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

High-level resistance to isoniazid and ethionamide in multidrug-resistant Mycobacterium tuberculosis of the Lisboa family is associated with inhA double mutations

(2013) Diana Machado et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Drug-resistant tuberculosis: time for visionary political leadership

(2013) Ibrahim Abubakar et al.   LANCET INFECTIOUS DISEASES

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

Effect of Mutation and Genetic Background on Drug Resistance in Mycobacterium tuberculosis

(2012) Lukas Fenner et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

(2012) Francesc Coll et al.   BIOINFORMATICS

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

(2012) A. Namouchi et al.   GENOME RESEARCH

Microevolution of extensively drug-resistant tuberculosis in Russia

(2012) N. Casali et al.   GENOME RESEARCH

SITVITWEB – A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology

(2012) Christophe Demay et al.   INFECTION GENETICS AND EVOLUTION

Adult tuberculosis in Israel and migration: trends and challenges between 1999 and 2010

(2012) Z. Mor et al.   INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE

From multidrug-resistant to extensively drug-resistant tuberculosis in Lisbon, Portugal: the stepwise mode of resistance acquisition

(2012) J. Perdigao et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Whole-Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Kerala, South India

(2012) G. K. Madhavilatha et al.   JOURNAL OF BACTERIOLOGY

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Fitness-compensatory mutations in rifampicin-resistant RNA polymerase

(2012) Gerrit Brandis et al.   MOLECULAR MICROBIOLOGY

Estimating the Impact of Newly Arrived Foreign-Born Persons on Tuberculosis in the United States

(2012) Yecai Liu et al.   PLoS One

The PE/PPE multigene family codes for virulence factors and is a possible source of mycobacterial antigenic variation: Perhaps more?

(2011) Yusuf Akhter et al.   BIOCHIMIE

Mutations outside the rifampicin resistance-determining region associated with rifampicin resistance in Mycobacterium tuberculosis

(2011) Gilman Kit Hang Siu et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

(2011) Kim Wong et al.   GENOME BIOLOGY

Travel and migration associated infectious diseases morbidity in Europe, 2008

(2010) Vanessa Field et al.   BMC INFECTIOUS DISEASES

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

(2010) Xin Fang et al.   BMC Systems Biology

IS6110-based global phylogeny of Mycobacterium tuberculosis

(2010) Nicola Thorne et al.   INFECTION GENETICS AND EVOLUTION

Variation among Genome Sequences of H37Rv Strains of Mycobacterium tuberculosis from Multiple Laboratories

(2010) T. R. Ioerger et al.   JOURNAL OF BACTERIOLOGY

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

(2010) Natacha Opalka et al.   PLOS BIOLOGY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

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

Genetic analysis of extensively drug-resistant Mycobacterium tuberculosis strains in Lisbon, Portugal

(2009) J. Perdigao et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints

(2009) Stefan Niemann et al.   PLoS One

Tuberculosis Transmission by Patients with Smear‐Negative Pulmonary Tuberculosis in a Large Cohort in The Netherlands

(2008) Alma Tostmann et al.   CLINICAL INFECTIOUS DISEASES

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Application of Sensitive and Specific Molecular Methods To Uncover Global Dissemination of the Major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis Spoligotype Family

(2008) A. L. Gibson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

RDRio Mycobacterium tuberculosis Infection Is Associated with a Higher Frequency of Cavitary Pulmonary Disease

(2008) L. C. O. Lazzarini et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multidrug-Resistant Tuberculosis in Lisbon, Portugal: A Molecular Epidemiological Perspective

(2008) João Perdigão et al.   Microbial Drug Resistance

The Co-Operonic PE25/PPE41 Protein Complex of Mycobacterium tuberculosis Elicits Increased Humoral and Cell Mediated Immune Response

(2008) Smanla Tundup et al.   PLoS One

Horizontally acquired genomic islands in the tubercle bacilli

(2008) Jichan Jang et al.   TRENDS IN MICROBIOLOGY

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography

(2008) Ruth Hershberg et al.   PLOS BIOLOGY