Tuberculosis Research and Epidemiology

The paper develops a 10-gene random forest signature to predict TB and HIV status and distinguishes TB/HIV co-infection from other conditions with high accuracy.

This study compares whole genome sequencing of Mycobacterium tuberculosis directly from sputum to sequencing from culture, finding greater genetic diversity in sputum-derived samples.

This study uses a multitask deep learning model to predict tuberculosis drug resistance from genomic data, achieving high accuracy in both first-line and second-line drug resistance prediction.

The paper presents a rapid, easy, and field-friendly protocol for detecting Mycobacterium tuberculosis using qPCR, showing high sensitivity and agreement with gold-standard methods.

This study uses time-resolved RNA-seq to analyze D. discoideum gene expression during M. marinum infection, identifying key pathways involved in host response to damage, stress, and metabolic adaptation.

The paper identifies a mutation in the papA2 gene of Mycobacterium tuberculosis that leads to loss of sulfolipids by disrupting protein stability and structure.

This study models how engaging private healthcare providers in tuberculosis control can reduce incidence and mortality in urban India when scaled to 75% of patient-provider interactions.

The paper identifies transcriptionally induced enhancers in macrophages infected with Mycobacterium tuberculosis and links them to immune gene activation.

This study conducts a sex-stratified genome-wide association study of tuberculosis, identifying sex-specific genetic interactions and candidate genes.

This paper predicts pyrazinamide resistance in Mycobacterium tuberculosis using machine learning models trained on pncA mutations and structural features, achieving 80.2% sensitivity and 76.9% specificity.

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.

The paper analyzes whole-genome sequences of Mycobacterium tuberculosis isolates from pulmonary and extrapulmonary tuberculosis patients in Russia to identify genetic substrains and drug resistance patterns.

The paper identifies stage-specific differentially expressed genes (DEGs) in tuberculosis (TB) using network analysis and classifies them into pathways, revealing potential biomarkers associated with TB progression.

The paper identifies novel drug potentiators in Mycobacterium tuberculosis using a network-based genetic screening approach to uncover stress response adaptations to isoniazid.

The paper uses mathematical models to predict that short-course bedaquiline regimens could reduce MDR-TB treatment to 18 weeks with high success rates.

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.

The paper assembles a complete genome of an XDR M. tuberculosis strain using Nanopore sequencing, identifies novel genetic variations in repetitive PE/PPE regions, and links these to drug resistance and virulence.

This study compares the transcriptomic and proteomic profiles of Mycobacterium tuberculosis and Mycobacterium bovis, revealing distinct host responses in bovine macrophages.

The paper shows that gene expression models based on the H37Rv strain poorly predict transcriptional diversity in Mycobacterium tuberculosis complex strains.

The paper characterizes two propionate catabolism pathways in mycobacteria, showing the methylcitrate pathway's high capacity and the methylmalonyl pathway's detoxification role.

This study analyzes 14 novel mutations in M. tuberculosis KatG using structural models to identify how they restrict access channels to the catalytic heme, potentially causing isoniazid resistance.

The paper uses gene expression in dendritic cells to predict tuberculosis susceptibility, finding differentially expressed genes and genetic polymorphisms associated with TB risk.

The paper updates the reference genome of Mycobacterium bovis AF2122/97 with new annotations, corrected SNPs, and confirms the presence of the RD900 locus.

This study reports crystal structures of Mycobacterium tuberculosis RNA polymerase with and without antituberculosis drugs, revealing a new class of inhibitors and their binding mechanisms.