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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Recon reconstructs genome-scale metabolic models for 410 Salmonella strains spanning 64 serovars to link specific metabolic capabilities with host range and nutritional niche and reveals growth differences that may reflect adaptation to particular colonization sites. Expand
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
The BOF generated by BOFdat resulted in the most concordant biomass composition, growth rate, and gene essentiality prediction accuracy when compared to other methods. Expand
BOFdat: generating biomass objective function stoichiometric coefficients from experimental data
BOFdat, a Python package that offers functions to generate biomass objective function stoichiometric coefficients (BOFsc) from macromolecular cell composition and relative abundances of macromolescules obtained from omic datasets, is presented. Expand
Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis
A comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, has identified the core genome and open pangenome of this species and suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. Expand
Minimal cells, maximal knowledge
Modeling all the chemical reactions that take place in a minimal cell will help us understand the fundamental interactions that power life.
The Use of In Silico Genome-Scale Models for the Rational Design of Minimal Cells
The most recent computational methods and protocols available for the reconstruction of genome-scale models, the formulation of objective functions, and the applications of models in the prediction of gene essentiality are reviewed. Expand
Estimating Cellular Goals from High-Dimensional Biological Data
The first approach to estimating constraint reactions from data that can scale to realistically large metabolic models is developed and recovered, enabling accurate prediction of metabolic states in hundreds of growth environments not seen in training data. Expand
Integrative characterization of the near‐minimal bacterium Mesoplasma florum
A broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches, including the first genome‐wide analysis of its transcriptome and proteome, notably revealing a conserved promoter motif, the organization of transcription units, and the transcription and protein expression levels of all protein‐coding sequences. Expand
Genome-scale estimation of cellular objectives
This work develops a new algorithm that extends existing approaches for de novo objective generation and solve it using the alternating direction method of multipliers (ADMM), and shows that it identifies de noVO objectives from measured fluxes with tunable sparsity. Expand
Genome‐scale metabolic modeling reveals key features of a minimal gene set
iJL208 is a stepping‐stone toward model‐driven whole‐genome engineering and was used to propose an in silico reduced genome and revealed key features of a minimal gene set. Expand