Barun Mathema

This study examines changes in cell envelope lipids of drug-resistant Mycobacterium tuberculosis strains and their impact on macrophage interactions.

The paper analyzes whole-genome sequencing data of Mycobacterium tuberculosis isolates to study lineage evolution and antigenic diversity in China and Zhejiang Province.

This study shows that different genomic variant calling methods lead to inconsistent transmission inferences and phylogenies in Mycobacterium tuberculosis outbreaks.

The paper introduces a transmission-based clustering method for identifying outbreak clusters using whole genome sequencing data, showing it outperforms SNP threshold methods in some scenarios.

Clusterflock uses a flocking algorithm to cluster orthologous gene families based on phylogenetic incongruence, outperforming existing methods in datasets with high missing data and rate heterogeneity.