Recent studies have brought forward the critical role of emergent properties in shaping
microbial communities and the ecosystems of which they are a part. Emergent properties …

Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …

Metabolism is a major regulator of immune cell function, but it remains difficult to study the
metabolic status of individual cells. Here, we present Compass, an algorithm to characterize …

Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …

Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

Abstract Machine learning provides researchers a unique opportunity to make metabolic
engineering more predictable. In this review, we offer an introduction to this discipline in …

Great strides have been made over the past decade toward comprehensive study of
metabolism. Mass spectrometry (MS) has played a central role by enabling measurement of …

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …

In their natural environment, plants are part of a rich ecosystem including numerous and
diverse microorganisms in the soil. It has been long recognized that some of these microbes …

Genome-scale network reconstructions have helped uncover the molecular basis of
metabolism. Here we present Recon3D, a computational resource that includes three …