Benjamin Sobkowiak

The paper identifies a rapidly expanding multidrug-resistant M. tuberculosis clade originating from Russia and circulating in Moldova, posing a threat to MDR-TB control.

The paper introduces e3SIM, a simulator that models epidemiological, ecological, and evolutionary processes in pathogens, demonstrating its use with SARS-CoV-2 and Mycobacterium tuberculosis.

This paper develops tiled amplicon sequencing panels for whole-genome sequencing of pathogenic bacteria without culturing, enabling drug resistance classification from clinical samples.

MixInfect2 accurately detects mixed Mycobacterium tuberculosis infections and estimates strain proportions, improving upon previous methods.

This study shows that including indels improves transmission reconstruction in a large Mtb outbreak by reducing clonal clusters and altering transmission networks.

This study compares seven transmission reconstruction tools for Mycobacterium tuberculosis using simulated and real-world data, finding that some tools better identify true transmission events than others.