Related papers: The Aging Metabolite Database with Summary Statist…
Widespread interest in non-destructive biomarkers of aging has led to a curse of plenty: a multitude of biological ages that each proffers a 'true' health-adjusted age of an individual. While each measure provides salient information on the…
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…
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…
Accurately identifying metabolites i.e. small molecules from mass spectrometry data remains a core challenge in metabolomics, with broad applications in drug discovery, environmental analysis, and clinical research. We address the Molecule…
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of…
It is well known that tumors originating from the same tissue have different prognosis and sensitivity to treatments. Over the last decade, cancer genomics consortia like the Cancer Genome Atlas (TCGA) have been generating thousands of…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the variety of existing bioinformatics tools, providing experimenters…
Introduction: Identification of blood-based metabolic changes might provide early and easy-to-obtain biomarkers. Methods: We included 127 AD patients and 121 controls with CSF-biomarker-confirmed diagnosis (cut-off tau/A$\beta_{42}$: 0.52).…
As the global population continues to age, there is an increasing demand for ways to accurately quantify the biological processes underlying aging. Biological age, unlike chronological age, reflects an individual's physiological state,…
Of the 2652 articles considered, 106 met the inclusion criteria. Review of the included papers resulted in identification of 43 chronic diseases, which were then further classified into 10 disease categories using ICD-10. The majority of…
Metabolite structure identification has become the major bottleneck of the mass spectrometry based metabolomics research. Till now, number of mass spectra databases and search algorithms have been developed to address this issue. However,…
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…
We propose a whole-body model of the metabolism in man as well as a generalized approach for modeling metabolic networks. Using this approach, we are able to write a large metabolic network in a systematic and compact way. We demonstrate…
System dynamics and agent based simulation models can both be used to model and understand interactions of entities within a population. Our modeling work presented here is concerned with understanding the suitability of the different types…
Generating synthetic tabular health data is challenging, and evaluating their quality is equally, if not more, complex. This systematic review highlights the critical importance of rigorous evaluation of synthetic health data to ensure…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
Mass spectrometry-based metabolomics generates complex, high-dimensional data that holds vast potential for biological discovery but remains difficult to integrate and interpret. Knowledge graphs (KGs) unify this heterogeneous information…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
Background: Most people with any long-term condition have multiple long-term conditions, but our understanding of how conditions cluster is limited. Many clustering studies identify clusters in the whole population, but the clusters that…