Related papers: Prediction of source nutrients for microorganisms …

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…

Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…

The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…

Metabolite biosynthesis is regulated via metabolic pathways, which can be activated and deactivated within organisms. Understanding and identifying an organism's metabolic pathway network is a crucial aspect for various research fields,…

In many key applications of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect changes in metabolic processes, usually represented in the form of pathways. As an alternative, a broader point of view…

Nutrient limitation is one of the most common triggers of antibiotic tolerance and persistence. Here, we present two microfluidic setups to study how spatial and temporal variation in nutrient availability lead to increased survival of…

We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…

The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide the first deep investigation of the predictive potential of machine…

Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…

Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…

This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The visual backbone of this comparative analysis is provided by a…

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…

Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…

Molecular gastronomy is a distinct sub-discipline of food science that takes an active role in examining chemical and physical properties of ingredients and as such lends itself to more scientific approaches to finding novel ingredient…

Metabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control. The focus is on control at the transcriptional level, serving as a means to…

In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…

The heterogeneity of reaction fluxes present in a metabolic network within a single flux state can be exploited to construct the so-called backbone as a reduced version of metabolism. The backbone maintains all significant fluxes producing…

Microorganisms are widely distributed in the human daily living environment. They play an essential role in environmental pollution control, disease prevention and treatment, and food and drug production. The analysis of microorganisms is…

Recent advances in single cell sequencing and multi-omics techniques have significantly improved our understanding of biological phenomena and our capacity to model them. Despite combined capture of data modalities showing similar progress,…

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…