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

EcoCyc is a bioinformatics database available online at EcoCyc. org that describes the
genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term …

Global environmental contamination with a complex mixture of xenobiotics has become a
major environmental issue worldwide. Many xenobiotic compounds severely impact the …

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 …

Genome-scale metabolic models are instrumental in uncovering operating principles of
cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in …

Figure 1 iML1515 genome-scale reconstruction.(a) The iML1515 model contains 1,515
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …

Metabolite-protein interactions control a variety of cellular processes, thereby playing a
major role in maintaining cellular homeostasis. Metabolites comprise the largest fraction of …

Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …

Genome-scale metabolic models are mathematically-structured knowledge bases that can
be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can …

Current machine learning techniques enable robust association of biological signals with
measured phenotypes, but these approaches are incapable of identifying causal …