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 …

Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …

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 …

To the Editor—Reconstructing metabolic reaction networks enables the development of
testable hypotheses of an organism's metabolism under different conditions 1. State-of-the …

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 …

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

Omic data analysis is steadily growing as a driver of basic and applied molecular biology
research. Core to the interpretation of complex and heterogeneous biological phenotypes …

To the Editor: Somatic recombination and accumulation of mutations in VDJ segments result
in vast heterogeneity of T-cell receptor (TCR) and immunoglobulin repertoires1, 2. High …

The human gut microbiome is known to be associated with various human disorders, but a
major challenge is to go beyond association studies and elucidate causalities. Mathematical …

Background Several genome-scale metabolic reconstruction software platforms have been
developed and are being continuously updated. These tools have been widely applied to …