Genomic insights into tuberculosis

Microbial Persistence and the Road to Drug Resistance

(2013) Nadia R. Cohen et al.   Cell Host & Microbe

The re-emergence of tuberculosis: what have we learnt from molecular epidemiology?

(2013) M.W. Borgdorff et al.   CLINICAL MICROBIOLOGY AND INFECTION

The evolutionary pressures that have molded Mycobacterium tuberculosis into an infectious adjuvant

(2013) David G Russell   CURRENT OPINION IN MICROBIOLOGY

Mutation rate and the emergence of drug resistance in Mycobacterium tuberculosis

(2013) M. McGrath et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Mycobacterium tuberculosis regulatory network and hypoxia

(2013) James E. Galagan et al.   NATURE

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

(2013) Iñaki Comas et al.   NATURE GENETICS

Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

(2013) Philip Supply et al.   NATURE GENETICS

Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

(2013) Christopher B Ford et al.   NATURE GENETICS

Dynamic Persistence of Antibiotic-Stressed Mycobacteria

(2013) Y. Wakamoto et al.   SCIENCE

Functional Roles of Pulsing in Genetic Circuits

(2013) J. H. Levine et al.   SCIENCE

The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations

(2013) Caitlin S. Pepperell et al.   PLoS Pathogens

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

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

Rib lesions in skeletons from early neolithic sites in Central Germany: On the trail of tuberculosis at the onset of agriculture

(2012) Nicole Nicklisch et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

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

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Inter- and Intra-subtype genotypic differences that differentiate Mycobacterium avium subspecies paratuberculosis strains

(2012) Franck Biet et al.   BMC MICROBIOLOGY

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

Totally drug-resistant tuberculosis (TDR-TB) in India: every dark cloud has a silver lining

(2012) Zarir Udwadia et al.   JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH

The Surprising Diversity of Mycobacterium tuberculosis: Change You Can Believe In

(2012) S. M. Fortune   JOURNAL OF INFECTIOUS DISEASES

Dynamic Population Changes in Mycobacterium tuberculosis During Acquisition and Fixation of Drug Resistance in Patients

(2012) Gang Sun et al.   JOURNAL OF INFECTIOUS DISEASES

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

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

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

Host-pathogen coevolution in human tuberculosis

(2012) S. Gagneux   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Independent Large Scale Duplications in Multiple M. tuberculosis Lineages Overlapping the Same Genomic Region

(2012) Brian Weiner et al.   PLoS One

Genotype of a historic strain of Mycobacterium tuberculosis

(2012) A. S. Bouwman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis

(2012) Borna Müller et al.   TRENDS IN GENETICS

Tuberculosis and HIV Co-Infection

(2012) Andrzej Pawlowski et al.   PLoS Pathogens

Impulse Control: Temporal Dynamics in Gene Transcription

(2011) Nir Yosef et al.   CELL

Mycobacterium tuberculosis and the intimate discourse of a chronic infection

(2011) David G. Russell   IMMUNOLOGICAL REVIEWS

DNA fingerprinting of Mycobacterium tuberculosis: From phage typing to whole-genome sequencing

(2011) Anita C. Schürch et al.   INFECTION GENETICS AND EVOLUTION

Characterization of the KstR-dependent promoter of the gene for the first step of the cholesterol degradative pathway in Mycobacterium smegmatis

(2011) I. Uhia et al.   MICROBIOLOGY-SGM

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford 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

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Phylogeny of Mycobacterium tuberculosis Beijing Strains Constructed from Polymorphisms in Genes Involved in DNA Replication, Recombination and Repair

(2011) Olga Mestre et al.   PLoS One

Dynamics of Antibiotic Resistant Mycobacterium tuberculosis during Long-Term Infection and Antibiotic Treatment

(2011) Solomon H. Mariam et al.   PLoS One

The rise and fall of the Mycobacterium tuberculosis genome

(2011) Frédéric J. Veyrier et al.   TRENDS IN MICROBIOLOGY

A role for systems epidemiology in tuberculosis research

(2011) Iñaki Comas et al.   TRENDS IN MICROBIOLOGY

Mycobacterium tuberculosis Uses Host Triacylglycerol to Accumulate Lipid Droplets and Acquires a Dormancy-Like Phenotype in Lipid-Loaded Macrophages

(2011) Jaiyanth Daniel et al.   PLoS Pathogens

The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa

(2010) Thomas R Ioerger et al.   BMC GENOMICS

Mycobacterium tuberculosis Wears What It Eats

(2010) David G. Russell et al.   Cell Host & Microbe

Clinical characteristics of the smooth tubercle bacilli ‘Mycobacterium canettii’ infection suggest the existence of an environmental reservoir

(2010) J.-L. Koeck et al.   CLINICAL MICROBIOLOGY AND INFECTION

Molecular characteristics of “Mycobacterium canettii” the smooth Mycobacterium tuberculosis bacilli

(2010) Michel Fabre et al.   INFECTION GENETICS AND EVOLUTION

Tuberculosis on the north coast of Peru: skeletal and molecular paleopathology of late pre-Hispanic and postcontact mycobacterial disease

(2010) Haagen D. Klaus et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Massive Gene Duplication Event among Clinical Isolates of the Mycobacterium tuberculosis W/Beijing Family

(2010) P. Domenech et al.   JOURNAL OF BACTERIOLOGY

Cholesterol utilization in mycobacteria is controlled by two TetR-type transcriptional regulators: kstR and kstR2

(2010) S. L. Kendall et al.   MICROBIOLOGY-SGM

Sublethal Antibiotic Treatment Leads to Multidrug Resistance via Radical-Induced Mutagenesis

(2010) Michael A. Kohanski et al.   MOLECULAR CELL

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

Cholesterol Metabolism Increases the Metabolic Pool of Propionate inMycobacterium tuberculosis

(2009) Xinxin Yang et al.   BIOCHEMISTRY

Emergence of New Forms of Totally Drug-Resistant Tuberculosis Bacilli

(2009) Ali Akbar Velayati et al.   CHEST

Role of reactive oxygen species in antibiotic action and resistance

(2009) Daniel J Dwyer et al.   CURRENT OPINION IN MICROBIOLOGY

A Thiolase of Mycobacterium tuberculosis Is Required for Virulence and Production of Androstenedione and Androstadienedione from Cholesterol

(2009) N. M. Nesbitt et al.   INFECTION AND IMMUNITY

Triacylglycerol Utilization Is Required for Regrowth of In Vitro Hypoxic Nonreplicating Mycobacterium bovis Bacillus Calmette-Guerin

(2009) K. L. Low et al.   JOURNAL OF BACTERIOLOGY

Tuberculosis and diabetes mellitus: convergence of two epidemics

(2009) Kelly E Dooley et al.   LANCET INFECTIOUS DISEASES

Foamy macrophages and the progression of the human tuberculosis granuloma

(2009) David G Russell et al.   NATURE IMMUNOLOGY

A replication clock for Mycobacterium tuberculosis

(2009) Wendy P Gill et al.   NATURE MEDICINE

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

Microfluidic devices for measuring gene network dynamics in single cells

(2009) Matthew R. Bennett et al.   NATURE REVIEWS GENETICS

Bacterial gene amplification: implications for the evolution of antibiotic resistance

(2009) Linus Sandegren et al.   NATURE REVIEWS MICROBIOLOGY

Genome Analysis of Multi- and Extensively-Drug-Resistant Tuberculosis from KwaZulu-Natal, South Africa

(2009) Thomas R. Ioerger et al.   PLoS One

Mycobacterium tuberculosis WhiB3 Maintains Redox Homeostasis by Regulating Virulence Lipid Anabolism to Modulate Macrophage Response

(2009) Amit Singh et al.   PLoS Pathogens

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY

Consensus generation and variant detection by Celera Assembler

(2008) G. Denisov et al.   BIOINFORMATICS

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

(2008) T. P. Stinear et al.   GENOME RESEARCH

IS6110, a Mycobacterium tuberculosis Complex-Specific Insertion Sequence, Is Also Present in the Genome of Mycobacterium smegmatis, Suggestive of Lateral Gene Transfer among Mycobacterial Species

(2008) A. Coros et al.   JOURNAL OF BACTERIOLOGY

Mycobacterium avium subsp. paratuberculosis and M. avium subsp. avium Are Independently Evolved Pathogenic Clones of a Much Broader Group of M. avium Organisms

(2008) C. Y. Turenne et al.   JOURNAL OF BACTERIOLOGY

Insertion and Deletion Events That Define the PathogenMycobacterium aviumsubsp.paratuberculosis

(2008) David C. Alexander et al.   JOURNAL OF BACTERIOLOGY

Mycobacterium du jour: what's on tomorrow's menu?

(2008) Marcel A. Behr   MICROBES AND INFECTION

Multispacer Sequence Typing for Mycobacterium tuberculosis Genotyping

(2008) Zoheira Djelouadji et al.   PLoS One

Detection and Molecular Characterization of 9000-Year-Old Mycobacterium tuberculosis from a Neolithic Settlement in the Eastern Mediterranean

(2008) Israel Hershkovitz et al.   PLoS One

CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA

(2008) Luciano A. Marraffini et al.   SCIENCE

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

Dynamics of Genome Rearrangement in Bacterial Populations

(2008) Aaron E. Darling et al.   PLoS Genetics

Foamy Macrophages from Tuberculous Patients' Granulomas Constitute a Nutrient-Rich Reservoir for M. tuberculosis Persistence

(2008) Pascale Peyron et al.   PLoS Pathogens

Origin, Spread and Demography of the Mycobacterium tuberculosis Complex

(2008) Thierry Wirth et al.   PLoS Pathogens