The human gut microbiome vastly extends the set of metabolic reactions catalysed by our
own cells, with far-reaching consequences for host health and disease. However, our …

Resource allocation affects the structure of microbiomes, including those associated with
living hosts. Understanding the degree to which this dependency determines interspecies …

Ocean metabolism constitutes a complex, multiscale ensemble of biochemical reaction
networks harbored within and between the boundaries of a myriad of organisms. Gaining a …

Genome-scale metabolic models are powerful tools for understanding cellular physiology.
Flux balance analysis (FBA), in particular, is an optimization-based approach widely …

Mechanistic, constraint-based models of microbial isolates or communities are a staple in
the metabolic analysis toolbox, but predictions about microbe-microbe and microbe …

Gliomas are the most common type of malignant brain tumors, with glioblastoma multiforme
(GBM) having a median survival of 15 months due to drug resistance and relapse. The …

Quantification of how different environmental cues affect protein allocation can provide
important insights for understanding cell physiology. While absolute quantification of …

Techniques to autonomously drive research have been prominent in Computational
Scientific Discovery, while Synthetic Biology is a field of science that focuses on designing …

Metabolic models condense biochemical knowledge about organisms in a structured and
standardised way. As large-scale network reconstructions are readily available for many …

We describe a datalog query evaluation approach based on efficient and composable
boolean matrix manipulation modules. We first define an overarching problem, Boolean …