Conor Joseph Meehan

This study evaluates reference-free methods for Mycobacterium tuberculosis lineage typing using simulated Illumina data, finding SKA2 to be the most accurate tool for strain classification.

The paper evaluates a SNP calling pipeline for Mycobacterium leprae using simulated reads and finds it robust and accurate with low false positives.

The paper provides a 5000-year-old dental calculus metagenomic dataset from 174 UK archaeological samples to study ancient human oral microbiomes and related topics like diet and antimicrobial resistance.

The paper evaluates pan-genome analysis methods using M. tuberculosis isolates, finding that annotation discrepancies and assembly quality affect results, and introduces panqc to address these issues.

This study evaluates the impact of DNA damage and contamination on detecting antibiotic and metal resistance genes in ancient metagenomic samples, finding contamination is more problematic than diagenetic damage.

This study evaluates binning tools for reconstructing metagenomic-assembled genomes from ancient oral microbiomes using simulated and real data.

The paper uses genomic data and phylodynamic models to show that Mycobacterium tuberculosis lineages have similar infectiousness durations but differ in onset timing, affecting transmission dynamics.

This study analyzes 665 Mycobacterium kansasii complex strains to identify unique and shared genomic signatures, revealing lineage splits, virulence factors, and drug resistance mechanisms.

The paper quantifies the MTBC pangenome, revealing a small, closed genome with lineage-specific regions of difference and implications for virulence and drug resistance.

hAMRonization standardizes AMR gene detection outputs from multiple tools into a unified format for easier analysis and integration.

The paper examines transmission rates of borderline and common rpoB mutations in MDR-TB isolates from Bangladesh, finding no difference in transmission clustering between mutation types.

The paper identifies conserved regions in ESX-1 related proteins by mapping SNVs from MTB isolates onto protein structures, highlighting potential therapeutic targets.

The paper identifies high within-lineage genomic diversity and gene content differences in Mycobacterium tuberculosis complex lineage 5 compared to H37Rv, affecting transmission analysis and suggesting the need for alternative reference genomes.

The paper analyzes genomes of Mycobacterium africanum strains to identify a new lineage and explore their evolutionary history and phylogeography.

The paper analyzes global S. maltophilia strains to show genetic diversity and intra-hospital transmission.

The paper constructs a genome-based taxonomy for the Lactobacillus Genus Complex using 2,459 genomes, identifying new species and resolving misclassifications.

The paper develops a tool to convert whole genome sequencing data into rifampicin-resistant tuberculosis diagnostic test results, enabling analysis of RR-TB burden across different data sources.

The paper compares the genomes of Mycobacterium africanum Lineage 5 and 6 from Ghana, finding genomic diversity and selection pressure differences suggesting distinct ecological niches.