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1
Ecology and evolution of Mycobacterium tuberculosis
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Ecology and evolution of Mycobacterium tuberculosis

Gagneux, Sebastien

Nature reviews. Microbiology, 2018-04, Vol.16 (4), p.202-213 [Peer Reviewed Journal]

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2
Host-pathogen coevolution in human tuberculosis
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Host-pathogen coevolution in human tuberculosis

Sebastien Gagneux

Philosophical transactions. Biological sciences, 2012-03-19, Vol.367 (1590), p.850-859

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3
Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives
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Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives

Gygli, Sebastian M ; Borrell, Sonia ; Trauner, Andrej ; Gagneux, Sebastien

FEMS microbiology reviews, 2017-05-01, Vol.41 (3), p.354-373 [Peer Reviewed Journal]

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4
Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes
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Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

COMAS, Inaki ; BORRELL, Sonia ; ROETZER, Andreas ; ROSE, Graham ; MALLA, Bijaya ; KATO-MAEDA, Midori ; GALAGAN, James ; NIEMANN, Stefan ; GAGNEUX, Sebastien

Nature genetics, 2012, Vol.44 (1), p.106-110 [Peer Reviewed Journal]

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5
KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes
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KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes

Steiner, Andreas ; Stucki, David ; Coscolla, Mireia ; Borrell, Sonia ; Gagneux, Sebastien

BMC genomics, 2014-10-09, Vol.15 (1), p.881-881 [Peer Reviewed Journal]

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6
Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage
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Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

Merker, Matthias ; Blin, Camille ; Mona, Stefano ; Duforet-Frebourg, Nicolas ; Lecher, Sophie ; Willery, Eve ; Blum, Michael G B ; Rüsch-Gerdes, Sabine ; Mokrousov, Igor ; Aleksic, Eman ; Allix-Béguec, Caroline ; Antierens, Annick ; Augustynowicz-Kopeć, Ewa ; Ballif, Marie ; Barletta, Francesca ; Beck, Hans Peter ; Barry, 3rd, Clifton E ; Bonnet, Maryline ; Borroni, Emanuele ; Campos-Herrero, Isolina ; Cirillo, Daniela ; Cox, Helen ; Crowe, Suzanne ; Crudu, Valeriu ; Diel, Roland ; Drobniewski, Francis ; Fauville-Dufaux, Maryse ; Gagneux, Sébastien ; Ghebremichael, Solomon ; Hanekom, Madeleine ; Hoffner, Sven ; Jiao, Wei-wei ; Kalon, Stobdan ; Kohl, Thomas A ; Kontsevaya, Irina ; Lillebæk, Troels ; Maeda, Shinji ; Nikolayevskyy, Vladyslav ; Rasmussen, Michael ; Rastogi, Nalin ; Samper, Sofia ; Sanchez-Padilla, Elisabeth ; Savic, Branislava ; Shamputa, Isdore Chola ; Shen, Adong ; Sng, Li-Hwei ; Stakenas, Petras ; Toit, Kadri ; Varaine, Francis ; Vukovic, Dragana ; Wahl, Céline ; Warren, Robin ; Supply, Philip ; Niemann, Stefan ; Wirth, Thierry

Nature genetics, 2015-03, Vol.47 (3), p.242-249 [Peer Reviewed Journal]

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7
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
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Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

Ford, Christopher B ; Shah, Rupal R ; Maeda, Midori Kato ; Gagneux, Sebastien ; Murray, Megan B ; Cohen, Ted ; Johnston, James C ; Gardy, Jennifer ; Lipsitch, Marc ; Fortune, Sarah M

Nature genetics, 2013-07-01, Vol.45 (7), p.784-790 [Peer Reviewed Journal]

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8
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans
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Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

Comas, Iñaki ; Coscolla, Mireia ; Luo, Tao ; Borrell, Sonia ; Holt, Kathryn E ; Kato-Maeda, Midori ; Parkhill, Julian ; Malla, Bijaya ; Berg, Stefan ; Thwaites, Guy ; Yeboah-Manu, Dorothy ; Bothamley, Graham ; Mei, Jian ; Wei, Lanhai ; Bentley, Stephen ; Harris, Simon R ; Niemann, Stefan ; Diel, Roland ; Aseffa, Abraham ; Gao, Qian ; Young, Douglas ; Gagneux, Sebastien

Nature genetics, 2013-10, Vol.45 (10), p.1176-1182 [Peer Reviewed Journal]

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9
Acquired Resistance to Bedaquiline and Delamanid in Therapy for Tuberculosis
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Acquired Resistance to Bedaquiline and Delamanid in Therapy for Tuberculosis

Bloemberg, Guido V ; Stuckia, David ; Coscolla, Mireia ; Feldmann, Julia ; Schulthess, Bettina ; Böttger, Erik C ; Gagneux, Sebastien ; Latshang, Tsogyal ; Hömke, Rico ; Rothe, Thomas ; Keller, Peter M ; Ritter, Claudia ; Trauner, Andrej ; Borrell, Sonia

The New England journal of medicine, 2015-11-12, Vol.373 (20), p.1986-1988 [Peer Reviewed Journal]

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10
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved
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Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

Niemann, Stefan ; Galagan, James ; Kremer, Kristin ; Gagneux, Sebastien ; Comas, Iñaki ; Ernst, Joel D ; Chakravartti, Jaidip ; Small, Peter M

Nature genetics, 2010-06, Vol.42 (6), p.498-503 [Peer Reviewed Journal]

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