Tuberculosis, Nature Reviews Disease Primers, vol.32, pp.16076-27784885, 2016. ,
DOI : 10.1183/09031936.00061808
The Global Burden of Latent Tuberculosis Infection: A Re-estimation Using Mathematical Modelling, PLOS Medicine, vol.87, issue.9, p.27780211, 2016. ,
DOI : 10.1371/journal.pmed.1002152.s007
Heterogeneity in tuberculosis pathology, microenvironments and therapeutic responses, Immunological Reviews, vol.74, issue.Suppl 1, pp.288-307, 2015. ,
DOI : 10.1128/IAI.00064-06
URL : http://onlinelibrary.wiley.com/doi/10.1111/imr.12252/pdf
Mycobacterium tuberculosis and the intimate discourse of a chronic infection, Immunological Reviews, vol.8, issue.1, pp.252-268, 2011. ,
DOI : 10.1016/j.chom.2010.06.002
Lateral gene transfer and the nature of bacterial innovation, Nature, vol.2, issue.6784, pp.299-304, 2000. ,
DOI : 10.1128/9781555818180.ch15
Genomic islands in pathogenic and environmental microorganisms, Nature Reviews Microbiology, vol.37, issue.5, pp.414-424, 2004. ,
DOI : 10.1006/plas.1997.1280
Horizontal Gene Transfer: Evidence and Possible Consequences, Annual Review of Genetics, vol.28, issue.1, pp.237-261, 1994. ,
DOI : 10.1146/annurev.ge.28.120194.001321
A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent, Molecular Microbiology, vol.69, issue.5, pp.835-852, 2014. ,
DOI : 10.1111/2049-632X.12096
Contribution of Horizontally Acquired Genomic Islands to the Evolution of the Tubercle Bacilli, Molecular Biology and Evolution, vol.24, issue.8, pp.1861-1871, 2007. ,
DOI : 10.1093/molbev/msm111
Horizontally acquired genomic islands in the tubercle bacilli, Trends in Microbiology, vol.16, issue.7, pp.303-308, 2008. ,
DOI : 10.1016/j.tim.2008.04.005
Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis, Genome Research, vol.18, issue.5, 2008. ,
DOI : 10.1101/gr.075069.107
Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis, BMC Evolutionary Biology, vol.9, issue.1, 2009. ,
DOI : 10.1186/1471-2148-9-196
Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria, Proceedings of the National Academy of Sciences, vol.2, issue.1, pp.9876-9881, 2016. ,
DOI : 10.2217/fmb.13.113
Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis, Nature Genetics, vol.174, issue.2, pp.172-179, 2013. ,
DOI : 10.1093/infdis/jiq089
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence, Nature, vol.25, issue.6685, pp.537-544, 1998. ,
DOI : 10.1093/nar/25.5.0955
Biosynthesis and Insertion of the Molybdenum Cofactor, EcoSal Plus, vol.6, 2015. ,
pathogenesis?, Critical Reviews in Microbiology, vol.286, issue.1, pp.18-29, 2014. ,
DOI : 10.1074/jbc.R110.172833
URL : https://hal.archives-ouvertes.fr/hal-00540163
Molybdenum enzymes in bacteria and their maturation, Coordination Chemistry Reviews, vol.255, issue.9-10, pp.1159-1178, 2011. ,
DOI : 10.1016/j.ccr.2010.12.031
The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis, Microbiology, vol.173, issue.22, pp.1332-1339, 2009. ,
DOI : 10.1046/j.1365-2958.2000.01794.x
Presence of multiple lesion types with vastly different microenvironments in C3HeB/FeJ mice following aerosol infection with Mycobacterium tuberculosis, Disease Models & Mechanisms, vol.8, issue.6, pp.591-602, 2015. ,
DOI : 10.1242/dmm.019570
-Molybdopterin Guanine Dinucleotide Is Required for Persistence of Mycobacterium tuberculosis in Guinea Pigs, Infection and Immunity, vol.83, issue.2, pp.544-550, 2015. ,
DOI : 10.1128/IAI.02722-14
latency, Cellular Microbiology, vol.95, issue.8, pp.1151-1159, 2009. ,
DOI : 10.1111/j.1462-5822.2009.01325.x
The Enduring Hypoxic Response of Mycobacterium tuberculosis, PLoS ONE, vol.98, issue.1, p.18231589, 2008. ,
DOI : 10.1371/journal.pone.0001502.s005
The Mycobacterium tuberculosis regulatory network and hypoxia, Nature, vol.9, issue.7457, pp.178-183, 2013. ,
DOI : 10.4161/rna.20105
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4087036/pdf
Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network, Genome Biology, vol.26, issue.11, pp.502-25380655, 2014. ,
DOI : 10.1093/bioinformatics/btq602
High Genetic Diversity Revealed by Variable-Number Tandem Repeat Genotyping and Analysis of hsp65 Gene Polymorphism in a Large Collection of "Mycobacterium canettii" Strains Indicates that the M. tuberculosis Complex Is a Recently Emerged Clone of "M. canettii", Journal of Clinical Microbiology, vol.42, issue.7, pp.3248-3255, 2004. ,
DOI : 10.1128/JCM.42.7.3248-3255.2004
URL : https://hal.archives-ouvertes.fr/hal-01158318
Clinical characteristics of the smooth tubercle bacilli ???Mycobacterium canettii??? infection suggest the existence of an environmental reservoir, Clinical Microbiology and Infection, vol.17, issue.7, pp.1013-1019, 2011. ,
DOI : 10.1111/j.1469-0691.2010.03347.x
pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence, Nature Microbiology, vol.66, issue.2, pp.15019-27571976 ,
DOI : 10.4049/jimmunol.174.6.3570
URL : https://hal.archives-ouvertes.fr/pasteur-01265519
Identification of a small molecule with activity against drug-resistant and persistent tuberculosis, Proceedings of the National Academy of Sciences, vol.169, issue.1, pp.2510-2517, 2013. ,
DOI : 10.1002/hlca.19920750718
Survival of mice infected with Mycobacterium smegmatis containing large DNA fragments from Mycobacterium tuberculosis, Tubercle and Lung Disease, vol.79, issue.3, pp.171-180, 1999. ,
DOI : 10.1054/tuld.1998.0201
Construction of Conditional Knockdown Mutants in Mycobacteria, Methods Mol Biol, vol.29, issue.11, pp.151-175, 2015. ,
DOI : 10.1016/S0378-1097(03)00823-1
QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR, BMC Bioinformatics, vol.9, issue.1, pp.465-18976492, 2008. ,
DOI : 10.1186/1471-2105-9-465
Ensembl Genomes 2016: more genomes, more complexity, Nucleic Acids Research, vol.30, issue.D1, pp.574-580, 2016. ,
DOI : 10.1093/bioinformatics/btt637
URL : https://academic.oup.com/nar/article-pdf/44/D1/D574/9483009/gkv1209.pdf
How to Interpret an Anonymous Bacterial Genome: Machine Learning Approach to Gene Identification, Genome Research, vol.12, issue.11, pp.1154-1171, 1998. ,
DOI : 10.1093/bioinformatics/10.6.613
Exploration of phylogenetic data using a global sequence analysis method, BMC Evolutionary Biology, vol.5, issue.1, pp.63-16280081, 2005. ,
DOI : 10.1186/1471-2148-5-63
URL : https://hal.archives-ouvertes.fr/inserm-00091302
BLAST+: architecture and applications, BMC Bioinformatics, vol.10, issue.1, p.421, 2009. ,
DOI : 10.1186/1471-2105-10-421
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-421?site=bmcbioinformatics.biomedcentral.com
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database, Bioinformatics, vol.16, issue.23, pp.2672-2676, 2008. ,
DOI : 10.1093/bioinformatics/16.10.944
URL : https://academic.oup.com/bioinformatics/article-pdf/24/23/2672/16886102/btn529.pdf
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: e11147. https, p.20593022, 2010. ,
DOI : 10.1371/journal.pone.0011147
Genomic signature: characterization and classification of species assessed by chaos game representation of sequences, Molecular Biology and Evolution, vol.16, issue.10, pp.1391-1399, 1999. ,
DOI : 10.1093/oxfordjournals.molbev.a026048