Sudaraka Mallawaarachchi

StrainSpy fits zero-inflated beta mixed models to containment ANI, reaching >98% simulated sensitivity versus ~79% for logistic regression and detecting colorectal-cancer E. coli strain shifts.

This study traces the evolutionary path from ST131-B to ST131-C clades in E. coli by analyzing genomic data from ST131-B0 isolates, revealing genetic changes associated with antibiotic resistance and host adaptation.

The paper investigates the evolutionary dynamics of colibactin production and resistance in E. coli, showing clonal expansions linked to co-evolution between production and immunity.

This study sequenced 4,475 H. influenzae isolates from Thailand and combined them with global data to show pervasive recombination and purifying selection, with MDR lineages widespread and not restricted to disease-causing subpopulations.

TRACS improves transmission inference by accurately estimating SNP-level genetic distances, outperforming existing methods in multiple datasets and revealing species-specific transmission rates between mothers and infants.

PAN-GWES identifies co-selected and epistatic genomic variations in bacterial genomes using de Bruijn graphs to analyze drug resistance and adaptation traits.

The paper introduces LDWeaver, a method to detect co-selection in bacterial genomes by analyzing both short- and long-range linkage disequilibrium, and validates findings using functional annotation and phenotypic measurements.

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

This study finds increased delta and theta oscillatory power in OCD patients compared to controls but no significant differences in connectivity measures.

This study examines ERP differences in OCD patients compared to healthy controls, finding altered frontal brain activity across multiple tasks but no link to symptom severity.

This paper applies genome-wide association, prediction, and heritability analyses to bacterial data, identifying genetic factors influencing antibiotic resistance and within-host survival in Streptococcus pneumoniae.