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   https://doi.org/10.1186/s12915-019-0691-z  

   Kirst, Henning; Kerfeld, Cheryl A. (December 2019, BMC Biology)
2. Interpreting metabolic complexity via isotope-assisted metabolic flux analysis

   https://doi.org/10.1016/j.tibs.2023.02.001  

   Moiz, Bilal; Sriram, Ganesh; Clyne, Alisa Morss (June 2023, Trends in Biochemical Sciences)
3. Integrating metabolic scaling and coexistence theories

   https://doi.org/10.1002/ecy.70173  

   Saavedra, Serguei; Arroyo, José Ignacio; Deng, Jie; Marquet, Pablo A; Kempes, Christopher P (August 2025, Ecology)

   Abstract Metabolic scaling theory has been pivotal in formalizing the expected energy expenditures across populations as a function of body size. Coexistence theory has provided a mathematization of the environmental conditions compatible with multispecies coexistence. Yet, it has been challenging to explain how observed community‐wide patterns, such as the inverse relationship between population abundance density and body size, can be unified under both theories. Here, we provide the foundation for a tractable, scalable, and extendable framework to study the coexistence of resource‐mediated competing populations as a function of their body size. For a given thermal domain and response, this integration reveals that the metabolically predicted 1/4 power dependence of carrying capacity of biomass density on body size can be understood as the average distribution of carrying capacities across feasible environmental conditions, especially for large communities. In line with empirical observations, our integration predicts that such average distribution leads to communities in which population biomass densities at equilibrium are independent from body size, and consequently, population abundance densities are inversely related to body size. This integration opens new opportunities to increase our understanding of how metabolic scaling relationships at the population level can shape processes at the community level under changing environments. 

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4. Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases

   https://doi.org/10.3390/metabo11070431  

   Jin, Huan; Moseley, Hunter N. (July 2021, Metabolites)

   null (Ed.)

   Metabolic models have been proven to be useful tools in system biology and have been successfully applied to various research fields in a wide range of organisms. A relatively complete metabolic network is a prerequisite for deriving reliable metabolic models. The first step in constructing metabolic network is to harmonize compounds and reactions across different metabolic databases. However, effectively integrating data from various sources still remains a big challenge. Incomplete and inconsistent atomistic details in compound representations across databases is a very important limiting factor. Here, we optimized a subgraph isomorphism detection algorithm to validate generic compound pairs. Moreover, we defined a set of harmonization relationship types between compounds to deal with inconsistent chemical details while successfully capturing atom-level characteristics, enabling a more complete enabling compound harmonization across metabolic databases. In total, 15,704 compound pairs across KEGG (Kyoto Encyclopedia of Genes and Genomes) and MetaCyc databases were detected. Furthermore, utilizing the classification of compound pairs and EC (Enzyme Commission) numbers of reactions, we established hierarchical relationships between metabolic reactions, enabling the harmonization of 3856 reaction pairs. In addition, we created and used atom-specific identifiers to evaluate the consistency of atom mappings within and between harmonized reactions, detecting some consistency issues between the reaction and compound descriptions in these metabolic databases. 

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5. Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies

   https://doi.org/10.1128/msystems.00070-22  

   Forchielli, Elena; Sher, Daniel; Segrè, Daniel (August 2022, mSystems)

   Shank, Elizabeth Anne (Ed.)

   Half of the Earth’s annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. 

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