Related papers: Microbial correlation: a semi-parametric model for…
The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit…
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…
Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…
The gut-muscle axis has been proposed to link gut microbiota with skeletal muscle physiology, yet its universality across livestock species remains unclear. Using aged laying hens, a livestock model with a relatively short digestive tract,…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…
The mathematical modelling of biological systems has historically followed one of two approaches: comprehensive and minimal. In comprehensive models, the involved biological pathways are modelled independently, then brought together as an…
The human microbiome can contribute to pathogeneses of many complex diseases by mediating disease-leading causal pathways. However, standard mediation analysis methods are not adequate to analyze the microbiome as a mediator due to the…
Due to the aging of the world population and westernization of lifestyles, the prevalence of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD) is rapidly rising and is expected to put a strong…
More and more diseases have been found to be strongly correlated with disturbances in the microbiome constitution, e.g., obesity, diabetes, or some cancer types. Thanks to modern high-throughput omics technologies, it becomes possible to…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
The diverse metabolic pathways are fundamental to all living organisms, as they harvest energy, synthesize biomass components, produce molecules to interact with the microenvironment, and neutralize toxins. While discovery of new…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Biological systems operate under simultaneous energetic and informational constraints, yet direct evidence that such constraints shape real metabolic networks is limited. The Network-Weighted Action Principle predicts that networks under…
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…
High throughput metabolomics data are fraught with both non-ignorable missing observations and unobserved factors that influence a metabolite's measured concentration, and it is well known that ignoring either of these complications can…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Mediation analysis is an important tool for studying causal associations in biomedical and other scientific areas and has recently gained attention in microbiome studies. Using a microbiome study of acute myeloid leukemia (AML) patients, we…
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…
Gut microbes play a key role in colorectal carcinogenesis, yet reaching a consensus on microbial signatures remains a challenge. This is in part due to a reliance on mean value estimates. We present an extreme value analysis for overcoming…