Hongwu Ma

ProGenFixer corrects prokaryotic genome sequences using a mapping-free algorithm, achieving high speed and accuracy compared to existing tools.

This paper develops a synthetic biology toolkit for Bacillus methanolicus to study plasmid-dependent methylotrophy and enhance methanol-based biosynthesis of L-arginine.

SynBioGPT v2.0 improves synthetic biology strain design by using query decomposition and keyword-based retrieval to enhance accuracy over its previous version.

This paper introduces a computational framework, AdaptUC, to predict metabolic engineering strategies for microbial adaptation to unadapted carbon sources, showing improved driving forces and reduced substrate requirements in case studies.

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

Standard-GEM provides a template for reproducible genome-scale metabolic model development following FAIR principles and software best practices.

This paper identifies prediction anomalies in a constraint-based metabolic model by incorporating enzyme compartmentalization, improving pathway structure accuracy and resolving constraint conflicts.

This paper introduces a method that integrates enzymatic and thermodynamic constraints into genome-scale metabolic models to improve pathway prediction accuracy.

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.