monitoring molecular, cellular and metabolic dynamics using mass spectrometry imaging

Gamcsik, M. P., Bruce, E. R., & Muddiman, D. C. (2025) · Bioanalysis · doi:10.1080/17576180.2025.2580293

Simulation and modeling of metabolic networks

Klipp, E. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-99507-8.00008-1

Non-targeted metabolomics profiling of Vaccinium dunalianum Wight: UPLC-MS/MS analysis of metabolite variability across different tissues

Yao, C., Yu, Y., Dong, X., An, X., Xia, J., Zhao, P., Zou, L.-H., Xie, S., Feng, J. T., & Yang, X. (2025) · Natural Product Research · doi:10.1080/14786419.2025.2588333

Additional file 4 of Network pharmacology combined with metabolomics to explore the mechanism for Lonicerae Japonicae flos against respiratory syncytial virus

Ding, J., Li, J., Zhang, Z., Du, Y., Liu, Y., Wang, P., & Du, H. (2024) · Figshare · doi:10.6084/m9.figshare.26652687

Additional file 2 of Network pharmacology combined with metabolomics to explore the mechanism for Lonicerae Japonicae flos against respiratory syncytial virus

Ding, J., Li, J., Zhang, Z., Du, Y., Liu, Y., Wang, P., & Du, H. (2024) · Figshare · doi:10.6084/m9.figshare.24798103

Additional file 1 of Network pharmacology combined with metabolomics to explore the mechanism for Lonicerae Japonicae flos against respiratory syncytial virus

Ding, J., Li, J., Zhang, Z., Du, Y., Liu, Y., Wang, P., & Du, H. (2023) · Figshare · doi:10.6084/m9.figshare.24797807

Additional file 3 of Network pharmacology combined with metabolomics to explore the mechanism for Lonicerae Japonicae flos against respiratory syncytial virus

Ding, J., Li, J., Zhang, Z., Du, Y., Liu, Y., Wang, P., & Du, H. (2024) · Figshare · doi:10.6084/m9.figshare.26652684

Improved flux profiling in genome-scale modeling of human cell metabolism

Huijer, C., Xiang, J., Chen, Y., & Yu, R. (2026) · Cell Reports Methods · doi:10.1016/j.crmeth.2025.101275

Two Decades of Genome-Scale Metabolic Modeling for Saccharomyces cerevisiae

Kocabaş, P. (2026) · GAZI UNIVERSITY JOURNAL OF SCIENCE · doi:10.35378/gujs.1840536

MetaKnogic-Alpha: A Hyper-Relational Knowledge Base for Grounded Metabolic ReasoningPreprint

Dang, P., Swaminathan, P., Guo, T., Wan, C., Cao, S., & Zhang, C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.05.704050

Advances in genome-scale metabolic modeling of Bacillus subtilis

Kocabaş, P. (2026) · Biotechnology Letters · doi:10.1007/s10529-026-03712-w

Taxonomie et inférence fonctionnelle des procaryotes : développement de MACADAM, une base de données de voies métaboliques associées à une taxonomie

Boulch, M. L. (2019) · theses.fr (ABES) · doi:10.70675/51a9bc1az041fz4060zb55dz54ff94022843

Computational modeling to design and analyze synthetic metabolic circuits

Koch, M. (2019) · theses.fr (ABES) · doi:10.70675/c62d36ffz8c11z4509zad56ze764c2cee027

Logic programming tools for metabolic fluxes analysis and biological applications

Mahout, M. (2023) · theses.fr (ABES) · doi:10.70675/a4f76dc9z54aaz4c4bza3aez5a23506df981

A Novel Topology-Based Candidate Reaction Prediction Approach for Gap-Fillings of Genome-Scale Metabolic Models

Qu, J., & Wang, K. (2026) · Metabolites · doi:10.3390/metabo16040258

Biology Tools for Optimizing Bacterial Cellulose Production

Pacheco, M., Montenegro-Silva, P., Dourado, F., Gama, M., Domingues, L., & Dias, Ó. (2026) · Springer eBooks · doi:10.1007/978-3-032-07042-5_2

Hypergraph learning with multi-dimensional metabolite feature extractions and static–dynamic attention mechanisms to fill missing reactions in metabolic networks

Wang, K., Qu, J., Liu, F. M., Luan, X., & Zhou, J. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag314

Sense to synthesis: Metabolic adaptation to environments

Yu, J., Huang, Y., & Huang, A. C. (2026) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2026.102935

Virtual screening identifies specnuezhenide as a potential therapeutic agent for rosacea via KLK5/TLR4/NF-κB pathway inhibition and metabolic modulation

Xu, J., Li, X., Chen, M., Di, S., Zhang, Y., Xu, Y., Xu, B., Guo, J., Xu, J., Li, Y., et al. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1886252

Metabolic Supercharging: Active Learning Strategies for Increasing Student Engagement With Metabolism

Johnson, R. J., Genova, L. A., & Grimes, C. L. (2026) · Biochemistry and Molecular Biology Education · doi:10.1002/bmb.70077

Integrated volatilomic and metabolomic analyses reveal the metabolic mechanisms underlying strain-dependent aroma differentiation in Lepista mycelial fermentationPreprint

Gu, M., Chen, Q., Huang, C., Shi, A., Gontard, N., & Gao, W. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7349242

Engineering alternative proteins for future foods: Advances in cultivated meat, precision fermentation, and plant protein structuring

Verma, V., Pandey, V. K., Sharma, R., & Verma, P. (2026) · Food Bioscience · doi:10.1016/j.fbio.2026.109846

PMPIHGLL: predicting metabolite–protein interactions using dual hypergraph convolutional networks and large language models

Chen, L., Jin, Z., Shao, Y., & Zhou, B. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag489

Bidirectional time-series state transfer network: a computational framework for target-directed control optimization of metabolic processes

Xu, S., Zhang, Y., & Chen, X. (2026) · Bioresource Technology · doi:10.1016/j.biortech.2026.135852

Enterobacteriaceae for succinic acid biomanufacturing: metabolic blueprints, systems-level engineering and future perspectives

Szczerba, H., Carranza‐Saavedra, D., Kuzdraliński, A., Moreno, F., Nogales, J., & Ostrowska, M. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.109052

The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein–Protein Interactions (PPIs)

Yakubu, R. (2026) · Advances in experimental medicine and biology · doi:10.1007/978-3-032-29437-1_28

Bioconversion of carbon dioxide into biofuels and value-added chemicals

Mamimin, C., In-chan, S., Chaikitkaew, S., Reungsang, A., & O‐Thong, S. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-40457-3.00010-x

Pretreatment with Feining Granules Mitigates LPS-Induced Lung Injury in Mice: Pharmacological and Serum Metabolomics Evidence

Tan, Z., Li, K., Zhang, L., Yin, Y., Bi, B., He, Z., & Bao, J. (2026) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2026.122579

Background

(2015) · BENTHAM SCIENCE PUBLISHERS eBooks · doi:10.2174/9781681080864115010004

Thermodynamics-based Significance Ranking of Candidates for Metabolomics

Kiparissides, A., & Vassily Hatzimanikatis, A. (2013) · Infoscience (Ecole Polytechnique Fédérale de Lausanne)

Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models

Dahal, S., Yurkovich, J. T., Xu, H., Palsson, B. Ø., & Yang, L. (2020) · PROTEOMICS · doi:10.1002/pmic.201900282 · Cited by 55

Quantitative modeling of human metabolism: A call for a community effort

Masid, M., & Vassily Hatzimanikatis, A. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.04.008 · Cited by 7

From Gene Expression to Metabolic Fluxes

Oliveira, A. P., Jewett, M. C., & Nielsen, J. (2008) · Humana Press eBooks · doi:10.1007/978-1-59745-531-2_3 · Cited by 7