Mathematical modeling of microbial community dynamics: a methodological review
Microorganisms in nature form diverse communities that dynamically change in structure
and function in response to environmental variations. As a complex adaptive system …
and function in response to environmental variations. As a complex adaptive system …
Dynamic models of metabolism: Review of the cybernetic approach
D Ramkrishna, HS Song - AIChE Journal, 2012 - Wiley Online Library
The cybernetic approach to metabolic modeling tracing its progress from its early beginnings
to its current state with regard to its relationship to other modeling approaches, applications …
to its current state with regard to its relationship to other modeling approaches, applications …
Mapping the evolution of cybernetics: a bibliometric perspective
In this study, we undertake a comprehensive bibliometric analysis of the cybernetics
research field. We compile a dataset of 4856 papers from the ISI Web of Science database …
research field. We compile a dataset of 4856 papers from the ISI Web of Science database …
DRUM: a new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae
Metabolic modeling is a powerful tool to understand, predict and optimize bioprocesses,
particularly when they imply intracellular molecules of interest. Unfortunately, the use of …
particularly when they imply intracellular molecules of interest. Unfortunately, the use of …
CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention
Microbial variations in the human gut are harbored in temporal and spatial heterogeneity,
and quantitative prediction of spatiotemporal dynamic changes in the gut microbiota is …
and quantitative prediction of spatiotemporal dynamic changes in the gut microbiota is …
[HTML][HTML] Modeling the metabolic dynamics at the genome-scale by optimized yield analysis
The hybrid cybernetic model (HCM) approach is a dynamic modeling framework that
integrates enzyme synthesis and activity regulation. It has been widely applied in …
integrates enzyme synthesis and activity regulation. It has been widely applied in …
Combining kinetic and constraint-based modelling to better understand metabolism dynamics
C Moulin, L Tournier, S Peres - Processes, 2021 - mdpi.com
To understand the phenotypic capabilities of organisms, it is useful to characterise cellular
metabolism through the analysis of its pathways. Dynamic mathematical modelling of …
metabolism through the analysis of its pathways. Dynamic mathematical modelling of …
A method of accounting for enzyme costs in flux balance analysis reveals alternative pathways and metabolite stores in an illuminated Arabidopsis leaf
CYM Cheung, RG Ratcliffe, LJ Sweetlove - Plant Physiology, 2015 - academic.oup.com
Flux balance analysis of plant metabolism is an established method for predicting metabolic
flux phenotypes and for exploring the way in which the plant metabolic network delivers …
flux phenotypes and for exploring the way in which the plant metabolic network delivers …
Representing organic matter thermodynamics in biogeochemical reactions via substrate-explicit modeling
Predictive biogeochemical modeling requires data-model integration that enables explicit
representation of the sophisticated roles of microbial processes that transform substrates …
representation of the sophisticated roles of microbial processes that transform substrates …
Cybernetic models based on lumped elementary modes accurately predict strain‐specific metabolic function
HS Song, D Ramkrishna - Biotechnology and Bioengineering, 2011 - Wiley Online Library
In a recent article, Song and Ramkrishna (Song and Ramkrishna [2010]. Biotechnol Bioeng
106 (2): 271–284) proposed a lumped hybrid cybernetic model (L‐HCM) towards extracting …
106 (2): 271–284) proposed a lumped hybrid cybernetic model (L‐HCM) towards extracting …