Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action

(2017) Ruth McNerney et al.   INTERNATIONAL JOURNAL OF 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

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

(2016) Jody Phelan et al.   BMC Medicine

Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a TBNET/RESIST-TB consensus statement

(2016) J. Domínguez et al.   INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance

(2016) Christopher A Desjardins et al.   NATURE GENETICS

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

(2016) Jody Phelan et al.   Genome Medicine

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

(2016) Sarah G. Earle et al.   Nature Microbiology

Genotypic Analysis of Genes Associated with Independent Resistance and Cross-Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis Clinical Isolates

(2015) Johana Rueda et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG

(2015) Giorgia Mori et al.   CHEMISTRY & BIOLOGY

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

(2015) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

(2015) Francesc Coll et al.   Genome Medicine

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

Energy Metabolism and Drug Efflux in Mycobacterium tuberculosis

(2014) P. A. Black et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genetic Determinants Involved inp-Aminosalicylic Acid Resistance in Clinical Isolates from Tuberculosis Patients in Northern China from 2006 to 2012

(2014) Xiaobing Zhang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

(2014) João Perdigão et al.   BMC GENOMICS

Treatment Outcomes of Patients With Multidrug-Resistant and Extensively Drug-Resistant Tuberculosis According to Drug Susceptibility Testing to First- and Second-line Drugs: An Individual Patient Data Meta-analysis

(2014) M. L. Bastos et al.   CLINICAL INFECTIOUS DISEASES

Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association

(2014) Md Tauqeer Alam et al.   Genome Biology and Evolution

Revisiting susceptibility testing in MDR-TB by a standardized quantitative phenotypic assessment in a European multicentre study

(2014) E. Cambau et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2014) Nicola Casali et al.   NATURE GENETICS

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

(2014) Francesc Coll et al.   Nature Communications

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

(2014) Claire Chewapreecha et al.   PLoS Genetics

Global control of tuberculosis: from extensively drug-resistant to untreatable tuberculosis

(2014) Keertan Dheda et al.   Lancet Respiratory Medicine

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

GidB mutation as a phylogenetic marker for Q1 cluster Mycobacterium tuberculosis isolates and intermediate-level streptomycin resistance determinant in Lisbon, Portugal

(2013) J. Perdigão et al.   CLINICAL MICROBIOLOGY AND INFECTION

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

(2013) Maha R Farhat et al.   NATURE GENETICS

Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-D-arabinose biosynthetic and utilization pathway genes

(2013) Hassan Safi 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

Whole-Genome Sequencing for Rapid Susceptibility Testing of M. tuberculosis

(2013) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Correction: Drug-Associated Adverse Events and Their Relationship with Outcomes in Patients Receiving Treatment for Extensively Drug-Resistant Tuberculosis in South Africa

(2013) Karen Shean et al.   PLoS One

Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients

(2013) Matthias Merker et al.   PLoS One

Putative Compensatory Mutations in the rpoC Gene of Rifampin-Resistant Mycobacterium tuberculosis Are Associated with Ongoing Transmission

(2012) M. de Vos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

(2012) Francesc Coll et al.   BIOINFORMATICS

Upregulation of the Phthiocerol Dimycocerosate Biosynthetic Pathway by Rifampin-Resistant,rpoBMutant Mycobacterium tuberculosis

(2012) Gregory P. Bisson et al.   JOURNAL OF BACTERIOLOGY

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Mutations ingidBConfer Low-Level Streptomycin Resistance in Mycobacterium tuberculosis

(2011) Sharon Y. Wong et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Alanine racemase mutants of Mycobacterium tuberculosis require D-alanine for growth and are defective for survival in macrophages and mice

(2011) D. Awasthy et al.   MICROBIOLOGY-SGM

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

(2011) Iñaki Comas et al.   NATURE GENETICS

Pyrazinamide Inhibits Trans-Translation in Mycobacterium tuberculosis

(2011) W. Shi et al.   SCIENCE

Microscopic-observation drug susceptibility and thin layer agar assays for the detection of drug resistant tuberculosis: a systematic review and meta-analysis

(2010) Jessica Minion et al.   LANCET INFECTIOUS DISEASES

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Overexpression of the chromosomally encoded aminoglycoside acetyltransferase eis confers kanamycin resistance in Mycobacterium tuberculosis

(2009) M. A. Zaunbrecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY