Items where Author is "Gagneux, Sebastien"
Number of items: 91. 2020Ngabonziza, Jean Claude Semuto and Loiseau, Chloé and Marceau, Michael and Jouet, Agathe and Menardo, Fabrizio and Tzfadia, Oren and Antoine, Rudy and Niyigena, Esdras Belamo and Mulders, Wim and Fissette, Kristina and Diels, Maren and Gaudin, Cyril and Duthoy, Stéphanie and Ssengooba, Willy and André, Emmanuel and Kaswa, Michel K. and Habimana, Yves Mucyo and Brites, Daniela and Affolabi, Dissou and Mazarati, Jean Baptiste and de Jong, Bouke Catherine and Rigouts, Leen and Gagneux, Sebastien and Meehan, Conor Joseph and Supply, Philip. (2020) A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nature Communications, 11. p. 2917. Loiseau, Chloé and Menardo, Fabrizio and Aseffa, Abraham and Hailu, Elena and Gumi, Balako and Ameni, Gobena and Berg, Stefan and Rigouts, Leen and Robbe-Austerman, Suelee and Zinsstag, Jakob and Gagneux, Sebastien and Brites, Daniela. (2020) An African origin for Mycobacterium bovis. Evolution, medicine, and public health, 2020. pp. 49-59. McHenry, Michael L. and Bartlett, Jacquelaine and Igo, Robert P. and Wampande, Eddie M. and Benchek, Penelope and Mayanja-Kizza, Harriet and Fluegge, Kyle and Hall, Noemi B. and Gagneux, Sebastien and Tishkoff, Sarah A. and Wejse, Christian and Sirugo, Giorgio and Boom, W. Henry and Joloba, Moses and Williams, Scott M. and Stein, Catherine M.. (2020) Interaction between host genes and Mycobacterium tuberculosis lineage can affect tuberculosis severity: evidence for coevolution? PLoS genetics, 16 (4). e1008728. Øyås, Ove and Borrell, Sonia and Trauner, Andrej and Zimmermann, Michael and Feldmann, Julia and Liphardt, Thomas and Gagneux, Sebastien and Stelling, Jörg and Sauer, Uwe and Zampieri, Mattia. (2020) Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America, 117 (15). pp. 8494-8502. Sousa, Jeremy and Cá, Baltazar and Maceiras, Ana Raquel and Simões-Costa, Luisa and Fonseca, Kaori L. and Fernandes, Ana Isabel and Ramos, Angélica and Carvalho, Teresa and Barros, Leandro and Magalhães, Carlos and Chiner-Oms, Álvaro and Machado, Henrique and Veiga, Maria Isabel and Singh, Albel and Pereira, Rui and Amorim, António and Vieira, Jorge and Vieira, Cristina P. and Bhatt, Apoorva and Rodrigues, Fernando and Rodrigues, Pedro N. S. and Gagneux, Sebastien and Castro, António Gil and Guimarães, João Tiago and Bastos, Helder Novais and Osório, Nuno S. and Comas, Iñaki and Saraiva, Margarida. (2020) Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production. Nature Communications, 11. p. 1949. Castro, Rhastin A. D. and Ross, Amanda and Kamwela, Lujeko and Reinhard, Miriam and Loiseau, Chloé and Feldmann, Julia and Borrell, Sonia and Trauner, Andrej and Gagneux, Sebastien. (2020) The genetic background modulates the evolution of fluoroquinolone-resistance in Mycobacterium tuberculosis. Molecular biology and evolution, 37 (1). pp. 195-207. Asare, Prince and Otchere, Isaac Darko and Bedeley, Edmund and Brites, Daniela and Loiseau, Chloé and Baddoo, Nyonuku Akosua and Asante-Poku, Adwoa and Osei-Wusu, Stephen and Prah, Diana Ahu and Borrell, Sonia and Reinhard, Miriam and Forson, Audrey and Koram, Kwadwo Ansah and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2020) Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana. Frontiers in medicine, 7. p. 161. 2019Maghradze, Nino and Jugheli, Levan and Borrell, Sonia and Tukvadze, Nestani and Aspindzelashvili, Rusudan and Avaliani, Zaza and Reither, Klaus and Gagneux, Sebastien. (2019) Classifying recurrent Mycobacterium tuberculosis cases in Georgia using MIRU-VNTR typing. PLoS ONE, 14 (10). e0223610. Zürcher, Kathrin and Ballif, Marie and Fenner, Lukas and Borrell, Sonia and Keller, Peter M. and Gnokoro, Joachim and Marcy, Olivier and Yotebieng, Marcel and Diero, Lameck and Carter, E. Jane and Rockwood, Neesha and Wilkinson, Robert J. and Cox, Helen and Ezati, Nicholas and Abimiku, Alash'le G. and Collantes, Jimena and Avihingsanon, Anchalee and Kawkitinarong, Kamon and Reinhard, Miriam and Hömke, Rico and Huebner, Robin and Gagneux, Sebastien and Böttger, Erik C. and Egger, Matthias and International epidemiology Databases to Evaluate Aids consortium, . (2019) Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries : a multicentre cohort study. The Lancet infectious diseases, 19 (3). pp. 298-307. Wampande, Eddie M. and Naniima, Peter and Mupere, Ezekiel and Kateete, David P. and Malone, LaShaunda L. and Stein, Catherine M. and Mayanja-Kizza, Harriet and Gagneux, Sebastien and Boom, W. Henry and Joloba, Moses L.. (2019) Genetic variability and consequence of Mycobacterium tuberculosis lineage 3 in Kampala-Uganda. PLoS ONE, 14 (9). e0221644. Chiner-Oms, Álvaro and Berney, Michael and Boinett, Christine and González-Candelas, Fernando and Young, Douglas B. and Gagneux, Sebastien and Jacobs, William R. and Parkhill, Julian and Cortes, Teresa and Comas, Iñaki. (2019) Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex. Nature Communications, 10. p. 3994. Rutaihwa, Liliana K. and Sasamalo, Mohamed and Jaleco, Aladino and Hella, Jerry and Kingazi, Ally and Kamwela, Lujeko and Kingalu, Amri and Malewo, Bryceson and Shirima, Raymond and Doetsch, Anna and Feldmann, Julia and Reinhard, Miriam and Borrell, Sonia and Brites, Daniela and Reither, Klaus and Doulla, Basra and Fenner, Lukas and Gagneux, Sebastien. (2019) Insights into the genetic diversity of Mycobacterium tuberculosis in Tanzania. PLoS ONE, 14 (4). e0206334. Otchere, Isaac Darko and van Tonder, Andries J. and Asante-Poku, Adwoa and Sánchez-Busó, Leonor and Coscollá, Mireia and Osei-Wusu, Stephen and Asare, Prince and Aboagye, Samuel Yaw and Ekuban, Samuel Acquah and Yahayah, Abdallah Iddrisu and Forson, Audrey and Baddoo, Akosua and Laryea, Clement and Parkhill, Julian and Harris, Simon R. and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2019) Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana. PLoS ONE, 14 (3). e0209395. Conceição, Emilyn Costa and Refregier, Guislaine and Gomes, Harrison Magdinier and Olessa-Daragon, Xavier and Coll, Francesc and Ratovonirina, Noël Harijaona and Rasolofo-Razanamparany, Voahangy and Lopes, Maria Luiza and van Soolingen, Dick and Rutaihwa, Liliana and Gagneux, Sebastien and Bollela, Valdes Roberto and Suffys, Philip Noel and Duarte, Rafael Silva and Lima, Karla Valéria Batista and Sola, Christophe Noel. (2019) Mycobacterium tuberculosis lineage 1 genetic diversity in Pará, Brazil, suggests common ancestry with east-African isolates potentially linked to historical slave trade. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 73. pp. 337-341. Borrell, Sònia and Trauner, Andrej and Brites, Daniela and Rigouts, Leen and Loiseau, Chloe and Coscolla, Mireia and Niemann, Stefan and De Jong, Bouke and Yeboah-Manu, Dorothy and Kato-Maeda, Midori and Feldmann, Julia and Reinhard, Miriam and Beisel, Christian and Gagneux, Sebastien. (2019) Reference set of Mycobacterium tuberculosis clinical strains: a tool for research and product development. PLoS ONE, 14 (3). e0214088. Loiseau, Chloé and Brites, Daniela and Moser, Irmgard and Coll, Francesc and Pourcel, Christine and Robbe-Austerman, Suelee and Escuyer, Vincent and Musser, Kimberlee A. and Peacock, Sharon J. and Feuerriegel, Silke and Kohl, Thomas A. and Niemann, Stefan and Gagneux, Sebastien and Köser, Claudio U.. (2019) Revised interpretation of the Hain Lifescience GenoType MTBC to differentiate Mycobacterium canettii and members of the M. tuberculosis complex. Antimicrobial agents and chemotherapy, 63 (6). e00159-19. Asante-Poku, Adwoa and Asare, Prince and Baddoo, Nyonuku Akosua and Forson, Audrey and Klevor, Pius and Otchere, Isaac Darko and Aboagye, Sammy Yaw and Osei-Wusu, Stephen and Danso, Emelia Konadu and Koram, Kwadwo and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2019) TB-diabetes co-morbidity in Ghana : the importance of Mycobacterium africanum infection. PLoS ONE, 14 (2). e0211822. Menardo, Fabrizio and Duchêne, Sebastian and Brites, Daniela and Gagneux, Sebastien. (2019) The molecular clock of Mycobacterium tuberculosis. PLoS Pathogens, 15 (9). e1008067. Payne, Joshua L. and Menardo, Fabrizio and Trauner, Andrej and Borrell, Sonia and Gygli, Sebastian M. and Loiseau, Chloe and Gagneux, Sebastien and Hall, Alex R.. (2019) Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. PLoS Biology, 17 (5). e3000265. Meehan, Conor J. and Goig, Galo A. and Kohl, Thomas A. and Verboven, Lennert and Dippenaar, Anzaan and Ezewudo, Matthew and Farhat, Maha R. and Guthrie, Jennifer L. and Laukens, Kris and Miotto, Paolo and Ofori-Anyinam, Boatema and Dreyer, Viola and Supply, Philip and Suresh, Anita and Utpatel, Christian and van Soolingen, Dick and Zhou, Yang and Ashton, Philip M. and Brites, Daniela and Cabibbe, Andrea M. and de Jong, Bouke C. and de Vos, Margaretha and Menardo, Fabrizio and Gagneux, Sebastien and Gao, Qian and Heupink, Tim H. and Liu, Qingyun and Loiseau, Chloé and Rigouts, Leen and Rodwell, Timothy C. and Tagliani, Elisa and Walker, Timothy M. and Warren, Robin M. and Zhao, Yanlin and Zignol, Matteo and Schito, Marco and Gardy, Jennifer and Cirillo, Daniela M. and Niemann, Stefan and Comas, Inaki and Van Rie, Annelies. (2019) Whole genome sequencing of Mycobacterium tuberculosis : current standards and open issues. Nature Reviews Microbiology, 17 (9). pp. 533-545. Gygli, Sebastian M. and Keller, Peter M. and Ballif, Marie and Blöchliger, Nicolas and Hömke, Rico and Reinhard, Miriam and Loiseau, Chloé and Ritter, Claudia and Sander, Peter and Borrell, Sonia and Collantes Loo, Jimena and Avihingsanon, Anchalee and Gnokoro, Joachim and Yotebieng, Marcel and Egger, Matthias and Gagneux, Sebastien and Böttger, Erik C.. (2019) Whole-genome sequencing for drug resistance profile prediction in Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy, 63 (4). e02175-18. 2018Hella, Jerry and Cercamondi, Colin I. and Mhimbira, Francis and Sasamalo, Mohamed and Stoffel, Nicole and Zwahlen, Marcel and Bodmer, Thomas and Gagneux, Sebastien and Reither, Klaus and Zimmermann, Michael B. and Risch, Lorenz and Fenner, Lukas. (2018) Anemia in tuberculosis cases and household controls from Tanzania: contribution of disease, coinfections, and the role of hepcidin. PLoS ONE, 13 (4). e0195985. Liu, Qingyun and Ma, Aijing and Wei, Lanhai and Pang, Yu and Wu, Beibei and Luo, Tao and Zhou, Yang and Zheng, Hong-Xiang and Jiang, Qi and Gan, Mingyu and Zuo, Tianyu and Liu, Mei and Yang, Chongguang and Jin, Li and Comas, Iñaki and Gagneux, Sebastien and Zhao, Yanlin and Pepperell, Caitlin S. and Gao, Qian. (2018) China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. Nature ecology & evolution, 2 (12). pp. 1982-1992. Otchere, Isaac Darko and Coscollá, Mireia and Sánchez-Busó, Leonor and Asante-Poku, Adwoa and Brites, Daniela and Loiseau, Chloe and Meehan, Conor and Osei-Wusu, Stephen and Forson, Audrey and Laryea, Clement and Yahayah, Abdallah Iddrisu and Baddoo, Akosua and Ansa, Gloria Akosua and Aboagye, Samuel Yaw and Asare, Prince and Borrell, Sonia and Gehre, Florian and Beckert, Patrick and Kohl, Thomas A. and N'dira, Sanoussi and Beisel, Christian and Antonio, Martin and Niemann, Stefan and de Jong, Bouke C. and Parkhill, Julian and Harris, Simon R. and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2018) Comparative genomics of Mycobacterium africanum lineage 5 and lineage 6 from Ghana suggests distinct ecological niches. Scientific reports, 8. p. 11269. Merker, Matthias and Barbier, Maxime and Cox, Helen and Rasigade, Jean-Philippe and Feuerriegel, Silke and Kohl, Thomas Andreas and Diel, Roland and Borrell, Sonia and Gagneux, Sebastien and Nikolayevskyy, Vladyslav and Andres, Sönke and Nübel, Ulrich and Supply, Philip and Wirth, Thierry and Niemann, Stefan. (2018) Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia. eLife, 7. e38200. Seth-Smith, Helena M. B. and Imkamp, Frank and Tagini, Florian and Cuénod, Aline and Hömke, Rico and Jahn, Kathleen and Tschacher, Anne and Grendelmeier, Peter and Bättig, Veronika and Erb, Stefan and Reinhard, Miriam and Rütimann, Gottfried and Borrell, Sonia and Gagneux, Sebastien and Casanova, Carlo and Droz, Sara and Osthoff, Michael and Tamm, Michael and Nübel, Ulrich and Greub, Gilbert and Keller, Peter M. and Egli, Adrian. (2018) Discovery and characterization of Mycobacterium basiliense sp. nov., a nontuberculous mycobacterium isolated from human lungs. Frontiers in Microbiology, 9. p. 3184. Gagneux, Sebastien. (2018) Ecology and evolution of Mycobacterium tuberculosis. Nature Reviews Microbiology, 16 (4). pp. 202-213. Boillat-Blanco, Noémie and Tumbo, Anneth-Mwasi N. and Perreau, Matthieu and Amelio, Patrizia and Ramaiya, Kaushik L. and Mganga, Maliwaza and Schindler, Christian and Gagneux, Sebastien and Reither, Klaus and Probst-Hensch, Nicole and Pantaleo, Giuseppe and Daubenberger, Claudia and Portevin, Damien. (2018) Hyperglycaemia is inversely correlated with live M. bovis BCG-specific CD4; +; T cell responses in Tanzanian adults with latent or active tuberculosis. Immunity, inflammation and disease, 6 (2). pp. 345-353. Ezewudo, Matthew and Borens, Amanda and Chiner-Oms, Álvaro and Miotto, Paolo and Chindelevitch, Leonid and Starks, Angela M. and Hanna, Debra and Liwski, Richard and Zignol, Matteo and Gilpin, Christopher and Niemann, Stefan and Kohl, Thomas Andreas and Warren, Robin M. and Crook, Derrick and Gagneux, Sebastien and Hoffner, Sven and Rodrigues, Camilla and Comas, Iñaki and Engelthaler, David M. and Alland, David and Rigouts, Leen and Lange, Christoph and Dheda, Keertan and Hasan, Rumina and McNerney, Ruth and Cirillo, Daniela M. and Schito, Marco and Rodwell, Timothy C. and Posey, James. (2018) Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Scientific Reports, 8 (1). p. 15382. Sanoussi, C. N'Dira and de Jong, Bouke C. and Odoun, Mathieu and Arekpa, Karamatou and Ali Ligali, Moulikatou and Bodi, Ousman and Harris, Simon and Ofori-Anyinam, Boatema and Yeboah-Manu, Dorothy and Otchere, Isaac Darko and Asante-Poku, Adwoa and Anagonou, Severin and Gagneux, Sebastien and Coscolla, Mireia and Rigouts, Leen and Affolabi, Dissou. (2018) Low sensitivity of the MPT64 identification test to detect lineage 5 of the Mycobacterium tuberculosis complex. Journal of medical microbiology, 67 (12). pp. 1718-1727. Asare, Prince and Asante-Poku, Adwoa and Prah, Diana Ahu and Borrell, Sonia and Osei-Wusu, Stephen and Otchere, Isaac Darko and Forson, Audrey and Adjapong, Gloria and Koram, Kwadwo Ansah and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2018) Reduced transmission of Mycobacterium africanum compared to Mycobacterium tuberculosis in urban West Africa. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 73. pp. 30-42. Bastos, Helder Novais and Osório, Nuno S. and Gagneux, Sebastien and Comas, Iñaki and Saraiva, Margarida. (2018) The troika host-pathogen-extrinsic factors in Tuberculosis: modulating inflammation and clinical outcomes. Frontiers in Immunology, 8. p. 1948. Carey, Allison F. and Rock, Jeremy M. and Krieger, Inna V. and Chase, Michael R. and Fernandez-Suarez, Marta and Gagneux, Sebastien and Sacchettini, James C. and Ioerger, Thomas R. and Fortune, Sarah M.. (2018) TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathogens, 14 (3). e1006939. Menardo, Fabrizio and Loiseau, Chloé and Brites, Daniela and Coscolla, Mireia and Gygli, Sebastian M. and Rutaihwa, Liliana K. and Trauner, Andrej and Beisel, Christian and Borrell, Sonia and Gagneux, Sebastien. (2018) Treemmer : a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC bioinformatics, 19 (1). p. 164. 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. 2017Miotto, Paolo and Tessema, Belay and Tagliani, Elisa and Chindelevitch, Leonid and Starks, Angela M. and Emerson, Claudia and Hanna, Debra and Kim, Peter S. and Liwski, Richard and Zignol, Matteo and Gilpin, Christopher and Niemann, Stefan and Denkinger, Claudia M. and Fleming, Joy and Warren, Robin M. and Crook, Derrick and Posey, James and Gagneux, Sebastien and Hoffner, Sven and Rodrigues, Camilla and Comas, Iñaki and Engelthaler, David M. and Murray, Megan and Alland, David and Rigouts, Leen and Lange, Christoph and Dheda, Keertan and Hasan, Rumina and Ranganathan, Uma Devi K. and McNerney, Ruth and Ezewudo, Matthew and Cirillo, Daniela M. and Schito, Marco and Köser, Claudio U. and Rodwell, Timothy C.. (2017) A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. The European respiratory journal, 50 (6). p. 1701354. Gygli, Sebastian M. and Borrell, Sonia and Trauner, Andrej and Gagneux, Sebastien. (2017) Antimicrobial resistance in Mycobacterium tuberculosis : mechanistic and evolutionary perspectives. FEMS Microbiology Reviews, 41 (3). pp. 354-373. 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. Yahyaoui-Azami, Hind and Aboukhassib, Hamid and Bouslikhane, Mohammed and Berrada, Jaouad and Rami, Soukaina and Reinhard, Miriam and Gagneux, Sebastien and Feldmann, Julia and Borrell, Sonia and Zinsstag, Jakob. (2017) Molecular characterization of bovine tuberculosis strains in two slaughterhouses in Morocco. BMC Veterinary Research, 13. p. 272. Hiza, Hellen and Doulla, Basra and Sasamalo, Mohamed and Hella, Jerry and Kamwela, Lujeko and Mhimbira, Francis and Reither, Klaus and Gagneux, Sebastien and Jugheli, Levan and Fenner, Lukas. (2017) Preservation of sputum samples with cetylpyridinium chloride (CPC) for tuberculosis cultures and Xpert MTB/RIF in a low-income country. BMC Infectious Diseases, 17. p. 542. Blondiaux, Nicolas and Moune, Martin and Desroses, Matthieu and Frita, Rosangela and Flipo, Marion and Mathys, Vanessa and Soetaert, Karine and Kiass, Mehdi and Delorme, Vincent and Djaout, Kamel and Trebosc, Vincent and Kemmer, Christian and Wintjens, René and Wohlkönig, Alexandre and Antoine, Rudy and Huot, Ludovic and Hot, David and Coscolla, Mireia and Feldmann, Julia and Gagneux, Sebastien and Locht, Camille and Brodin, Priscille and Gitzinger, Marc and Déprez, Benoit and Willand, Nicolas and Baulard, Alain R.. (2017) Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420. Science, 355 (6330). pp. 1206-1211. Koch, Anastasia S. and Brites, Daniela and Stucki, David and Evans, Joanna C. and Seldon, Ronnett and Heekes, Alexa and Mulder, Nicola and Nicol, Mark and Oni, Tolu and Mizrahi, Valerie and Warner, Digby F. and Parkhill, Julian and Gagneux, Sebastien and Martin, Darren P. and Wilkinson, Robert J.. (2017) The influence of HIV on the evolution of Mycobacterium tuberculosis. Molecular biology and evolution, 34 (7). pp. 1654-1668. Brites, Daniela and Gagneux, Sebastien. (2017) The nature and evolution of genomic diversity in the Mycobacterium tuberculosis complex. Advances in experimental medicine and biology, 1019. pp. 1-26. Trauner, Andrej and Liu, Qingyun and Via, Laura E. and Liu, Xin and Ruan, Xianglin and Liang, Lili and Shi, Huimin and Chen, Ying and Wang, Ziling and Liang, Ruixia and Zhang, Wei and Wei, Wang and Gao, Jingcai and Sun, Gang and Brites, Daniela and England, Kathleen and Zhang, Guolong and Gagneux, Sebastien and Barry, Clifton E. and Gao, Qian. (2017) The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy. Genome biology, 18. p. 71. 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. Hella, Jerry and Morrow, Carl and Mhimbira, Francis and Ginsberg, Samuel and Chitnis, Nakul and Gagneux, Sebastien and Mutayoba, Beatrice and Wood, Robin and Fenner, Lukas. (2017) Tuberculosis transmission in public locations in Tanzania: A novel approach to studying airborne disease transmission. Journal of Infection, 75 (3). pp. 191-197. 2016Boillat-Blanco, Noémie and Bovet, Pascal and Ramaiya, Kaushik L. and Mganga, Maliwasa and Minja, Lilian T. and Saleh, Lanja and Imboden, Medea and Schindler, Christian and Gagneux, Sebastien and Daubenberger, Claudia and Reither, Klaus and Probst-Hensch, Nicole. (2016) Association between tuberculosis, diabetes and 25 hydroxyvitamin D in Tanzania: a longitudinal case control study. BMC Infectious Diseases, 16 (1). p. 626. Asante-Poku, Adwoa and Otchere, Isaac Darko and Osei-Wusu, Stephen and Sarpong, Esther and Baddoo, Akosua and Forson, Audrey and Laryea, Clement and Borrell, Sonia and Bonsu, Frank and Hattendorf, Jan and Ahorlu, Collins and Koram, Kwadwo A. and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2016) Molecular epidemiology of Mycobacterium africanum in Ghana. BMC Infectious Diseases, 16. p. 385. Stucki, David and Brites, Daniela and Jeljeli, Leïla and Coscolla, Mireia and Liu, Qingyun and Trauner, Andrej and Fenner, Lukas and Rutaihwa, Liliana and Borrell, Sonia and Luo, Tao and Gao, Qian and Kato-Maeda, Midori and Ballif, Marie and Egger, Matthias and Macedo, Rita and Mardassi, Helmi and Moreno, Milagros and Vilanova, Griselda Tudo and Fyfe, Janet and Globan, Maria and Thomas, Jackson and Jamieson, Frances and Guthrie, Jennifer L. and Asante-Poku, Adwoa and Yeboah-Manu, Dorothy and Wampande, Eddie and Ssengooba, Willy and Joloba, Moses and Boom, W. Henry and Basu, Indira and Bower, James and Saraiva, Margarida and Vasconcellos, Sidra E. G. and Suffys, Philip and Koch, Anastasia and Wilkinson, Robert and Gail-Bekker, Linda and Malla, Bijaya and Ley, Serej D. and Beck, Hans-Peter and de Jong, Bouke C. and Toit, Kadri and Sanchez-Padilla, Elisabeth and Bonnet, Maryline and Gil-Brusola, Ana and Frank, Matthias and Penlap Beng, Veronique N. and Eisenach, Kathleen and Alani, Issam and Ndung'u, Perpetual Wangui and Revathi, Gunturu and Gehre, Florian and Akter, Suriya and Ntoumi, Francine and Stewart-Isherwood, Lynsey and Ntinginya, Nyanda E. and Rachow, Andrea and Hoelscher, Michael and Cirillo, Daniela Maria and Skenders, Girts and Hoffner, Sven and Bakonyte, Daiva and Stakenas, Petras and Diel, Roland and Crudu, Valeriu and Moldovan, Olga and Al-Hajoj, Sahal and Otero, Larissa and Barletta, Francesca and Carter, E. Jane and Diero, Lameck and Supply, Philip and Comas, Iñaki and Niemann, Stefan and Gagneux, Sebastien. (2016) Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature genetics, 48 (12). pp. 1535-1543. Yeboah-Manu, Dorothy and Asare, P. and Asante-Poku, A. and Otchere, I. D. and Osei-Wusu, S. and Danso, E. and Forson, A. and Koram, K. A. and Gagneux, Sebastien. (2016) Spatio-temporal distribution of Mycobacterium tuberculosis complex strains in Ghana. PLoS ONE, 11 (8). e0161892. Stucki, David and Ballif, Marie and Egger, Matthias and Furrer, Hansjakob and Altpeter, Ekkehardt and Battegay, Manuel and Droz, Sara and Bruderer, Thomas and Coscolla, Mireia and Borrell, Sonia and Zürcher, Kathrin and Janssens, Jean-Paul and Calmy, Alexandra and Mazza Stalder, Jesica and Jaton, Katia and Rieder, Hans L. and Pfyffer, Gaby E. and Siegrist, Hans H. and Hoffmann, Matthias and Fehr, Jan and Dolina, Marisa and Frei, Reno and Schrenzel, Jacques and Böttger, Erik C. and Gagneux, Sebastien and Fenner, Lukas. (2016) Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low-incidence country. Journal of clinical microbiology, 54 (7). pp. 1862-1870. Boillat-Blanco, Noémie and Ramaiya, Kaushik L. and Mganga, Maliwasa and Minja, Lilian T. and Bovet, Pascal and Schindler, Christian and Von Eckardstein, Arnold and Gagneux, Sebastien and Daubenberger, Claudia and Reither, Klaus and Probst-Hensch, Nicole. (2016) Transient hyperglycemia in patients with tuberculosis in Tanzania : implications for diabetes screening algorithms. Journal of Infectious Diseases, 213 (7). pp. 1163-1172. Copin, Richard and Wang, Xueying and Louie, Eddie and Escuyer, Vincent and Coscolla, Mireia and Gagneux, Sebastien and Palmer, Guy H. and Ernst, Joel D.. (2016) Within host evolution selects for a dominant genotype of Mycobacterium tuberculosis while T cells increase pathogen genetic diversity. PLoS Pathogens, 12 (12). e1006111. 2015Wampande, Eddie M. and Hatzios, Stavroula K. and Achan, Beatrice and Mupere, Ezekiel and Nsereko, Mary and Mayanja, Harriet K. and Eisenach, Kathleen and Boom, W. Henry and Gagneux, Sebastien and Joloba, Moses L. and Tuberculosis Research Unit, . (2015) A single-nucleotide-polymorphism real-time PCR assay for genotyping of mycobacterium tuberculosis complex in peri-urban Kampala. BMC infectious diseases, Vol. 15 , 396. Bloemberg, Guido V. and Keller, Peter M. and Stucki, David and Stuckia, David and Trauner, Andrej and Borrell, Sonia and Latshang, Tsogyal and Coscolla, Mireia and Rothe, Thomas and Hömke, Rico and Ritter, Claudia and Feldmann, Julia and Schulthess, Bettina and Gagneux, Sebastien and Böttger, Erik C.. (2015) Acquired resistance to bedaquiline and delamanid in therapy for tuberculosis. The New England journal of medicine, 373 (20). pp. 1986-1988. Brites, Daniela and Gagneux, Sebastien. (2015) Co-evolution of Mycobacterium tuberculosis and Homo sapiens. Immunological reviews, Vol. 264, H. 1. pp. 6-24. Rock, Jeremy M. and Lang, Ulla F. and Chase, Michael R. and Ford, Christopher B. and Gerrick, Elias R. and Gawande, Richa and Coscolla, Mireia and Gagneux, Sebastien and Fortune, Sarah M. and Lamers, Meindert H.. (2015) DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader. Nature genetics, Vol. 47, H. 6. pp. 677-681. Wampande, Eddie M. and Mupere, Ezekiel and Jaganath, Devan and Nsereko, Mary and Mayanja, Harriet K. and Eisenach, Kathleen and Boom, W. Henry and Gagneux, Sebastien and Joloba, Moses L. and Tuberculosis Research Unit, . (2015) Distribution and transmission of mycobacterium tuberculosis complex lineages among children in peri-urban Kampala, Uganda. BMC pediatrics, Vol. 15 , 140. Coscolla, Mireia and Barry, Pennan M. and Oeltmann, John E. and Koshinsky, Heather and Shaw, Tambi and Cilnis, Martin and Posey, Jamie and Rose, Jordan and Weber, Terry and Fofanov, Viacheslav Y. and Gagneux, Sebastien and Kato-Maeda, Midori and Metcalfe, John Z.. (2015) Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread. Journal of infectious diseases, Vol. 212, H. 2. pp. 302-310. Berg, Stefan and Schelling, Esther and Hailu, Elena and Firdessa, Rebuma and Gumi, Balako and Erenso, Girume and Gadisa, Endalamaw and Mengistu, Araya and Habtamu, Meseret and Hussein, Jemal and Kiros, Teklu and Bekele, Shiferaw and Mekonnen, Wondale and Derese, Yohannes and Zinsstag, Jakob and Ameni, Gobena and Gagneux, Sebastien and Robertson, Brian D. and Tschopp, Rea and Hewinson, Glyn and Yamuah, Lawrence and Gordon, Stephen V. and Aseffa, Abraham. (2015) 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. BMC infectious diseases, Vol. 15 , 112. Young, David C. and Layre, Emilie and Pan, Shih-Jung and Tapley, Asa and Adamson, John and Seshadri, Chetan and Wu, Zhongtao and Buter, Jeffrey and Minnaard, Adriaan J. and Coscolla, Mireia and Gagneux, Sebastien and Copin, Richard and Ernst, Joel D. and Bishai, William R. and Snider, Barry B. and Moody, D. Branch. (2015) In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection. Chemistry & biology, Vol. 22, H. 4. pp. 516-526. Coscolla, Mireia and Copin, Richard and Sutherland, Jayne and Gehre, Florian and de Jong, Bouke and Owolabi, Olumuiya and Mbayo, Georgetta and Giardina, Federica and Ernst, Joel D. and Gagneux, Sebastien. (2015) M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens. Cell host & microbe, 18 (5). pp. 538-548. 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. Comas, Iñaki and Hailu, Elena and Kiros, Teklu and Bekele, Shiferaw and Mekonnen, Wondale and Gumi, Balako and Tschopp, Rea and Ameni, Gobena and Hewinson, R. Glyn and Robertson, Brian D. and Goig, Galo A. and Stucki, David and Gagneux, Sebastien and Aseffa, Abraham and Young, Douglas and Berg, Stefan. (2015) Population genomics of Mycobacterium tuberculosis in Ethiopia contradicts the virgin soil hypothesis for human tuberculosis in sub-saharan Africa. Current biology, 25 (24). pp. 3260-3206. Luo, Tao and Comas, Iñaki and Luo, Dan and Lu, Bing and Wu, Jie and Wei, Lanhai and Yang, Chongguang and Liu, Qingyun and Gan, Mingyu and Sun, Gang and Shen, Xin and Liu, Feiying and Gagneux, Sebastien and Mei, Jian and Lan, Rushu and Wan, Kanglin and Gao, Qian. (2015) Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proceedings of the National Academy of Sciences of the United States of America, Vol. 112, no. 26. pp. 8136-8141. 2014Coscolla, Mireia and Gagneux, Sebastien. (2014) Consequences of genomic diversity in Mycobacterium tuberculosis. Seminars in immunology, Vol. 26, H. 6. pp. 431-444. Ley, Serej D. and Harino, Paul and Vanuga, Kilagi and Kamus, Ruben and Carter, Robyn and Coulter, Christopher and Pandey, Sushil and Feldmann, Julia and Ballif, Marie and Siba, Peter M. and Phuanukoonnon, Suparat and Gagneux, Sebastien and Beck, Hans-Peter. (2014) Diversity of Mycobacterium tuberculosis and drug resistance in different provinces of Papua New Guinea. BMC microbiology, Vol. 14 , 307. Asante-Poku, Adwoa and Nyaho, Michael Selasi and Borrell, Sonia and Comas, Iñaki and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2014) Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana. PLoS ONE, Vol. 9, H. 3 , e92675. Trauner, Andrej and Borrell, Sonia and Reither, Klaus and Gagneux, Sebastien. (2014) Evolution of drug resistance in tuberculosis : recent progress and implications for diagnosis and therapy. Drugs, Vol. 74, H. 10. pp. 1063-1072. Copin, Richard and Coscollá, Mireia and Efstathiadis, Efstratios and Gagneux, Sebastien and Ernst, Joel D.. (2014) Impact of in vitro evolution on antigenic diversity of Mycobacterium bovis bacillus Calmette-Guerin (BCG). Vaccine : the official journal of the International Society for Vaccines, 32 (45). pp. 5998-6004. 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. Portevin, Damien and Sukumar, Sudarkodi and Coscolla, Mireia and Shui, Guanghou and Li, Bowen and Guan, Xue Li and Bendt, Anne K. and Young, Douglas and Gagneux, Sebastien and Wenk, Markus R.. (2014) Lipidomics and genomics of Mycobacterium tuberculosis reveal lineage-specific trends in mycolic acid biosynthesis. MicrobiologyOpen, Vol. 3, H. 6. pp. 823-835. Coll, Francesc and Preston, Mark and Guerra-Assunção, José Afonso and Hill-Cawthorn, Grant and Harris, David and Perdigão, João and Viveiros, Miguel and Portugal, Isabel and Drobniewski, Francis and Gagneux, Sebastien and Glynn, Judith R. and Pain, Arnab and Parkhill, Julian and McNerney, Ruth and Martin, Nigel and Clark, Taane G.. (2014) PolyTB : a genomic variation map for Mycobacterium tuberculosis. Tuberculosis, Vol. 94, H. 3. pp. 346-354. Copin, Richard and Coscollá, Mireia and Seiffert, Salome N. and Bothamley, Graham and Sutherland, Jayne and Mbayo, Georgetta and Gagneux, Sebastien and Ernst, Joel D.. (2014) Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. mBio, Vol. 5, H. 1 , e00960-13. 2013Via, Laura E. and Weiner, Danielle M. and Schimel, Daniel and Lin, Philana Ling and Dayao, Emmanuel and Tankersley, Sarah L. and Cai, Ying and Coleman, M. Teresa and Tomko, Jaime and Paripati, Praveen and Orandle, Marlene and Kastenmayer, Robin J. and Tartakovsky, Michael and Rosenthal, Alexander and Portevin, Damien and Eum, Seok Yong and Lahouar, Saher and Gagneux, Sebastien and Young, Douglas B. and Flynn, Joanne L. and Barry, Clifton E.. (2013) Differential virulence and disease progression following Mycobacterium tuberculosis complex infection of the common marmoset (Callithrix jacchus). Infection and immunity, Vol. 81, H. 8. pp. 2909-2919. Borrell, Sònia and Teo, Youjin and Giardina, Federica and Streicher, Elizabeth M. and Klopper, Marisa and Feldmann, Julia and Müller, Borna and Victor, Tommie C. and Gagneux, Sebastien. (2013) Epistasis between antibiotic resistance mutations drives the evolution of extensively drug-resistant tuberculosis. Evolution, medicine, and public health, H. 1. pp. 65-74. Osório, Nuno S. and Rodrigues, Fernando and Gagneux, Sebastien and Pedrosa, Jorge and Pinto-Carbó, Marta and Castro, António G. and Young, Douglas and Comas, Iñaki and Saraiva, Margarida. (2013) Evidence for diversifying selection in a set of Mycobacterium tuberculosis genes in response to antibiotic- and nonantibiotic-related pressure. Molecular biology and evolution, Vol. 30, no. 6. pp. 1326-1336. Gagneux, Sebastien. (2013) Genetic diversity in Mycobacterium tuberculosis. Current topics in microbiology and immunology, Vol. 374. pp. 1-25. Farhat, Maha R. and Shapiro, B. Jesse and Kieser, Karen J. and Sultana, Razvan and Jacobson, Karen R. and Victor, Thomas C. and Warren, Robin M. and Streicher, Elizabeth M. and Calver, Alistair and Sloutsky, Alex and Kaur, Devinder and Posey, Jamie E. and Plikaytis, Bonnie and Oggioni, Marco R. and Gardy, Jennifer L. and Johnston, James C. and Rodrigues, Mabel and Tang, Patrick K. C. and Kato-Maeda, Midori and Borowsky, Mark L. and Muddukrishna, Bhavana and Kreiswirth, Barry N. and Kurepina, Natalia and Galagan, James and Gagneux, Sebastien and Birren, Bruce and Rubin, Eric J. and Lander, Eric S. and Sabeti, Pardis C. and Murray, Megan. (2013) Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nature genetics, Vol. 45, H. 10. pp. 1183-1189. Fenner, Lukas and Egger, Matthias and Bodmer, Thomas and Furrer, Hansjakob and Ballif, Marie and Battegay, Manuel and Helbling, Peter and Fehr, Jan and Gsponer, Thomas and Rieder, Hans L. and Zwahlen, Marcel and Hoffmann, Matthias and Bernasconi, Enos and Cavassini, Matthias and Calmy, Alexandra and Dolina, Marisa and Frei, Reno and Janssens, Jean-Paul and Borrell, Sonia and Stucki, David and Schrenzel, Jacques and Böttger, Erik C. and Gagneux, Sebastien and Swiss HIV Cohort, and Molecular Epidemiology of Tuberculosis Study Groups, . (2013) HIV infection disrupts the sympatric host-pathogen relationship in human tuberculosis. PLoS genetics, Vol. 9, H. 3 , e1003318. Rose, Graham and Cortes, Teresa and Comas, Iñaki and Coscolla, Mireia and Gagneux, Sebastien and Young, Douglas B.. (2013) Mapping of genotype-phenotype diversity among clinical isolates of Mycobacterium tuberculosis by sequence-based transcriptional profiling. Genome biology and evolution, Vol. 5, H. 10. pp. 1849-1862. Ford, Christopher B. and Shah, Rupal R. and Maeda, Midori Kato and Gagneux, Sebastien and Murray, Megan B. and Cohen, Ted and Johnston, James C. and Gardy, Jennifer and Lipsitch, Marc and Fortune, Sarah M.. (2013) Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nature genetics, Vol. 45, H. 7. pp. 784-790. Coscolla, Mireia and Lewin, Astrid and Metzger, Sonja and Maetz-Rennsing, Kerstin and Calvignac-Spencer, Sébastien and Nitsche, Andreas and Dabrowski, Pjotr Wojtek and Radonic, Aleksandar and Niemann, Stefan and Parkhill, Julian and Couacy-Hymann, Emmanuel and Feldman, Julia and Comas, Iñaki and Boesch, Christophe and Gagneux, Sebastien and Leendertz, Fabian H.. (2013) Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerging infectious diseases, Vol. 19, H. 6. pp. 969-976. Comas, Iñaki and Coscolla, Mireia and Luo, Tao and Borrell, Sonia and Holt, Kathryn E. and Kato-Maeda, Midori and Parkhill, Julian and Malla, Bijaya and Berg, Stefan and Thwaites, Guy and Yeboah-Manu, Dorothy and Bothamley, Graham and Mei, Jian and Wei, Lanhai and Bentley, Stephen and Harris, Simon R. and Niemann, Stefan and Diel, Roland and Aseffa, Abraham and Gao, Qian and Young, Douglas and Gagneux, Sebastien. (2013) Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature genetics, Vol. 45, H. 10. pp. 1176-1182. Müller, Borna and Chihota, Violet N. and Pillay, Manormoney and Klopper, Marisa and Streicher, Elizabeth M. and Coetzee, Gerrit and Trollip, Andre and Hayes, Cindy and Bosman, Marlein E. and Gey van Pittius, Nicolaas C. and Victor, Thomas C. and Gagneux, Sebastien and van Helden, Paul D. and Warren, Robin M.. (2013) Programmatically selected multidrug-resistant strains drive the emergence of extensively drug-resistant tuberculosis in South Africa. PLoS ONE, Vol. 8, H. 8 , e70919. 2012Luo, Tao and Yang, Chongguang and Gagneux, Sebastien and Gicquel, Brigitte and Jian, Mei and Gao, Qian. (2012) Combination of single nucleotide polymorphism and variable-number tandem repeats for genotyping a homogenous population of Mycobacterium tuberculosis Beijing strains in China. Journal of clinical microbiology, Vol. 50, H. 3. pp. 633-639. Brites, Daniela and Gagneux, Sebastien. (2012) Old and new selective pressures on Mycobacterium tuberculosis. Infection, genetics and evolution, Vol. 12, H. 4. pp. 678-685. Comas, Iñaki and Borrell, Sonia and Roetzer, Andreas and Rose, Graham and Malla, Bijaya and Kato-Maeda, Midori and Galagan, James and Niemann, Stefan and Gagneux, Sebastien. (2012) Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nature genetics, Vol. 44, H. 1. pp. 106-110. 2011Fenner, Lukas and Malla, Bijaya and Ninet, Béatrice and Dubuis, Olivier and Stucki, David and Borrell, Sonia and Huna, Thembela and Bodmer, Thomas and Egger, Matthias and Gagneux, Sebastien. (2011) "Pseudo-Beijing" : evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. PLoS ONE, Vol. 6, H. 9 , e24737. Sherman, David R. and Gagneux, Sebastien. (2011) Estimating the mutation rate of Mycobacterium tuberculosis during infection. Nature genetics, Vol. 43, H. 5. pp. 400-401. 2007Leimkugel, Julia and Forgor, Abudulai Adams and Dangy, Jean-Pierre and Pflüger, Valentin and Gagneux, Sebastien and Hodgson, Abraham and Pluschke, Gerd. (2007) Genetic diversification of Neisseria meningitidis during waves of colonization and disease in the meningitis belt of sub-Saharan Africa. Vaccine : the official journal of the International Society for Vaccines, 25 (1). A18-A23. |
