Daniela Brites

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

The paper introduces the Microbiology Galaxy Lab, a community-driven platform for reproducible and FAIR microbial data analysis, offering tools for various omics data types and use cases.

Evolutionary dynamics of the insertion sequence IS6110 in the Mycobacterium tuberculosis complex

The paper analyzes the evolutionary dynamics of IS6110 in Mycobacterium tuberculosis complex strains using ancestral state reconstruction and identifies patterns of insertion and selection.

Stringent proteogenomic discovery of novel small proteins in Mycobacterium tuberculosis clinical reference strains

The paper uses long-read assemblies and proteogenomic analysis to discover novel small proteins in Mycobacterium tuberculosis strains.

Clinical and bacterial determinants of unfavorable tuberculosis treatment outcomes: an observational study in Georgia

This study identifies patient and bacterial factors associated with unfavorable tuberculosis treatment outcomes in Georgia using genomic and clinical data from 4,536 patients.

Variability in intrinsic drug tolerance in Mycobacterium tuberculosis corresponds with phylogenetic lineage

The paper measures drug tolerance in Mycobacterium tuberculosis lineages and finds higher tolerance in L3 and L4 strains, with heritable patterns and enrichment of mutations in specific metabolic pathways.

Large contribution of repeats to genetic variation in a transmission cluster of Mycobacterium tuberculosis

The paper characterizes repeat-associated mutations in Mycobacterium tuberculosis genomes using long-read sequencing, revealing their significant contribution to genetic variation in an outbreak.

Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages

The paper uses genomic data and phylodynamic models to show that Mycobacterium tuberculosis lineages have similar infectiousness durations but differ in onset timing, affecting transmission dynamics.

Human genetic ancestry, Mycobacterium tuberculosis diversity and tuberculosis disease severity in Dar es Salaam, Tanzania

This study examines the relationship between human genetic ancestry, Mycobacterium tuberculosis diversity, and TB disease severity in Dar es Salaam, Tanzania, finding no significant genetic influence on disease severity.

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

The paper improves genotype imputation in underrepresented populations by adding population-specific SNPs to existing reference panels, showing improved accuracy in a Tanzanian cohort.

Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history

The paper analyzes genomes of Mycobacterium africanum strains to identify a new lineage and explore their evolutionary history and phylogeography.

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

The paper analyzes whole genome sequences of Mycobacterium tuberculosis lineages L1 and L3 to show South Asia's role in their dispersion and identify local adaptation at the esxH locus.

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests different ecological niches

The paper compares the genomes of Mycobacterium africanum Lineage 5 and 6 from Ghana, finding genomic diversity and selection pressure differences suggesting distinct ecological niches.

Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity

Treemmer reduces large phylogenetic datasets by removing redundant leaves, preserving diversity while simplifying the dataset.