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

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

(2018) Kathryn E. Holt et al.   NATURE GENETICS

Treatment of isoniazid-resistant tuberculosis with first-line drugs: a systematic review and meta-analysis

(2017) Medea Gegia et al.   LANCET INFECTIOUS DISEASES

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance

(2017) Abigail L Manson et al.   NATURE GENETICS

Antibiotic tolerance facilitates the evolution of resistance

(2017) Irit Levin-Reisman et al.   SCIENCE

Digitally Barcoding Mycobacterium tuberculosis Reveals In Vivo Infection Dynamics in the Macaque Model of Tuberculosis

(2017) Constance J. Martin et al.   mBio

Distinguishing between resistance, tolerance and persistence to antibiotic treatment

(2016) Asher Brauner et al.   NATURE REVIEWS MICROBIOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence

(2016) Bram Van den Bergh et al.   Nature Microbiology

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

(2015) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Southern East Asian origin and coexpansion ofMycobacterium tuberculosisBeijing family with Han Chinese

(2015) Tao Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

(2015) Keira A. Cohen et al.   PLOS MEDICINE

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area

(2015) JA Guerra-Assunção et al.   eLife

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

(2014) Ofer Fridman et al.   NATURE

Evolution and transmission of drug-resistant tuberculosis in a Russian population

(2014) Nicola Casali et al.   NATURE GENETICS

A Four-Month Gatifloxacin-Containing Regimen for Treating Tuberculosis

(2014) Corinne S. Merle et al.   NEW ENGLAND JOURNAL OF MEDICINE

Four-Month Moxifloxacin-Based Regimens for Drug-Sensitive Tuberculosis

(2014) Stephen H. Gillespie et al.   NEW ENGLAND JOURNAL OF MEDICINE

High-Dose Rifapentine with Moxifloxacin for Pulmonary Tuberculosis

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

Methylcitrate cycle defines the bactericidal essentiality of isocitrate lyase for survival ofMycobacterium tuberculosison fatty acids

(2014) Hyungjin Eoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Meta-Analysis of Self-Administered vs Directly Observed Therapy Effect on Microbiologic Failure, Relapse, and Acquired Drug Resistance in Tuberculosis Patients

(2013) Jotam G. Pasipanodya et al.   CLINICAL INFECTIOUS DISEASES

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

(2013) Iñaki Comas et al.   NATURE GENETICS

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis

(2013) Maha R Farhat 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

Cholesterol Catabolism by Mycobacterium tuberculosis Requires Transcriptional and Metabolic Adaptations

(2012) Jennifer E. Griffin et al.   CHEMISTRY & BIOLOGY

Microevolution of extensively drug-resistant tuberculosis in Russia

(2012) N. Casali et al.   GENOME RESEARCH

National Survey of Drug-Resistant Tuberculosis in China

(2012) Yanlin Zhao et al.   NEW ENGLAND JOURNAL OF MEDICINE

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

A Novel Role of the PrpR as a Transcription Factor Involved in the Regulation of Methylcitrate Pathway in Mycobacterium tuberculosis

(2012) Paweł Masiewicz et al.   PLoS One

Drug Tolerance in Replicating Mycobacteria Mediated by a Macrophage-Induced Efflux Mechanism

(2011) Kristin N. Adams et al.   CELL

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mycobacterium smegmatis RNase J is a 5′-3′ exo-/endoribonuclease and both RNase J and RNase E are involved in ribosomal RNA maturation

(2011) Valerio Taverniti et al.   MOLECULAR MICROBIOLOGY

Characterization and Transcriptome Analysis of Mycobacterium tuberculosis Persisters

(2011) I. Keren et al.   mBio

Persister Cells

(2010) Kim Lewis   Annual Review of Microbiology

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Emergence of Pseudomonas aeruginosa Strains Producing High Levels of Persister Cells in Patients with Cystic Fibrosis

(2010) L. R. Mulcahy et al.   JOURNAL OF BACTERIOLOGY

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

Simultaneous Analysis of Multiple Mycobacterium tuberculosis Knockdown Mutants In Vitro and In Vivo

(2010) Antje Blumenthal et al.   PLoS One

Mycobacterium tuberculosis persistence mutants identified by screening in isoniazid-treated mice

(2010) N. Dhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patients with Long-Term Oral Carriage Harbor High-Persister Mutants of Candida albicans

(2009) M. D. LaFleur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Role of the Transcriptional Regulator RamB (Rv0465c) in the Control of the Glyoxylate Cycle in Mycobacterium tuberculosis

(2009) J. C. Micklinghoff et al.   JOURNAL OF BACTERIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tuberculosis Drug Resistance Mutation Database

(2009) Andreas Sandgren et al.   PLOS MEDICINE

Functional Characterization of a Vitamin B12-Dependent Methylmalonyl Pathway in Mycobacterium tuberculosis: Implications for Propionate Metabolism during Growth on Fatty Acids

(2008) S. Savvi et al.   JOURNAL OF BACTERIOLOGY

Mycobacterial persistence requires the utilization of host cholesterol

(2008) A. K. Pandey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA