Mapping of Genotype–Phenotype Diversity among Clinical Isolates of Mycobacterium tuberculosis by Sequence-Based Transcriptional Profiling

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

(2013) Iñaki Comas et al.   NATURE GENETICS

Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis

(2013) Teresa Cortes et al.   Cell Reports

Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

(2012) Kira S Makarova et al.   Biology Direct

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Mycobacterium tuberculosis Lacking All Mycolic Acid Cyclopropanation Is Viable but Highly Attenuated and Hyperinflammatory in Mice

(2012) Daniel Barkan et al.   INFECTION AND IMMUNITY

Ppm1-Encoded Polyprenyl Monophosphomannose Synthase Activity Is Essential for Lipoglycan Synthesis and Survival in Mycobacteria

(2012) Amrita K. Rana et al.   PLoS One

Non-coding RNA and its potential role in Mycobacterium tuberculosis pathogenesis

(2012) Kristine Arnvig et al.   RNA Biology

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

The complex architecture of mycobacterial promoters

(2012) Mae Newton-Foot et al.   TUBERCULOSIS

Antisense Transcription Is Pervasive but Rarely Conserved in Enteric Bacteria

(2012) R. Raghavan et al.   mBio

Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis

(2012) Yanjia J. Zhang et al.   PLoS Pathogens

Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes

(2011) Xiaobin Zheng et al.   BMC GENOMICS

Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype

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

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

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

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis

(2011) Kristine B. Arnvig et al.   PLoS Pathogens

Human Macrophage Responses to Clinical Isolates from the Mycobacterium tuberculosis Complex Discriminate between Ancient and Modern Lineages

(2011) Damien Portevin et al.   PLoS Pathogens

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Strains of the East Asian (W/Beijing) Lineage of Mycobacterium tuberculosis Are DosS/DosT-DosR Two-Component Regulatory System Natural Mutants

(2010) A. Fallow et al.   JOURNAL OF BACTERIOLOGY

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

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

Possible underlying mechanisms for successful emergence of the Mycobacterium tuberculosis Beijing genotype strains

(2010) Ida Parwati et al.   LANCET INFECTIOUS DISEASES

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

(2010) Iñaki Comas et al.   NATURE GENETICS

Diversity in Mycobacterium tuberculosis mannosylated cell wall determinants impacts adaptation to the host

(2010) Jordi B. Torrelles et al.   TUBERCULOSIS

TubercuList – 10 years after

(2010) Jocelyne M. Lew et al.   TUBERCULOSIS

Functional Genetic Diversity among Mycobacterium tuberculosis Complex Clinical Isolates: Delineation of Conserved Core and Lineage-Specific Transcriptomes during Intracellular Survival

(2010) Susanne Homolka et al.   PLoS Pathogens

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Inactivation of Mycobacterium tuberculosis mannosyltransferase pimB reduces the cell wall lipoarabinomannan and lipomannan content and increases the rate of bacterial-induced human macrophage cell death

(2009) J. B Torrelles et al.   GLYCOBIOLOGY

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies

(2009) Iñaki Comas et al.   PLoS One

The Past and Future of Tuberculosis Research

(2009) Iñaki Comas et al.   PLoS Pathogens

Recent and Rapid Emergence of W‐Beijing Strains ofMycobacterium tuberculosisin Cape Town, South Africa

(2008) Donna Cowley et al.   CLINICAL INFECTIOUS DISEASES

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Genome-wide regulon and crystal structure of BlaI (Rv1846c) fromMycobacterium tuberculosis

(2008) Claudia Sala et al.   MOLECULAR MICROBIOLOGY

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

(2008) Ruth Hershberg et al.   PLOS BIOLOGY