William T. Scott

A metadata managed FAIR end-to-end workflow for microbial community Omics data analysis

The paper presents a metadata-managed FAIR end-to-end workflow for microbial community Omics data analysis, demonstrating its reliability and reproducibility through mock datasets.

Unraveling the metabolic interactions of a Dehalobacter-containinganaerobic mixed culture for bioremediation

The paper uses genome-resolved metagenomics and metabolic modeling to study microbial interactions in a Dehalobacter-containing community for chlorinated benzene degradation.

Metabolic modeling unveils potential probiotic roles of Flavonifractor plautii in reshaping the Western gut microbiota landscape

This study develops a genome-scale metabolic model of Flavonifractor plautii to explore its probiotic potential and ecological roles in the gut microbiota.

Deep sequencing of 16 Ixodes ricinus ticks unveils insights into their interactions with endosymbionts

This study uses deep sequencing on 16 Ixodes ricinus ticks to analyze symbionts, revealing genome sequences, transmission modes, and genetic variability in Rickettsia helvetica.

Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations

This paper develops a genome-scale metabolic model for Clostridium luticellarii to improve syngas fermentation, showing its potential for producing value-added biochemicals.

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

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

Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data

Yeast9 improves yeast metabolic modeling by integrating multi-omics data, showing better prediction of growth rates and gene function than transcriptomics.

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

This study evaluates COBRA-based tools for microbial consortia modeling using FAIR criteria and experimental data, finding that newer, better-documented tools generally outperform older ones in quality and performance.

Dynamic genome-scale modeling of Saccharomyces cerevisiae unravels mechanisms for ester formation during alcoholic fermentation

The paper uses dynamic flux balance analysis to identify conserved and strain-specific metabolic mechanisms in Saccharomyces cerevisiae that influence ester formation during alcoholic fermentation.

Regulating microbiome metabolic stability for stable indigenous liquor fermentation

The paper investigates factors affecting microbiome metabolic stability in traditional Chinese liquor fermentation and identifies strategies to enhance stability through initial conditions and microbial inoculation ratios.