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List of works by Sébastien Gagneux

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Variable host-pathogen compatibility in Mycobacterium tuberculosis

scientific article (publication date: 21 February 2006)
Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development.

scientific article published on May 2007
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

scientific article (publication date: October 2013)
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

scientific article
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography

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

scientific article published on 18 December 2011
Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

scientific article
The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis

scientific article
Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

scientific article published on 19 January 2015
Host–pathogen coevolution in human tuberculosis

scientific article published on March 19, 2012
Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

scientific article (publication date: 23 October 2014)
Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages

scientific article
Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis

scientific article
The W-Beijing lineage of Mycobacterium tuberculosis overproduces triglycerides and has the DosR dormancy regulon constitutively upregulated

scientific article published on 19 January 2007
Consequences of genomic diversity in Mycobacterium tuberculosis

scientific article published on October 22, 2014
An outbreak of serotype 1 Streptococcus pneumoniae meningitis in northern Ghana with features that are characteristic of Neisseria meningitidis meningitis epidemics

scientific article published on 10 June 2005
Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis

scientific article
Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia.

scientific article published on March 2013
Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa

scientific article
Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

scientific article published on 31 October 2016
Relationship between Mycobacterium tuberculosis genotype and the clinical phenotype of pulmonary and meningeal tuberculosis

scientific article published on 20 February 2008
Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints

scientific article
Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis.

scientific article published on December 2009
The past and future of tuberculosis research

scientific article
Does M. tuberculosis genomic diversity explain disease diversity?

scientific article
Co‐evolution of M ycobacterium tuberculosis and H omo sapiens

scientific article published on March 1, 2015
The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis

scientific article published on December 13, 2012
A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis

scientific article published on 28 December 2017
Two new rapid SNP-typing methods for classifying mycobacterium tuberculosis complex into the main phylogenetic lineages

scientific article (publication date: 2012)
Clonal waves of Neisseria colonisation and disease in the African meningitis belt: eight- year longitudinal study in northern Ghana

scientific article published in March 2007
M. tuberculosis T Cell Epitope Analysis Reveals Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens

scientific article published on 21 October 2015
Ecology and evolution of Mycobacterium tuberculosis.

scientific article
KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes.

scientific article
Differential virulence and disease progression following Mycobacterium tuberculosis complex infection of the common marmoset (Callithrix jacchus)

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

scientific article published on January 2016
Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese

scientific article published on 15 June 2015
Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition

scientific article published on 14 January 2014
The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy

scientific article
Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis

scientific article published on June 1, 2011
Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis

scientific article
Mycobacterium africanum elicits an attenuated T cell response to early secreted antigenic target, 6 kDa, in patients with tuberculosis and their household contacts.

scientific article
Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak

scientific article
"Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis

scientific article
Epistasis between antibiotic resistance mutations drives the evolution of extensively drug-resistant tuberculosis.

scientific article published on January 2013
Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints

scientific article published on 4 April 2012
The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex

scientific article published on 28 February 2012
Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing

scientific article published on 30 October 2014
HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis

scientific article
PolyTB: a genomic variation map for Mycobacterium tuberculosis

scientific article
Mapping of genotype-phenotype diversity among clinical isolates of mycobacterium tuberculosis by sequence-based transcriptional profiling

scientific article published on January 2013

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