Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa by Seth Duwor, Daniela Brites, Pascal Mäser

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The molecular clock of Mycobacterium tuberculosis. by Fabrizio Menardo, Sebastian Duchêne, Daniela Brites, Sebastien Gagneux

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Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila. by Daniela Brites, Francisco Encinas-Viso, Dieter Ebert, Louis Du Pasquier, Christoph R Haag

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Tuberculosis outbreak investigation using phylodynamic analysis by Denise Kühnert, Mireia Coscolla, Daniela Brites, David Stucki, John Metcalfe, Lukas Fenner, Sebastien Gagneux, Tanja Stadler

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Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity by Fabrizio Menardo, Chloé Loiseau, Daniela Brites, Mireia Coscolla, Sebastian M. Gygli, Liliana K. Rutaihwa, Andrej Trauner, Christian Beisel, Sonia Borrell, Sebastien Gagneux

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A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics [version 2; peer review: 2 approved] by Anna Dötsch, Dick Van Soolingen, Miriam Reinhard, Michaela Zwyer, Giovanni Ghielmetti, Cengiz Çavusoglu, Erika Scaltriti, Sebastien Gagneux, Maria Lodovica Pacciarini, Daniela Brites

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Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana by Prince Asare, Prince Asare, Prince Asare, Isaac Darko Otchere, Edmund Bedeley, Daniela Brites, Daniela Brites, Chloé Loiseau, Chloé Loiseau, Nyonuku Akosua Baddoo, Adwoa Asante-Poku, Stephen Osei-Wusu, Diana Ahu Prah, Sonia Borrell, Sonia Borrell, Miriam Reinhard, Miriam Reinhard, Audrey Forson, Kwadwo Ansah Koram, Sebastien Gagneux, Sebastien Gagneux, Dorothy Yeboah-Manu, Dorothy Yeboah-Manu

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Dispersal of Mycobacterium tuberculosis Driven by Historical European Trade in the South Pacific by Claire V. Mulholland, Claire V. Mulholland, Abigail C. Shockey, Htin L. Aung, Htin L. Aung, Ray T. Cursons, Ronan F. O’Toole, Ronan F. O’Toole, Sanjay S. Gautam, Daniela Brites, Daniela Brites, Sebastien Gagneux, Sebastien Gagneux, Sally A. Roberts, Noel Karalus, Gregory M. Cook, Gregory M. Cook, Caitlin S. Pepperell, Caitlin S. Pepperell, Vickery L. Arcus, Vickery L. Arcus

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Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania by Hellen Hiza, Michaela Zwyer, Jerry Hella, Ainhoa Arbués, Mohamed Sasamalo, Sonia Borrell, Zhi Ming Xu, Amanda Ross, Daniela Brites, Jacques Fellay, Klaus Reither, Sébastien Gagneux, Damien Portevin

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HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa. by Etthel M Windels, Eddie M Wampande, Moses L Joloba, W Henry Boom, Galo A Goig, Helen Cox, Jerry Hella, Sonia Borrell, Sebastien Gagneux, Daniela Brites, Tanja Stadler

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Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development. by Sònia Borrell, Andrej Trauner, Daniela Brites, Leen Rigouts, Chloe Loiseau, Mireia Coscolla, Stefan Niemann, Bouke De Jong, Dorothy Yeboah-Manu, Midori Kato-Maeda, Julia Feldmann, Miriam Reinhard, Christian Beisel, Sebastien Gagneux

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Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon. by Miriam Bolz, Martin W Bratschi, Sarah Kerber, Jacques C Minyem, Alphonse Um Boock, Moritz Vogel, Pierre Franklin Bayi, Thomas Junghanss, Daniela Brites, Simon R Harris, Julian Parkhill, Gerd Pluschke, Araceli Lamelas Cabello

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Insights into the genetic diversity of Mycobacterium tuberculosis in Tanzania. by Liliana K Rutaihwa, Mohamed Sasamalo, Aladino Jaleco, Jerry Hella, Ally Kingazi, Lujeko Kamwela, Amri Kingalu, Bryceson Malewo, Raymond Shirima, Anna Doetsch, Julia Feldmann, Miriam Reinhard, Sonia Borrell, Daniela Brites, Klaus Reither, Basra Doulla, Lukas Fenner, Sebastien Gagneux

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Genomic epidemiological analysis identifies high relapse among individuals with recurring tuberculosis and provides evidence of recent household-related transmission of tuberculosi... by Prince Asare, Stephen Osei-Wusu, Nyonuku Akosua Baddoo, Edmund Bedeley, Isaac Darko Otchere, Daniela Brites, Chloé Loiseau, Adwoa Asante-Poku, Diana Ahu Prah, Sonia Borrell, Miriam Reinhard, Michael Amo Omari, Audrey Forson, Kwadwo Ansah Koram, Sebastien Gagneux, Dorothy Yeboah-Manu

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The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot by Chloé Loiseau, Etthel M. Windels, Sebastian M. Gygli, Levan Jugheli, Nino Maghradze, Daniela Brites, Amanda Ross, Galo Goig, Miriam Reinhard, Sonia Borrell, Andrej Trauner, Anna Dötsch, Rusudan Aspindzelashvili, Rebecca Denes, Klaus Reither, Christian Beisel, Nestani Tukvadze, Zaza Avaliani, Tanja Stadler, Sebastien Gagneux

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The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy by Andrej Trauner, Qingyun Liu, Laura E. Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England, Guolong Zhang, Sebastien Gagneux, Clifton E. Barry, Qian Gao

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A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region by Jean Claude Semuto Ngabonziza, Chloé Loiseau, Michael Marceau, Agathe Jouet, Fabrizio Menardo, Oren Tzfadia, Rudy Antoine, Esdras Belamo Niyigena, Wim Mulders, Kristina Fissette, Maren Diels, Cyril Gaudin, Stéphanie Duthoy, Willy Ssengooba, Emmanuel André, Michel K. Kaswa, Yves Mucyo Habimana, Daniela Brites, Dissou Affolabi, Jean Baptiste Mazarati, Bouke Catherine de Jong, Leen Rigouts, Sebastien Gagneux, Conor Joseph Meehan, Philip Supply

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Genetic Characterization and Population Structure of Drug-Resistant <i>Mycobacterium tuberculosis</i> Isolated from Brazilian Patients Using Whole-Genome Sequencing by Leonardo Souza Esteves, Lia Lima Gomes, Daniela Brites, Fátima Cristina Onofre Fandinho, Marcela Bhering, Márcia Aparecida da Silva Pereira, Emilyn Costa Conceição, Richard Salvato, Bianca Porphirio da Costa, Reginalda Ferreira de Melo Medeiros, Paulo Cesar de Souza Caldas, Paulo Redner, Margareth Pretti Dalcolmo, Vegard Eldholm, Sebastien Gagneux, Maria Lucia Rossetti, Afrânio Lineu Kritski, Philip Noel Suffys

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Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim [version 2; peer review: 3 approved] by Fabrizio Menardo, Liliana K. Rutaihwa, Michaela Zwyer, Sonia Borrell, Iñaki Comas, Emilyn Costa Conceição, Mireia Coscolla, Helen Cox, Moses Joloba, Horng-Yunn Dou, Julia Feldmann, Lukas Fenner, Janet Fyfe, Qian Gao, Darío García de Viedma, Alberto L. Garcia-Basteiro, Sebastian M. Gygli, Jerry Hella, Hellen Hiza, Levan Jugheli, Lujeko Kamwela, Midori Kato-Maeda, Qingyun Liu, Serej D. Ley, Chloe Loiseau, Surakameth Mahasirimongkol, Bijaya Malla, Prasit Palittapongarnpim, Niaina Rakotosamimanana, Voahangy Rasolofo, Miriam Reinhard, Klaus Reither, Mohamed Sasamalo, Rafael Silva Duarte, Christophe Sola, Philip Suffys, Karla Valeria Batista Lima, Dorothy Yeboah-Manu, Christian Beisel, Daniela Brites, Sebastien Gagneux

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Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania. by Michaela Zwyer, Liliana K Rutaihwa, Etthel Windels, Jerry Hella, Fabrizio Menardo, Mohamed Sasamalo, Gregor Sommer, Lena Schmülling, Sonia Borrell, Miriam Reinhard, Anna Dötsch, Hellen Hiza, Christoph Stritt, George Sikalengo, Lukas Fenner, Bouke C De Jong, Midori Kato-Maeda, Levan Jugheli, Joel D Ernst, Stefan Niemann, Leila Jeljeli, Marie Ballif, Matthias Egger, Niaina Rakotosamimanana, Dorothy Yeboah-Manu, Prince Asare, Bijaya Malla, Horng Yunn Dou, Nicolas Zetola, Robert J Wilkinson, Helen Cox, E Jane Carter, Joachim Gnokoro, Marcel Yotebieng, Eduardo Gotuzzo, Alash'le Abimiku, Anchalee Avihingsanon, Zhi Ming Xu, Jacques Fellay, Damien Portevin, Klaus Reither, Tanja Stadler, Sebastien Gagneux, Daniela Brites

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