The endometrial cycle is known to be mediated via the endocrine system, with both estradiol and progesterone hormones heavily implicated in menstruation. Throughout this cycle, the tissue undergoes vast changes in tissue and cellular-level function, including phagocytosis and apoptosis, cell proliferation, both tissue and vascular remodelling, and extracellular matrix construction. Macrophages...
Rice (Oryza sativa) is highly sensitive to cold stress, imposing major constraints on its productivity and geographical distribution. Elucidating cold-induced metabolic reprogramming is essential for understanding the underlying mechanisms of rice adaptive responses.
Constraint-based metabolic modeling is a powerful framework for capturing metabolic interactions. A key challenge, however,...
Genomic sequencing data can be used to identify gene-protein-reaction (GPR) rules for microbial species, which determine how the genes corresponding to enzymes catalyse specific metabolic reactions. GPRs can thus be combined to create genome-scale metabolic models (GEMs) for any organism for which a genome sequence is available. Mathematically, GEMs are large stoichiometric matrices that can...
Isotopically non-stationary metabolic flux analysis (INST-MFA) enables the estimation of intracellular fluxes from time-resolved labeling data but remains limited to medium-scale networks due to experimental constraints on metabolite coverage. Extending INST-MFA toward large-scale models with high confidence in flux estimates requires extensive labeling datasets. Here, we employ a neural...
The prevalence of -omics data is steadily increasing within the biological and ecological sciences, and it is widely accepted within the community that data is published open access alongside journal articles. Consequently, this provides mechanistic modellers with a wealth of accessible data with which to parameterise and validate models. However, understanding the complexities of this data...
