Timothy D. Read

The paper identifies four immune state types (ISTs) in trachoma patients using protein profiling, linking them to infection, inflammation, and scarring outcomes.

This study uses comparative genomics to analyze Sympodiorosea fungi, revealing that selective pressures on metabolic genes drive genome evolution and functional diversification in ant-associated fungi.

The paper introduces MetaChlam, a pipeline for strain typing Chlamydia trachomatis in metagenomes, showing it outperforms existing tools and detects contaminants.

The paper identifies ocular microbiome community state types (CSTs) in Ethiopian villagers, linking specific microbial compositions to trachoma prevalence and potential therapeutic implications.

This study compares single colony and pooled colony isolates of Staphylococcus aureus from cystic fibrosis patients to reveal hidden intraspecific diversity in chronic infections.

This study shows that host and antibiotic exposure together increase virulence in Staphylococcus aureus, with distinct evolutionary outcomes for methicillin-resistant and -sensitive strains.

The paper analyzes azithromycin resistance mutations in Chlamydia trachomatis genomes, finding common mutations in rplV that predate azithromycin's clinical use.

This study examines how azithromycin affects microbial composition, function, and resistance genes in endocervical, vaginal, and rectal microbiomes of women with Chlamydia trachomatis infection.

This study uses ANI to group S. aureus strains and identifies strain-specific genes in the pangenome by analyzing gene distribution patterns.

This paper introduces Com-2seq, a method that integrates 16S and shotgun metagenomic data to improve statistical efficiency in testing differential abundance.

The paper reconstructs the pre-epidemic evolution of the USA300 MRSA lineage using genomic data and identifies a third major clade and molecular markers for classification.

The paper develops a coevolution score method to detect coevolving genes in bacterial genomes, finding coordinated gene gain/loss patterns in S. aureus related to antibiotic resistance.

The paper analyzes the agr operon across S. aureus genomes to identify frameshift mutations and their evolutionary patterns, finding over 5% of strains have non-functional agr systems.

This study benchmarks nine bioinformatics tools for detecting AMR genes in shotgun metagenomic data using simulated samples and a custom pipeline.

The paper analyzes the whale shark genome to study vertebrate gene family evolution, finding patterns in immunity, gigantism, and cancer-related gene expansion.

The paper improves whole-genome sequencing of Chlamydia trachomatis from clinical samples by redesigning an RNA bait library, achieving 100% efficiency and identifying genomic recombination in paired specimens.

Bactopia provides a flexible pipeline for analyzing bacterial genomes, including quality control, assembly, and post-processing tools for comparative genomics.

This study tracks USA300 MRSA persistence on multiple body sites post-infection, finding clonal lineages persist up to a year with genetic changes.