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List of works by Sébastien Gagneux

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

scientific article

A New Phylogenetic Framework for the Animal-Adapted Complex

scientific article published on 27 November 2018

A New Phylogenetic Framework for the Animal-adapted Mycobacterium tuberculosis Complex

scholarly article published 3 August 2018

A case of cutaneous tuberculosis in a Buruli ulcer-endemic area

scientific article

A role for systems epidemiology in tuberculosis research

scientific article

A single-nucleotide-polymorphism real-time PCR assay for genotyping of Mycobacterium tuberculosis complex in peri-urban Kampala.

scientific article published on 30 September 2015

A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

scientific article published on 09 June 2020

A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis

scientific article published on 28 December 2017

A19 The impact of HIV-1 on the evolution of Mycobacterium tuberculosis.

scientific article

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

Analysis of potential household transmission events of tuberculosis in the city of Belem, Brazil

scientific article published on 02 October 2018

Annie Darwin's death, the evolution of tuberculosis and the need for systems epidemiology

scientific article published on 01 December 2009

Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives.

scientific article published on 25 March 2017

Association between tuberculosis, diabetes and 25 hydroxyvitamin D in Tanzania: a longitudinal case control study

scientific article

Author Correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

scientific article published on 21 February 2020

China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis

article

Classifying recurrent Mycobacterium tuberculosis cases in Georgia using MIRU-VNTR typing

scientific article published on 18 October 2019

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

scientific article published on January 2016

Clonal groupings in serogroup X Neisseria meningitidis

scientific article published on May 2002

Clonal waves of Neisseria colonisation and disease in the African meningitis belt: eight- year longitudinal study in northern Ghana

scientific article

Co-evolution of Mycobacterium tuberculosis and Homo sapiens

scientific article

Combination of single nucleotide polymorphism and variable-number tandem repeats for genotyping a homogenous population of Mycobacterium tuberculosis Beijing strains in China

scientific article published on 11 January 2012

Comment on: characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array

scientific article published on 20 April 2014

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

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

scientific article published in Scientific Reports

Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia

scientific article published on 30 October 2018

Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria.

scientific article published on 21 September 2016

Consequences of genomic diversity in Mycobacterium tuberculosis

scientific article

Correction: Clonal Waves of Neisseria Colonisation and Disease in the African Meningitis Belt: Eight-Year Longitudinal Study in Northern Ghana.

scientific article published on 29 May 2007

DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader.

scientific article published on 20 April 2015

Detection and characterization of drug-resistant conferring genes in Mycobacterium tuberculosis complex strains: A prospective study in two distant regions of Ghana

scientific article published on 03 June 2016

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

scientific article

Discovery and Characterization of Mycobacterium basiliense sp. nov., a Nontuberculous Mycobacterium Isolated From Human Lungs

scientific article published on 01 January 2018

Dispersal of Mycobacterium tuberculosis Driven by Historical European Trade in the South Pacific

scientific article published on 04 December 2019

Dispersal of Mycobacterium tuberculosis to indigenous populations driven by historical European trade in the South Pacific

scholarly article published 8 May 2019

Distribution and transmission of Mycobacterium tuberculosis complex lineages among children in peri-urban Kampala, Uganda.

scientific article published on 30 September 2015

Diversity of Mycobacterium tuberculosis and drug resistance in different provinces of Papua New Guinea

scientific article published on 5 December 2014

Does M. tuberculosis genomic diversity explain disease diversity?

scientific article

Does resistance to pyrazinamide accurately indicate the presence of Mycobacterium bovis?

scientific article published on July 2005

Drug resistance-conferring mutations in Mycobacterium tuberculosis from Madang, Papua New Guinea

scientific article published on 4 September 2012

EVOLUTION OF MYCOBACTERIUM TUBERCULOSIS AND IMPLICATIONS FOR VACCINE DEVELOPMENT.

scientific article published on April 2016

Ecology and evolution of Mycobacterium tuberculosis.

scientific article

Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis

scientific article

Emergence of W135 meningococcal meningitis in Ghana

scientific article published in December 2005

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

scientific article published on January 2013

Estimating the mutation rate of Mycobacterium tuberculosis during infection

scientific article published on 01 May 2011

Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana

scientific article

Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar.

scientific article

Evidence for diversifying selection in a set of Mycobacterium tuberculosis genes in response to antibiotic- and nonantibiotic-related pressure.

scientific article published on 28 February 2013

Evolution of drug resistance in tuberculosis: recent progress and implications for diagnosis and therapy

scientific article

Evolutionary forces in Mycobacterium tuberculosis

scientific article published on 01 January 2010

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

scientific article published on 19 January 2015

Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance

scientific article published on 06 July 2021

First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal

scientific article

Genetic Diversity in Mycobacterium tuberculosis ⬇️

scientific article published on January 1, 2013

Genetic diversification of Neisseria meningitidis during waves of colonization and disease in the meningitis belt of sub-Saharan Africa.

scientific article

Genetic diversity of Mycobacterium tuberculosis in Madang, Papua New Guinea.

scientific article published on 14 June 2012

Genetic diversity within Mycobacterium tuberculosis complex impacts on the accuracy of genotypic pyrazinamide drug-susceptibility assay

scientific article

Genetic variability and consequence of Mycobacterium tuberculosis lineage 3 in Kampala-Uganda

scientific article published on 09 September 2019

Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex

scientific article published on 05 September 2019

Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections

scientific article published on 11 May 2021

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

scientific article

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

scientific article published on 12 June 2019

Genomic determinants of sympatric speciation of theMycobacterium tuberculosiscomplex across evolutionary timescales

Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints

scientific article

Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread

scientific article published on 18 January 2015

Genomic interrogation of ancestral Mycobacterium tuberculosis from south India

scientific article published on 29 September 2007

Genotypic diversity and drug susceptibility patterns among M. tuberculosis complex isolates from South-Western Ghana

scientific article

Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

scientific article

Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development.

scientific article published on May 2007

HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis

scientific article

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

scientific article

High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds.

scientific article published in February 2018

Home-Based and Facility-Based Directly Observed Therapy of Tuberculosis Treatment under Programmatic Conditions in Urban Tanzania

scientific article

Host–pathogen coevolution in human tuberculosis ⬇️

scientific article published on March 19, 2012

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

scientific article

Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages

scientific article

Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis

scientific article

Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin (BCG)

scientific article

In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection

scientific article published on April 2015

Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region

scientific article

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

scientific article published on December 2009

Influence of M. tuberculosis lineage variability within a clinical trial for pulmonary tuberculosis

scientific article

Insights into the genetic diversity of Mycobacterium tuberculosis in Tanzania

scholarly article by Liliana K Rutaihwa et al published 2019 in PLOS ONE

Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

scientific article published in Scientific Reports

Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: Evidence for coevolution?

scientific article published on 30 April 2020

Interplay of strain and race/ethnicity in the innate immune response to M. tuberculosis.

scientific article

Investigation of the high rates of extrapulmonary tuberculosis in Ethiopia reveals no single driving factor and minimal evidence for zoonotic transmission of Mycobacterium bovis infection

scientific article

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

scientific article

Large sequence polymorphisms classify Mycobacterium tuberculosis strains with ancestral spoligotyping patterns.

scientific article

Leprosy in wild chimpanzees

scientific article published in 2021

Lipidomics and genomics of Mycobacterium tuberculosis reveal lineage-specific trends in mycolic acid biosynthesis

scientific article

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

scientific article published in 2021

Long-term dominance of Mycobacterium tuberculosis Uganda family in peri-urban Kampala-Uganda is not associated with cavitary disease

scientific article

Low sensitivity of the MPT64 identification test to detect lineage 5 of the Mycobacterium tuberculosis complex

scientific article published on 02 November 2018

M. tuberculosis T Cell Epitope Analysis Reveals Paucity of Antigenic Variation and Identifies Rare Variable TB Antigens

scientific article published on 21 October 2015

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

scientific article published on January 2013

Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis

scientific article published on 30 March 2020

Molecular characterization of bovine tuberculosis strains in two slaughterhouses in Morocco.

scientific article published on 25 August 2017

Molecular epidemiology of Mycobacterium africanum in Ghana

scientific article

Multiple Introductions of the Mycobacterium tuberculosis Lineage 2 Beijing into Africa over centuries

scholarly article published 10 September 2018

Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia.

scientific article published on March 2013

Mycobacterium africanum Is Associated with Patient Ethnicity in Ghana

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

Mycobacterium africanum--review of an important cause of human tuberculosis in West Africa

scientific article

Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production

scientific article published on 23 April 2020

Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade

scientific article published on 03 June 2019

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

scientific article published on 31 October 2016

Mycobacterium tuberculosis transmission in a country with low tuberculosis incidence: role of immigration and HIV infection

scientific article published on 23 November 2011

Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee

scientific article published on June 2013

Old and new selective pressures on Mycobacterium tuberculosis.

scientific article published on 17 August 2011

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

scientific article (publication date: October 2013)

PolyTB: a genomic variation map for Mycobacterium tuberculosis

scientific article

Population Genomics of Mycobacterium tuberculosis in Ethiopia Contradicts the Virgin Soil Hypothesis for Human Tuberculosis in Sub-Saharan Africa.

scientific article

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

scientific article (publication date: 23 October 2014)

Prevalence and clinical relevance of helminth co-infections among tuberculosis patients in urban Tanzania

scientific article

Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study.

scientific article

Prevalence of fluoroquinolone resistance among tuberculosis patients in Shanghai, China.

scientific article published on 13 April 2009

Programmatically selected multidrug-resistant strains drive the emergence of extensively drug-resistant tuberculosis in South Africa

scientific article (publication date: 2013)

Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa

scientific article published on 04 June 2018

Reference Set ofMycobacterium tuberculosisClinical Strains: A tool for research and product development

article

Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development

research work

Relationship between Mycobacterium tuberculosis genotype and the clinical phenotype of pulmonary and meningeal tuberculosis

scientific article published on 20 February 2008

Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420.

scientific article

Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex

scientific article published on 24 May 2019

Risk factors for meningococcal meningitis in northern Ghana ⬇️

scientific article published on September 1, 2001

Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition

scientific article published on 14 January 2014

Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum

scientific article published on 4 March 2017

Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database ⬇️

scientific article published on December 21, 2012

Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese

scientific article published on 15 June 2015

Spatio-temporal distribution of Mycobacterium tuberculosis complex strains in Ghana

scientific article

Strain classification of Mycobacterium tuberculosis: congruence between large sequence polymorphisms and spoligotypes.

scientific article published on January 2011

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

scientific article published on June 1, 2011

Survival and sequelae of meningococcal meningitis in Ghana.

scientific article published on December 2001

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

scientific article published in 2022

The Influence of HIV on the Evolution of Mycobacterium tuberculosis

scientific article

The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex.

scientific article published in January 2017

The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study

scientific article published on 20 August 2021

The Troika Host-Pathogen-Extrinsic Factors in Tuberculosis: Modulating Inflammation and Clinical Outcomes.

scientific article published in January 2017

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

scientific article published on 19 January 2007

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

The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis ⬇️

scientific article published on December 13, 2012

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

scientific article

The molecular clock of Mycobacterium tuberculosis

scientific article published on 12 September 2019

The past and future of tuberculosis research

scientific article

The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy

scientific article

TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities.

scientific article published on 5 March 2018

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

Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis.

scientific article published on 13 May 2019

Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity.

scientific article

Tuberculosis in HIV-Negative and HIV-Infected Patients in a Low-Incidence Country: Clinical Characteristics and Treatment Outcomes ⬇️

scientific article published on March 30, 2012

Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequencing.

scientific article published on 7 November 2017

Tuberculosis outbreak investigation using phylodynamic analysis

scholarly article published by David Stucki in 2018

Two new rapid SNP-typing methods for classifying mycobacterium tuberculosis complex into the main phylogenetic lineages

scientific article (publication date: 2012)

Use of spoligotyping and large sequence polymorphisms to study the population structure of the Mycobacterium tuberculosis complex in a cohort study of consecutive smear-positive tuberculosis cases in The Gambia

scientific article published on 04 February 2009

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

scientific article

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

scientific article published on 13 January 2022

Variable host-pathogen compatibility in Mycobacterium tuberculosis

scientific article (publication date: 21 February 2006)

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

scientific article published on 01 September 2019

Whole-Genome Sequencing Has the Potential To Improve Treatment for Rifampicin-Resistant Tuberculosis in High-Burden Settings: a Retrospective Cohort Study

scientific article published on 16 March 2022

Whole-Genome Sequencing for Drug Resistance Profile Prediction in

scientific article published on 27 March 2019

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

scientific article published on 18 December 2011

Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity

scientific article

complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv

scientific article published in 2021

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