A Caenorhabditis elegans genome-scale metabolic network model

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Applications of genome‐scale metabolic reconstructions

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Using Genome-scale Models to Predict Biological Capabilities

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BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

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Carnitine biosynthesis in mammals

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Rictor/TORC2 regulates fat metabolism, feeding, growth, and life span in Caenorhabditis elegansPreprint

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Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

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Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism

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Dauer

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Global analysis of dauer gene expression inCaenorhabditis elegans

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Diet-Induced Developmental Acceleration Independent of TOR and Insulin in C. elegans

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The Influence of Bacterial Diet on Fat Storage in C. elegans

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Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits

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Fatty Acid Desaturation and the Regulation of Adiposity in Caenorhabditis elegans

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Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

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BRENDA in 2015: exciting developments in its 25th year of existence

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A 13C Isotope Labeling Strategy Reveals the Influence of Insulin Signaling on Lipogenesis in C. elegans

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Trehalose Renders the Dauer Larva of Caenorhabditis elegans Resistant to Extreme Desiccation

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WormBase 2014: new views of curated biology

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Alternate metabolism during the dauer stage of the nematode Caenorhabditis elegans

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Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

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Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response

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Adaptive Capacity to Bacterial Diet Modulates Aging in C. elegans

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Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans

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Caenorhabditis elegans Genomic Response to Soil Bacteria Predicts Environment-Specific Genetic Effects on Life History Traits

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SAGE surveys C. elegans carbohydrate metabolism: evidence for an anaerobic shift in the long-lived dauer larva.

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Decreased Energy Metabolism Extends Life Span inCaenorhabditis elegansWithout Reducing Oxidative Damage

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Integration of metabolomics data into metabolic networks

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Intermediary metabolism

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Fertility and Germline Stem Cell Maintenance under Different Diets Requires nhr-114/HNF4 in C. elegans

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Worms, bacteria, and micronutrients: an elegant model of our diet

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Phospholipids from the free‐living nematodeCaenorhabditis elegans

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The C. elegans lethal gut-obstructed gob-1 gene is trehalose-6-phosphate phosphatase

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Metabolism of Glycogen and Neutral Lipids by Aphelenchus avenae and Caenorhabditis sp. in Aerobic, Microaerobic and Anaerobic Environments.

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Synthesis of paucimannose N-glycans by Caenorhabditis elegans requires prior actions of UDP-N-acetyl-d-glucosamine:alpha-3-d-mannoside beta1,2-N-acetylglucosaminyltransferase I, alpha3,6-mannosidase II and a specific membrane-bound beta-N-acetylglucosaminidase

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Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms

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Profiling the Anaerobic Response of C. elegans Using GC-MS

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Carbohydrates and glycosylation

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Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy

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Sex Differences in Carbohydrate Metabolism Are Linked to Gene Expression in Caenorhabditis elegans

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Carnitine protects the nematode Caenorhabditis elegans from glucose-induced reduction of survival depending on the nuclear hormone receptor DAF-12

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Isopentenyl-diphosphate isomerase is essential for viability of Caenorhabditis elegans

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Current status and applications of genome-scale metabolic models

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Metabolic Flexibility as an Adaptation to Energy Resources and Requirements in Health and Disease

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Lipid and Carbohydrate Metabolism in Caenorhabditis elegans

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DAF-16/FoxO in Caenorhabditis elegans and Its Role in Metabolic Remodeling

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Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans

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Genome-scale metabolic network reconstruction of model animals as a platform for translational research

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C. elegans and its bacterial diet as a model for systems-level understanding of host–microbiota interactions

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The nutritional requirements of Caenorhabditis elegans

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The C. elegans intestine: organogenesis, digestion, and physiology

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Stress sensor Ire1 deploys a divergent transcriptional program in response to lipid bilayer stress

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A delicate balance between bacterial iron and reactive oxygen species supports optimal C. elegans development

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Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion

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Caenorhabditis elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor

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Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing pan-neuronal human amyloid beta

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Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging

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A metabolic switch regulates the transition between growth and diapause in C. elegans

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Metabolic network modeling with model organisms

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Metabolomics and lipidomics in Caenorhabditis elegans using a single-sample preparation

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Integrative omics approaches provide biological and clinical insights: examples from mitochondrial diseases

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A Persistence Detector for Metabolic Network Rewiring in an Animal

Bulcha, J., Giese, G. E., Ali, M. Z., Lee, Y., Walker, M. D., Holdorf, A. D., Yilmaz, L. S., Brewster, R. C., & Walhout, A. J. M. (2019) · Cell Reports · doi:10.1016/j.celrep.2018.12.064 · Cited by 54 · see citing works

How choosing random-walk model and network representation matters for flow-based community detection in hypergraphs

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Caenorhabditis elegans as a Model Host to Monitor the Candida Infection Processes

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Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels

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Beyond Proteostasis: Lipid Metabolism as a New Player in ER Homeostasis

Xu, J., & Taubert, S. (2021) · Metabolites · doi:10.3390/metabo11010052 · Cited by 47 · see citing works

Genome‐wide characterization of Phytophthora infestans metabolism: a systems biology approach

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StanDep: Capturing transcriptomic variability improves context-specific metabolic models

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Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans

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Glycolate combats massive oxidative stress by restoring redox potential in Caenorhabditis elegans

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WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualizationPreprint

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C. elegans as a model for inter-individual variation in metabolism

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WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization

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Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the Nematode

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Nutrient control of growth and metabolism through mTORC1 regulation of mRNA splicing

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Systems-level design principles of metabolic rewiring in an animal

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Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets

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Tolerance to NADH/NAD+ imbalance anticipates aging and anti-aging interventions

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Identification of enzymes that have helminth-specific active sites and are required for Rhodoquinone-dependent metabolism as targets for new anthelmintics

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A systems-level, semi-quantitative landscape of metabolic flux in C. elegans

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A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential

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Stressful development: integrating endoderm development, stress, and longevity

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A metabolic regulatory network for the Caenorhabditis elegans intestine

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FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data

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Unveiling the potential of systems biology in biotechnology and biomedical research

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WormJam: A consensusC. elegansMetabolic Reconstruction and Metabolomics Community and Workshop Series

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Metabolic decisions in development and disease—a Keystone Symposia report

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Essential gene prediction using limited gene essentiality information–An integrative semi-supervised machine learning strategy

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Generating Bacterial Foods in Toxicology Studies with Caenorhabditis elegans

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Systems biology analysis using a genome-scale metabolic model shows that phosphine triggers global metabolic suppression in a resistant strain of C. elegansPreprint

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A genome-scale metabolic model of parasitic whipworm

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Transcriptional regulation of metabolic flux: A Caenorhabditis elegans perspective

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Genome‐scale metabolic models applied for human health and biopharmaceutical engineering

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Functional identification of microRNA-centered complexes in C. elegans

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Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model

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An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics

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Resolving tissue and cellular functions of parasitic nematodes

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Host–microbe interactions rewire metabolism in a C. elegans model of leucine breakdown deficiency

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CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

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Integrating metabolomics into the diagnosis and investigation of anthelmintic resistance

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Microbial degradation of herbicides in contaminated soils by following computational approaches

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Investigation of the threonine metabolism of Echinococcus multilocularis: The threonine dehydrogenase as a potential drug target in alveolar echinococcosis

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Lifespan extension in Caenorhabditis elegans insulin/IGF-1 signalling mutants is supported by non-vertebrate physiological traits

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Network Architecture and Mutational Sensitivity of the C. elegans Metabolome

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A Persistence Detector for Metabolic Network Rewiring in an AnimalPreprint

Bulcha, J., Giese, G. E., Ali, M. Z., Lee, Y., Walker, M. D., Holdorf, A. D., Yilmaz, L. S., Brewster, R. C., & Walhout, A. J. M. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/382507 · Cited by 4 · see citing works

Comparative Metabolic Network Flux Analysis to Identify Differences in Cellular Metabolism

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Identification of high sugar diet-induced dysregulated metabolic pathways in muscle using tissue-specific metabolic models in DrosophilaPreprint

Moon, S. J., Hu, Y., Dzieciątkowska, M., Kim, A., Chen, P.-L., Asara, J. M., D’Alessandro, A., & Perrimon, N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.24.591006 · Cited by 3 · see citing works

Biallelic variants in BBOX1 cause L-Carnitine deficiency and elevated γ-butyrobetaine

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Modeling tissue-specific Drosophila metabolism identifies high sugar diet-induced metabolic dysregulation in muscle at reaction and pathway levels

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Caenorhabditis elegans Gets Metabolic Network Models

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Cellular Genome-Scale Metabolic Modeling Identifies New Potential Drug Targets Against Hepatocellular Carcinoma

Jamialahmadi, O., Salehabadi, E., Hashemi‐Najafabadi, S., Motamedian, E., Bagheri, F., Mancina, R. M., & Romeo, S. (2022) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2022.0122 · Cited by 2 · see citing works

Biothermodynamic Analysis of Caenorhabditis elegans: Model of Growth and Metabolism Based on Empirical Formulas, Metabolism Reactions, and Thermodynamic Properties of Living Matter and Metabolism

Popovic, M. E., Popović, M., & Pei, D. (2025) · Biophysica · doi:10.3390/biophysica5020019 · Cited by 2 · see citing works

Using Genome-Scale Metabolic Networks for Analysis, Visualization, and Integration of Targeted Metabolomics Data

Hattwell, J. P. N., Hastings, J., Casanueva, O., Schirra, H. J., & Witting, M. A. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0239-3_18 · Cited by 2 · see citing works

An insulin, AMPK, and steroid hormone-mediated metabolic switch regulates the transition between growth and diapause in C. elegansPreprint

Penkov, S., Raghuraman, B. K., Erkut, C., Oertel, J., Galli, R., Ackerman, E. J. M., Vorkel, D., Verbavatz, J., Koch, E., Fahmy, K., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/323956 · Cited by 2 · see citing works

Identification of enzymes that are required for Rhodoquinone-dependent metabolism as targets for new species-specific inhibitorsPreprint

Lautens, M. J., Tan, J. H., Serrat, X., Borrello, S. D., Schertzberg, M. R., & Fraser, A. G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.24.436840 · Cited by 2 · see citing works

scFLUX: a web server for metabolic flux and variation prediction using transcriptomics dataPreprint

Zhang, Z., Chang, W., Alghamdi, N., Fei, M., Wan, C., Lu, A. Z., Zang, Y., Xu, Y., Wu, W., Cao, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.18.496660 · Cited by 2 · see citing works

Flow with the flux: Systems biology tools predict metabolic drivers of ageing in C. elegans

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Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically diverse Caenorhabditis nematodes

Banse, S. A., Sedore, C. A., Coleman-Hulbert, A. L., Johnson, E., Onken, B., Hall, D., Segerdell, E., Jones, E. G., Song, Y., Osman, H., et al. (2025) · eLife · doi:10.7554/elife.104375.3 · Cited by 1 · see citing works

Modelling sponge-symbiont metabolism

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Investigation of the threonine metabolism of Echinococcus multilocularis : the threonine dehydrogenase as a potential drug target in alveolar echinococcosisPreprint

Kaethner, M., Zumstein, P., Preza, M., Grossenbacher, P., Bartetzko, A., Lochner, M., Schürch, S., Regnault, C., Ramírez, D. V., & Lundström‐Stadelmann, B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.27.605433 · Cited by 1 · see citing works

Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically diverse Caenorhabditis nematodesPreprint

Banse, S. A., Sedore, C. A., Coleman-Hulbert, A. L., Johnson, E., Onken, B., Hall, D., Segerdell, E., Jackson, E. G., Song, Y., Osman, H. C., et al. (2024) · eLife · doi:10.7554/elife.104375 · Cited by 1 · see citing works

Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically-diverse Caenorhabditis nematodesPreprint

Banse, S. A., Sedore, C. A., Coleman-Hulbert, A. L., Johnson, E., Onken, B., Hall, D., Segerdell, E., Jones, E. G., Song, Y., Osman, H., et al. (2024) · eLife · doi:10.7554/elife.104375.1 · Cited by 1 · see citing works

Uncovering oomycete metabolism using systems biology

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

Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer

Yang, G. M., Huang, S., Hu, K., Lu, A. Z., Yang, J., Meroueh, N., Dang, P., Wang, Y., Zhu, H., Cao, S., et al. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1117810

Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically-diverse Caenorhabditis nematodesPreprint

Banse, S. A., Sedore, C. A., Coleman-Hulbert, A. L., Johnson, E., Onken, B., Hall, D., Segerdell, E., Jones, E. G., Song, Y., Osman, H., et al. (2025) · eLife · doi:10.7554/elife.104375.2

Metabolic rewiring and osmoregulation in halotolerant Oceanimonas sp. GK1 under salinity stress: Insights from genome-scale modeling and transcriptomics for saline wastewater biotreatmentPreprint

Zhang, J., Xing, W., Hou, Y., Liu, J., Ren, N., Ma, H., Wang, A., Yuan, Q., & Huang, C. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.6065120

pAo : A Consensus Genome-Scale Metabolic Model for Aspergillus oryzae Capturing Intraspecies Diversity

Gilis, J., van der Luijt, C. R. B., Feller, M., Barba, C. S.-G., Sommer, M. O. A., Jahn, L. J., & Kerkhoven, E. J. (2026) · Computational and Structural Biotechnology Journal · doi:10.34133/csbj.0173

Neuropeptides NLP-10 and FLP-18 stimulate lipid catabolism in chronically diet-restricted Caenorhabditis elegansPreprint

Liu, J., Lin, L., Yao, L., Yu, Y., & Luo, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.17.752367

Caenorhabditis elegans Gets Metabolic Network Models

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A systems-level, semi-quantitative landscape of metabolic flux in C. elegans

Zhang, H., Li, X., Tseyang, T., Giese, G. E., Wang, H., Yao, B., Zhang, J., Neve, R. L., Shank, E. A., Spinelli, J. B., et al. (2025) · Nature · doi:10.1038/s41586-025-08635-6 · Cited by 16 · see citing works

A genome-scale database and reconstruction of Caenorhabditis elegans metabolism

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Modeling tissue‐relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels

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Metabolic influences on ageing in Caenorhabditis elegans: A time series multi-omics and metabolic modelling study

Hastings, J. (2019) · Apollo (University of Cambridge) · doi:10.17863/cam.43232