Microbial communities affect many facets of human health and well-being. Naturally
occurring bacteria, whether in nature or the human body, rarely exist in isolation. A deeper …

Engineering natural microbiomes for biotechnological applications remains challenging, as
metabolic interactions within microbiomes are largely unknown, and practical principles and …

Mechanistic models explicitly represent hypothesized biological knowledge. As such, they
offer more generalizability than data-driven models. However, identifying model curation …

Microbial communities play vital roles in biogeochemical cycles, allowing biodegradation of
a wide range of pollutants. Although many studies have shown the importance of …

The human gut microbiome impacts several aspects of human health and disease, including
digestion, drug metabolism and the propensity to develop various inflammatory …

Motivation Genome-scale metabolic network reconstructions (GENREs) are valuable for
understanding cellular metabolism in silico. Several tools exist for automatic GENRE …

The relationship between plants and soil microbial communities is complex and subtle, with
microbes playing a crucial role in plant growth. Autochthonous bioaugmentation and nutrient …

Background The efficient biological production of industrially and economically important
compounds is a challenging problem. Brute-force determination of the optimal pathways to …

Gap-filling is a necessary step to produce quality genome-scale metabolic reconstructions
capable of flux-balance simulation. Most available gap-filling tools use an organism …

While scientific software has become increasingly important to research, the ability to fully
understand the behavior of these tools has remained limited. This is, in part, due to the …