Swaine Lin Chen

Home is where the host is: Evolutionary history of geographic spread, host switching, and adaptive genomic signatures in two generalist Group B Streptococcus clonal groups

This study analyzes the evolutionary history and host adaptation of two GBS clonal groups, revealing host switching, regional AMR gene distribution differences, and biased sampling in multi-host pathogens.

A recipient-based anti-conjugation factor triggers an abortive mechanism by targeting the Type IV secretion system

The paper identifies AbjA, a bacterial protein that blocks plasmid conjugation by targeting the T4SS ATPase TrbE, inducing cell death and preventing horizontal gene transfer.

Three Accessory Gene Clusters Drive Host-Adaptation in Group B Streptococcus

The paper identifies three accessory gene clusters driving host adaptation in Group B Streptococcus across different hosts.

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

The paper characterizes the ecological and evolutionary dynamics of gut microbiomes colonized by carbapenemase-producing Enterobacteriaceae (CPE) using longitudinal metagenomics and whole genome sequencing.

GBS-SBG - GBS Serotyping by Genome Sequencing

This paper introduces GBS-SBG, a serotyping tool for Group B Streptococcus using genome sequencing, achieving high concordance with PCR-based methods on both short-read and assembly data.

A faster and more accurate algorithm for calculating population genetics statistics requiring sums of Stirling numbers of the first kind

The paper introduces a faster and more accurate method for calculating population genetics statistics by using the incomplete beta function to estimate sums of Stirling numbers of the first kind.

Gut microbiome recovery after antibiotic usage is mediated by specific bacterial species

The paper identifies specific bacterial species associated with gut microbiome recovery after antibiotic use and shows their role in promoting microbial diversity and preventing pathogen colonization.

Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

The paper reports high-quality genomes of six Orientia tsutsugamushi strains using long-read sequencing and identifies a small core genome and phylogenetic relationships.

Lacer: Accurate Base Quality Score Recalibration For Improving Variant Calling From Next-Generation Sequencing Data In Any Organism

Lacer improves variant calling accuracy by recalibrating base quality scores without needing variant databases or assumptions about correct bases, benefiting all organisms.