My H. Pham

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells

The paper reports mutation rates and mutational signatures across 53 normal human cell types, revealing variation in mutation accumulation and identifying known and unknown mutational processes.

Systemic mutagen exposures reported by normal kidney cell genomes

The paper identifies mutational signatures in normal kidney cells from multiple countries, revealing exposure to exogenous mutagens including aristolochic acids and unknown agents prevalent in Japan.

Landscape of parental postzygotic mutations in >11,000 rare disease trios

The paper identifies 1,015 high-confidence postzygotic mutations in 12,015 parent-offspring trios, showing they contribute to clinical phenotypes and can be detected from standard sequencing data.

Sperm sequencing reveals extensive positive selection in the male germline

This study uses sperm sequencing to show that positive selection in the male germline leads to a higher risk of disease-causing mutations in offspring.

The long-term effects of chemotherapy on normal blood cells

This study examines the long-term effects of chemotherapy on normal blood cells by analyzing mutation burdens and cell population structure in treated individuals.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.