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We present a whole-body model of human metabolism that utilizes a system of organs and blood vessels to simulate the enzymatic reactions. The model focuses on key organs, including the brain, heart and lungs, liver, gut, and kidney, as well…
Physiological whole-body models are valuable tools for the development of novel drugs where understanding the system aspects is important. This paper presents a generalized model that encapsulates the structure and flow of whole-body human…
We present and critically discuss five commonly used mathematical models of the meal glucose rate of appearance in humans. Such models are key to simulation of the metabolism in healthy people, people with diabetes, and obese people, and…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
Simulation of post-prandial pharmacokinetics, such as muscle protein synthesis (MPS) through mTORC1 and insulin-induced glucose uptake, is often challenging due to the computational intensity of the multi-compartmental approach. In this…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…
An imbalance between energy intake and energy expenditure will lead to a change in body weight (mass) and body composition (fat and lean masses). A quantitative understanding of the processes involved, which currently remains lacking, will…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
Integrated global food system analysis is hampered by the fragmentation of data among food types, processes, and scales. Studies also often neglect the connection to human metabolism -- the ultimate driver of food demand. Here we use a…
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop…
Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…
Type 2 diabetes progresses slowly and may be reversed through lifestyle changes, but quantifying the long-term impact of regular physical activity remains challenging due to sparse longitudinal data. Mechanistic models offer a powerful tool…
We propose a method for finding metabolic parameters of cells, organs and whole organisms, which is based on the earlier discovered general growth law. Based on the obtained results and analysis of available biological models, we propose a…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…