相关论文: Parameter Estimation and Identifiability in Kineti…
Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…
Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to…
Understanding transcription factor dynamics is crucial for unraveling the regulatory mechanisms of gene expression that underpin cellular function and development. Measurements of transcription factor subcellular movements are essential for…
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…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
Comprehension of metabolic pathways is considerably enhanced by metabolic flux analysis (MFA-ILE) in isotope labeling experiments. The balance equations are given by hundreds of algebraic (stationary MFA) or ordinary differential equations…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
Models in systems biology are mathematical descriptions of biological processes that are used to answer questions and gain a better understanding of biological phenomena. Dynamic models represent the network through rates of the production…
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of…
Detailed dynamical systems' models used in the life sciences may include hundreds of state variables and many input parameters, often with physical meaning. Therefore, efficient and unique input parameter identification, from experimental…
The Linear Multistep Method Particle Filter (LMM PF) is a method for predicting the evolution in time of a evolutionary system governed by a system of differential equations. If some of the parameters of the governing equations are…
The metabolic process in a cell is modeled with the use of the Fourier transformation. The histograms of the invariant measures of chaotic attractors are constructed. In particular, a scenario of adaptation of the metabolic process under a…
An Elementary Flux Mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find…
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…
Identifying unique parameters for mathematical models describing biological data can be challenging and often impossible. Parameter identifiability for partial differential equations models in cell biology is especially difficult given that…
Understanding the links between diet, metabolic changes, and health outcomes is a key focus in nutritional science and broader biological research. Analyzing relationships, such as those between ultra-processed food (UPF) intake and…
Metabolic flux analysis using 13C labeled substrates is an important tool for metabolic engineering. Although it has now been evolving for more than ten years, metabolic flux analysis has still not reached the limits of its application.…
Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…
This paper focuses on data arising from the field of metabolomics, a rapidly developing area concerned by the analysis of the chemical fingerprints (i.e. the metabolite profile). The metabolite profile is left by specific chemical processes…
Kinetic parameters such as the turnover number ($k_{cat}$) and Michaelis constant ($K_{\mathrm{M}}$) are essential for modelling enzymatic activity but experimental data remains limited in scale and diversity. Previous methods for…