Saeed Shoaie

Metacontam is a decontamination method for metagenomic data that improves detection of low-abundance contaminants without needing negative controls.

The paper identifies oral-gut microbial translocation in ACLD patients linked to intestinal barrier dysfunction and hepatic fibrosis, with prtC encoding bacteria as a biomarker.

This study investigates microbiome signatures in the oral-gut-brain axis and their role in Parkinson's disease and cognitive decline.

The paper identifies two types of antimicrobial resistant bacteria in the gut microbiome after antibiotic treatment and shows how one type persists and reshapes the microbial community.

The paper develops and evaluates optimized computational and experimental methods for analyzing the human mycobiome, identifying novel fungal species in oral and gut samples.

The paper introduces MIGRENE, a computational framework for constructing personalized microbiome metabolism models using metagenomic data.

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

Palidis identifies novel insertion sequences in metagenomic data by detecting inverted terminal repeats, revealing 519 previously uncharacterized sequences across 264 human metagenomes.

This study uses metabolic modeling of gut microbiome data from type 2 diabetes patients to show how metformin treatment alters microbial growth rates and metabolic pathways.

The paper identifies metabolic differences between Candida species using genomic, metabolomic, and gene expression data, highlighting unique pathways in the AGAu cluster.

GutMicroNet provides an interactive platform to explore gut microbiome interaction networks using data from the Human Gut Microbiome Atlas.

The paper introduces the reactobiome, a stratification method for the human gut microbiome, identifying five reactotypes with distinct metabolic features and validating them in a longitudinal cohort.

This study compares mucosal microbiota composition and function along the intestine using shotgun metagenomics, highlighting functional enrichments and antimicrobial resistance patterns.

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.