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Rutaihwa L, Menardo F. and Stucki D, Gygli S. M. and Ley SD, Malla B. and Feldmann J, Borrell S. and Beisel C, Middelkoop K. and Carter JE, Diero L. and Ballif M, Jugheli L. and Reither K, Fenner L. and Brites D, Gagneux S.. (2019) Multiple introductions of Mycobacterium tuberculosis lineage 2-Beijing into Africa over centuries. Frontiers in Ecology and Evolution, 7. p. 112.

Kühnert, Denise and Coscolla, Mireia and Brites, Daniela and Stucki, David and Metcalfe, John and Fenner, Lukas and Gagneux, Sebastien and Stadler, Tanja. (2018) Tuberculosis outbreak investigation using phylodynamic analysis. Epidemics, 25. pp. 47-53.

Ghielmetti, Giovanni and Coscolla, Mireia and Ruetten, Maja and Friedel, Ute and Loiseau, Chloé and Feldmann, Julia and Steinmetz, Hanspeter W. and Stucki, David and Gagneux, Sebastien. (2017) Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequencingle-number tandem-repeat analysis and whole-genome sequencing. Scientific reports, 7 (1). p. 14647.

Rasoahanitralisoa, Rondroarivelo and Rakotosamimanana, Niaina and Stucki, David and Sola, Christophe and Gagneux, Sebastien and Rasolofo Razanamparany, Voahangy. (2017) Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar. PLoS ONE, 12 (10). e0186088.

Asante-Poku, Adwoa and Yeboah-Manu, Dorothy and Otchere, Isaac Darko and Aboagye, Samuel Y. and Stucki, David and Hattendorf, Jan and Borrell, Sonia and Feldmann, Julia and Danso, Emelia and Gagneux, Sebastien. (2015) Mycobacterium africanum is associated with patient ethnicity in Ghana. PLoS neglected tropical diseases, Vol. 9, H. 1, e3370.

Stucki, David and Ballif, Marie and Bodmer, Thomas and Coscolla, Mireia and Maurer, Anne-Marie and Droz, Sara and Butz, Christa and Borrell, Sonia and Längle, Christel and Feldmann, Julia and Furrer, Hansjakob and Mordasini, Carlo and Helbling, Peter and Rieder, Hans L. and Egger, Matthias and Gagneux, Sébastien and Fenner, Lukas. (2015) Tracking a tuberculosis outbreak over 21 years : strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing. Journal of infectious diseases, Vol. 211, H. 8. pp. 1306-1316.

Steiner, Andreas and Stucki, David and Coscolla, Mireia and Borrell, Sonia and Gagneux, Sebastien. (2014) KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. BMC genomics, Vol. 15 , 881.

Stucki, D. and Gagneux, S.. (2013) Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database. Tuberculosis, Vol. 93, H. 1. pp. 30-39.