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 …
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 …
ZA King, J Lu, A Dräger, P Miller… - Nucleic acids …, 2016 - academic.oup.com
Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can …
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 …
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 …