Related papers: Numerical Representations of Metabolic Systems
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
Metabolomic data can potentially enable accurate, non-invasive and low-cost prediction of coronary artery disease. Regression-based analytical approaches however might fail to fully account for interactions between metabolites, rely on a…
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…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
Life science is entering a new era of petabyte-level sequencing data. Converting such big data to biological insights represents a huge challenge for computational analysis. To this end, we developed DeepMetabolism, a biology-guided deep…
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…
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…
Multimodal data modeling has emerged as a powerful approach in clinical research, enabling the integration of diverse data types such as imaging, genomics, wearable sensors, and electronic health records. Despite its potential to improve…
Life has a special status, it even has its own science: biology. In many ways, the logic of life seems to differ from that of atoms, molecules, planets, or any other `inanimate object'. However, life is increasingly measured using…
Obesity does not emerge abruptly; rather, it develops gradually over extended periods. The gradual progression often prevents early recognition of physiological changes until excess adiposity is established. A common belief is that weight…
Background: Determining sample sizes for metabolomic experiments is important but due to the complexity of these experiments, there are currently no standard methods for sample size estimation in metabolomics. Since pilot studies are rarely…
More advanced visualization tools are needed to assist with the analyses and interpretation of human metabolomics data, which are rapidly increasing in quantity and complexity. Using a dataset of several hundred bioactive lipid metabolites…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
Liquid chromatography mass spectrometry (LC-MS)-based metabolomics and exposomics aim to measure detectable small molecules in biological samples. The results facilitate hypothesis-generating discovery of metabolic changes and disease…
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…
Predicting cellular metabolic states is a central problem in biophysics. Conventional approaches, however, sensitively depend on the microscopic details of individual metabolic systems. In this Letter, we derived a universal linear…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…
Background: Data preparation, such as missing values imputation and transformation, is the first step in any data analysis and requires crucial attention. Particularly, analysis of metabolites demands more preparation since those small…
Data is omnipresent in the modern, digital world and a significant number of people need to make sense of data as part of their everyday social and professional life. Therefore, together with the rise of data, the design of graphical…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…