Ronan M. T. Fleming

StereoMapper clarifies metabolite identity by assigning stereochemically aware relationships, achieving high performance in benchmark datasets and improving GEM accuracy.

OpenKinetics Predictor unifies thirteen enzyme kinetic predictors behind one interface and API; on E. coli iML1515, eight kcat predictors correlate pairwise at r 0.08 to 0.67.

XomicsToModel integrates multi-omics data with a generic metabolic model to generate context-specific, thermodynamically consistent metabolic models.

APOLLO provides 247,092 genome-scale metabolic models of human microbes, enabling strain-level taxonomic prediction and disease-associated metabolite analysis.

mzQuality is a software tool for quality control in metabolomics data that corrects technical variation and prepares data for analysis.

fluxTrAM automates processing of tracer-based metabolomics data and integrates it with genome-scale metabolic models for flux analysis.

This paper introduces a new method for genome-scale metabolic flux inference using conserved moieties, demonstrating its computational efficiency and accuracy with isotopic labeling data.

This study uses whole-body metabolic models to show that isoleucine availability limits SARS-CoV-2 virus shedding and identifies potential therapeutic strategies.

The paper develops genome-scale metabolic models of human dopaminergic neurons to study metabolic dysfunction in Parkinson's disease using exometabolomic and transcriptomic data.

This study investigates neuronal activity in LRRK2-G2019S mutant neurons and finds increased spontaneous calcium transients and shorter inter-spike intervals.

AGORA2 reconstructs the human microbiome at scale, revealing individual-specific drug metabolism capabilities and correlations with clinical parameters.

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 simulates alpha-synuclein spread using a connectome model and finds connectivity alone is insufficient to explain observed pathology patterns in rats.

The paper integrates cancer signalling and metabolic networks to enable multi-omics data analysis and cross-talk studies in ovarian cancer subtypes.

The paper introduces a toolbox for modeling microbial interactions and communities using metagenomic data and extends the COBRA Toolbox.

The paper introduces the Virtual Metabolic Human database, which integrates human and gut microbiome metabolism with nutrition and disease data to support biomedical research.

The paper presents two gender-specific whole-body metabolism models, Harvey and Harvetta, that integrate physiological and omics data to predict metabolic processes and interactions across organs.

The paper uses personalized microbial community models to analyze bile acid metabolism in healthy and IBD individuals, revealing distinct metabolic potentials and strain contributions.