Tuberculosis treatment failure associated with evolution of antibiotic resilience

Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome

(2022) Maximillian Marin et al.   BIOINFORMATICS

Penicillin Binding Proteins and β-Lactamases of Mycobacterium tuberculosis: Reexamination of the Historical Paradigm

(2022) Gaurav Kumar et al.   mSphere

Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection

(2022) Álvaro Chiner-Oms et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

(2022) Timothy M Walker et al.   Lancet Microbe

Spatiotemporal localization of proteins in mycobacteria

(2021) Junhao Zhu et al.   Cell Reports

Dynamic imaging in patients with tuberculosis reveals heterogeneous drug exposures in pulmonary lesions

(2020) Alvaro A. Ordonez et al.   NATURE MEDICINE

A biphasic growth model for cell pole elongation in mycobacteria

(2020) Mélanie T. M. Hannebelle et al.   Nature Communications

Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments

(2020) Qingyun Liu et al.   Science Advances

Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis

(2020) Nathan D. Hicks et al.   PLoS Pathogens

Tuberculosis drugs’ distribution and emergence of resistance in patient’s lung lesions: A mechanistic model and tool for regimen and dose optimization

(2019) Natasha Strydom et al.   PLOS MEDICINE

Evaluation of Whole-Genome Sequence Method to Diagnose Resistance of 13 Anti-tuberculosis Drugs and Characterize Resistance Genes in Clinical Multi-Drug Resistance Mycobacterium tuberculosis Isolates From China

(2019) Xinchang Chen et al.   Frontiers in Microbiology

Citywide transmission of MDR-TB under China’s rapid urbanization: a retrospective population-based genomic spatial epidemiological study

(2019) Qi Jiang et al.   CLINICAL INFECTIOUS DISEASES

Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance

(2019) Hassan Safi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drug Penetration Gradients Associated with Acquired Drug Resistance in Tuberculosis Patients

(2018) Keertan Dheda et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Have compensatory mutations facilitated the current epidemic of multidrug-resistant tuberculosis?

(2018) Qingyun Liu et al.   Emerging Microbes & Infections

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

(2018)   NEW ENGLAND JOURNAL OF MEDICINE

Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance

(2018) Nathan D. Hicks et al.   Nature Microbiology

China’s tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis

(2018) Qingyun Liu et al.   Nature Ecology & Evolution

Drug detoxification dynamics explain the postantibiotic effect

(2017) Jaydeep K Srimani et al.   Molecular Systems Biology

Persistent bacterial infections and persister cells

(2017) Robert A. Fisher et al.   NATURE REVIEWS MICROBIOLOGY

Distinct Spatiotemporal Dynamics of Peptidoglycan Synthesis between Mycobacterium smegmatis and Mycobacterium tuberculosis

(2017) Helene Botella et al.   mBio

Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform

(2017) Jeremy M. Rock et al.   Nature Microbiology

Mechanisms of bacterial persistence during stress and antibiotic exposure

(2016) Alexander Harms et al.   SCIENCE

Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis Shows that WhiB Is a Transcription Factor That Cocontrols Its Regulon with WhiA To Initiate Developmental Cell Division in Streptomyces

(2016) Matthew J. Bush et al.   mBio

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis

(2016) Mingyu Gan et al.   PLoS One

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

(2015) S. J. Philips et al.   SCIENCE

Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment

(2015) Qingyun Liu et al.   Scientific Reports

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

(2014) Ofer Fridman et al.   NATURE

How sisters grow apart: mycobacterial growth and division

(2014) Karen J. Kieser et al.   NATURE REVIEWS MICROBIOLOGY

High-Dose Rifapentine with Moxifloxacin for Pulmonary Tuberculosis

(2014) Amina Jindani et al.   NEW ENGLAND JOURNAL OF MEDICINE

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

(2013) Iñaki Comas et al.   NATURE GENETICS

Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance

(2013) Hongtai Zhang et al.   NATURE GENETICS

Genes Required for Aerial Growth, Cell Division, and Chromosome Segregation Are Targets of WhiA before Sporulation in Streptomyces venezuelae

(2013) M. J. Bush et al.   mBio

Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

(2013) Josephine M Bryant et al.   Lancet Respiratory Medicine

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Automated imaging with ScanLag reveals previously undetectable bacterial growth phenotypes

(2010) Irit Levin-Reisman et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

(2008) Gregory I. Lang et al.   GENETICS