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This study uses ribosome profiling to show that steatohepatitis-associated HCC has extensive translational alterations affecting hundreds of genes and revealing novel translated regions.

This paper introduces NIS, a method to simplify genome-scale metabolic models for comparing metabolic capabilities across organisms, revealing conserved and divergent patterns in metabolism.

This study identifies RPL39L as an efficiency factor in cotranslational folding of alpha helical proteins by analyzing its expression, ribosome structure, and impact on translation dynamics.

NICEgame identifies and resolves metabolic gaps in genome-scale models by suggesting alternative reactions and genes, improving gene essentiality predictions in E. coli.

ZARP is an RNA-seq analysis workflow that automates data processing using Snakemake, reducing hands-on time for users by integrating best practices and generating detailed reports.

This paper introduces a constraint-based framework, Network Response Analysis (NRA), to improve metabolic engineering by incorporating physiological constraints and genome editing limitations.

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.

The paper analyzes how uncertainty in intracellular fluxes and concentrations affects kinetic models of E. coli metabolism and proposes a workflow to improve prediction reliability.

This paper uses retrobiosynthesis to discover and evaluate novel biosynthetic pathways for producing five MEK precursors in E. coli.