Items where Division is "09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Medical Parasitology and Infection Biology (MPI) > Tuberculosis Ecology and Evolution Unit (Gagneux)"

2017

Andre, E. and Goeminne, L. and Cabibbe, A. and Beckert, P. and Kabamba Mukadi, B. and Mathys, V. and Gagneux, S. and Niemann, S. and Van Ingen, J. and Cambau, E.. (2017) Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria. Clinical microbiology and infection, 23 (3). pp. 167-172.

Armitage, Sophie A. O. and Kurtz, Joachim and Brites, Daniela and Dong, Yuemei and Du Pasquier, Louis and Wang, Han-Ching. (2017) Dscam1 in pancrustacean immunity: current status and a look to the future. Frontiers in immunology, 8. p. 662.

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.

Borrell, Sonia and Trauner, Andrej. (2017) Strain diversity and the evolution of antibiotic resistance. Advances in experimental medicine and biology, 1019. pp. 263-279.

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.

Coscolla, Mireia. (2017) Biological and epidemiological consequences of MTBC diversity. Advances in experimental medicine and biology, 1019. pp. 95-116.

Fenner, Lukas and Atkinson, Andrew and Boulle, Andrew and Fox, Matthew P. and Prozesky, Hans and Zürcher, Kathrin and Ballif, Marie and Furrer, Hansjakob and Zwahlen, Marcel and Davies, Mary-Ann and Egger, Matthias and International Epidemiology Database to Evaluate Aids in Southern, . (2017) HIV viral load as an independent risk factor for tuberculosis in South Africa: collaborative analysis of cohort studies. Journal of the International AIDS Society, 20. p. 21327.

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.

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.

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.

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.

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.

Miotto, 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.

Ofori-Anyinam, B. and Dolganov, G. and Van, T. and Davis, J. L. and Walter, N. D. and Garcia, B. J. and Voskuil, M. and Fissette, K. and Diels, M. and Driesen, M. and Meehan, C. J. and Yeboah-Manu, D. and Coscolla, M. and Gagneuyx, S. and Antonio, M. and Schoolnik, G. K. and Gehre, F. and de Jong, B. C.. (2017) Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum. Tuberculosis, 104. pp. 58-64.

Reither, Klaus. Improving the diagnosis of tuberculosis - clinical evaluation of four new diagnostics. 2017, Doctoral Thesis, University of Basel, Faculty of Science.

Said, Khadija and Hella, Jerry and Mhalu, Grace and Chiryankubi, Mary and Masika, Edward and Maroa, Thomas and Mhimbira, Francis and Kapalata, Neema and Fenner, Lukas. (2017) Diagnostic delay and associated factors among patients with pulmonary tuberculosis in Dar es Salaam, Tanzania. Infectious Diseases of Poverty, 6. p. 64.

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.

4 January 2016

Swiss Institute of Bioinformatics Members, SIB. (2016) The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44 (D1). D27-D37.

2016

Boillat-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.

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.

Charles, M. Katherine and Lindegren, Mary Lou and Wester, C. William and Blevins, Meridith and Sterling, Timothy R. and Dung, Nguyen Thi and Dusingize, Jean Claude and Avit-Edi, Divine and Durier, Nicolas and Castelnuovo, Barbara and Nakigozi, Gertrude and Cortes, Claudia P. and Ballif, Marie and Fenner, Lukas. (2016) Implementation of tuberculosis intensive case finding, isoniazid preventive therapy, and infection control ("Three I's") and HIV-tuberculosis service integration in lower income countries. PLoS one, 11 (4). e0153243.

Demers, Anne-Marie and Venter, Amour and Friedrich, Sven O. and Rojas-Ponce, Gabriel and Mapamba, Daniel and Jugheli, Levan and Sasamalo, Mohammed and Almeida, Deepak and Dorasamy, Afton and Jentsch, Ute and Gibson, Mara and Everitt, Daniel and Eisenach, Kathleen D. and Diacon, Andreas H.. (2016) Direct susceptibility testing of Mycobacterium tuberculosis for pyrazinamide by use of the bactec MGIT 960 system. Journal of clinical microbiology, 54 (5). pp. 1276-1281.

Domínguez, J. and Boettger, E. C. and Cirillo, D. and Cobelens, F. and Eisenach, K. D. and Gagneux, S. and Hillemann, D. and Horsburgh, R. and Molina-Moya, B. and Niemann, S. and Tortoli, E. and Whitelaw, A. and Lange, C. and Tbnet, and Resist-TB networks, . (2016) Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis : a TBNET/RESIST-TB consensus statement. The international journal of tuberculosis and lung disease, 20 (1). pp. 24-42.

Mhimbira, Francis and Hella, Jerry and Maroa, Thomas and Kisandu, Shadrack and Chiryamkubi, Magreth and Said, Khadija and Mhalu, Grace and Mkopi, Abdallah and Mutayoba, Beatrice and Reither, Klaus and Gagneux, Sébastien and Fenner, Lukas. (2016) Home-based and facility-based directly observed therapy of tuberculosis treatment under programmatic conditions in urban Tanzania. PLoS one, 11 (8). e0161171.

Otchere, I. D. and Asante-Poku, A. and Osei-Wusu, S. and Baddoo, A. and Sarpong, E. and Ganiyu, A. H. and Aboagye, S. Y. and Forson, A. and Bonsu, F. and Yahayah, A. I. and Koram, K. and Gagneux, S. and Yeboah-Manu, D.. (2016) Detection and characterization of drug-resistant conferring genes in Mycobacterium tuberculosis complex strains : a prospective study in two distant regions of Ghana. Tuberculosis, 99. pp. 147-154.

Petrone, L. and Cannas, A. and Vanini, V. and Cuzzi, G. and Aloi, F. and Nsubuga, M. and Sserunkuma, J. and Nazziwa, R. A. and Jugheli, L. and Lukindo, T. and Giradi, E. and Antinori, A. and Pucci, L. and Reither, K. and Goletti, D.. (2016) Blood and urine inducible protein 10 as potential markers of disease activity. The international journal of tuberculosis and lung disease, 20 (11). pp. 1554-1561.

Pohl, Christian and Rutaihwa, Liliana K. and Haraka, Frederick and Nsubuga, Martin and Aloi, Francesco and Ntinginya, Nyanda E. and Mapamba, Daniel and Heinrich, Norbert and Hoelscher, Michael and Marais, Ben J. and Jugheli, Levan and Reither, Klaus. (2016) Limited value of whole blood Xpert(®) MTB/RIF for diagnosing tuberculosis in children. The journal of infection, 73 (4). pp. 326-335.

Sikalengo, George and Ramirez, Adria and Faini, Diana and Mwamelo, Kim and Battegay, Manuel and Jugheli, Levan and Hatz, Christoph and Reither, Klaus and Letang, Emilio. (2016) Tuberculous spondylitis diagnosed through Xpert MTB/RIF assay in urine: a case report. BMC Infectious Diseases, 16 (1). p. 514.

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.

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.

Zumla, Alimuddin and Rao, Martin and Wallis, Robert S. and Kaufmann, Stefan H. E. and Rustomjee, Roxana and Mwaba, Peter and Vilaplana, Cris and Yeboah-Manu, Dorothy and Chakaya, Jeremiah and Ippolito, Giuseppe and Azhar, Esam and Hoelscher, Michael and Maeurer, Markus and Host-Directed Therapies Network consortium, . (2016) Host-directed therapies for infectious diseases : current status, recent progress, and future prospects. The Lancet infectious diseases, 16 (4). e47-e63.

Zürcher, Kathrin and Ballif, Marie and Zwahlen, Marcel and Rieder, Hans L. and Egger, Matthias and Fenner, Lukas. (2016) Tuberculosis mortality and living conditions in Bern, Switzerland, 1856-1950. PLoS one, 11 (2). e0149195.

2015

Asante-Poku, A. and Otchere, I. D. and Danso, E. and Mensah, D. D. and Bonsu, F. and Gagneux, S. and Yeboah-Manu, D.. (2015) Evaluation of geno type(®) MTBDRplus for the rapid detection of drug-resistant tuberculosis in Ghana. The international journal of tuberculosis and lung disease, Vol. 19, H. 8. pp. 954-959.

Asante-Poku, Adwoa. Genotypic and epidemiological characterization of Mycobacterium tuberculosis complex in Ghana. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

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.

Ballif, Marie and Renner, Lorna and Claude Dusingize, Jean and Leroy, Valeriane and Ayaya, Samuel and Wools-Kaloustian, Kara and Cortes, Claudia P. and McGowan, Catherine C. and Graber, Claire and Mandalakas, Anna M. and Mofenson, Lynne M. and Egger, Matthias and Kumara Wati, Ketut Dewi and Nallusamy, Revathy and Reubenson, Gary and Davies, Mary-Ann and Fenner, Lukas and International Epidemiologic Databases to Evaluate Aids, and International Epidemiologic Databases to Evaluate Aids IeDEA, . (2015) Tuberculosis in pediatric antiretroviral therapy programs in low- and middle-income countries : diagnosis and screening practices. Journal of the Pediatric Infectious Diseases Society, Vol. 4, H. 1. pp. 30-38.

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 Du Pasquier, Louis. (2015) Somatic and germline diversification of a putative immunoreceptor within one Phylum : dscam in arthropods. Results and problems in cell differentiation, 57. pp. 131-158.

Brites, Daniela and Gagneux, Sebastien. (2015) Co-evolution of Mycobacterium tuberculosis and Homo sapiens. Immunological reviews, Vol. 264, H. 1. pp. 6-24.

Cabibbe, Andrea M. and Miotto, Paolo and Moure, Raquel and Alcaide, Fernando and Feuerriegel, Silke and Pozzi, Gianni and Nikolayevskyy, Vladislav and Drobniewski, Francis and Niemann, Stefan and Reither, Klaus and Cirillo, Daniela M.. (2015) Lab-on-chip-based platform for fast molecular diagnosis of multidrug-resistant tuberculosis. Journal of clinical microbiology, 53 (12). pp. 3876-3880.

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.

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. The Journal of Infectious Diseases, Vol. 212, H. 2. pp. 302-310.

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.

Dawson, Rodney and Diacon, Andreas H. and Everitt, Daniel and van Niekerk, Christo and Donald, Peter R. and Burger, Divan A. and Schall, Robert and Spigelman, Melvin and Conradie, Almari and Eisenach, Kathleen and Venter, Amour and Ive, Prudence and Page-Shipp, Liesl and Variava, Ebrahim and Reither, Klaus and Ntinginya, Nyanda E. and Pym, Alexander and von Groote-Bidlingmaier, Florian and Mendel, Carl M.. (2015) Efficiency and safety of the combination of moxifloxacin, pretomanid (PA-824), and pyrazinamide during the first 8 weeks of antituberculosis treatment : a phase 2b, open-label, partly randomised trial in patients with drug-susceptible or drug-resistant pulmonary tuberculosis. Lancet, Vol. 385, no. 9979. pp. 1738-1747.

Elkon, Ran and Milon, Beatrice and Morrison, Laura and Shah, Manan and Vijayakumar, Sarath and Racherla, Manoj and Leitch, Carmen C. and Silipino, Lorna and Hadi, Shadan and Weiss-Gayet, Michèle and Barras, Emmanuèle and Schmid, Christoph D. and Ait-Lounis, Aouatef and Barnes, Ashley and Song, Yang and Eisenman, David J. and Eliyahu, Efrat and Frolenkov, Gregory I. and Strome, Scott E. and Durand, Bénédicte and Zaghloul, Norann A. and Jones, Sherri M. and Reith, Walter and Hertzano, Ronna. (2015) RFX transcription factors are essential for hearing in mice. Nature communications, 6. p. 8549.

Heinrich, Norbert and Dawson, Rodney and du Bois, Jeannine and Narunsky, Kim and Horwith, Gary and Phipps, Andrew J. and Nacy, Carol A. and Aarnoutse, Rob E. and Boeree, Martin J. and Gillespie, Stephen H. and Venter, Amour and Henne, Sonja and Rachow, Andrea and Phillips, Patrick P. J. and Hoelscher, Michael and Diacon, Andreas H. and Pan African Consortium for the Evaluation of Antituberculosis An, and Pan African Consortium for the Evaluation of Antituberculosis An, . (2015) Early phase evaluation of SQ109 alone and in combination with rifampicin in pulmonary TB patients. The journal of antimicrobial chemotherapy, 70 (5). pp. 1558-1566.

Kroidl, Inge and Clowes, Petra and Reither, Klaus and Mtafya, Bariki and Rojas-Ponce, Gabriel and Ntinginya, Elias N. and Kalomo, Mariam and Minja, Lilian T. and Kowuor, Dickens and Saathoff, Elmar and Kroidl, Arne and Heinrich, Norbert and Maboko, Leonard and Bates, Matthew and O'Grady, Justin and Zumla, Alimuddin and Hoelscher, Michael and Rachow, Andrea. (2015) Performance of urine lipoarabinomannan assays for paediatric tuberculosis in Tanzania. The European respiratory journal, 46 (3). pp. 761-770.

Luisoni, Stefania and Suomalainen, Maarit and Boucke, Karin and Tanner, Lukas B. and Wenk, Markus R. and Guan, Xue Li and Grzybek, Michał and Coskun, Ünal and Greber, Urs F.. (2015) Co-option of membrane wounding enables virus penetration into cells. Cell host & microbe, Vol. 18, H. 1. pp. 75-85.

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.

Melendez, Jaime and van Ginneken, Bram and Maduskar, Pragnya and Philipsen, Rick H. H. M. and Reither, Klaus and Breuninger, Marianne and Adetifa, Ifedayo M. O. and Maane, Rahmatulai and Ayles, Helen and Sanchez, Clara I.. (2015) A novel multiple-instance learning-based approach to computer-aided detection of tuberculosis on chest x-rays. IEEE transactions on medical imaging, Vol. 34, H. 1. pp. 179-192.

Merker, Matthias and Blin, Camille and Mona, Stefano and Duforet-Frebourg, Nicolas and Lecher, Sophie and Willery, Eve and Blum, Michael G. B. and Rüsch-Gerdes, Sabine and Mokrousov, Igor and Aleksic, Eman and Allix-Béguec, Caroline and Antierens, Annick and Augustynowicz-Kopeć, Ewa and Ballif, Marie and Barletta, Francesca and Beck, Hans Peter and Barry, Clifton E. and Bonnet, Maryline and Borroni, Emanuele and Campos-Herrero, Isolina and Cirillo, Daniela and Cox, Helen and Crowe, Suzanne and Crudu, Valeriu and Diel, Roland and Drobniewski, Francis and Fauville-Dufaux, Maryse and Gagneux, Sébastien and Ghebremichael, Solomon and Hanekom, Madeleine and Hoffner, Sven and Jiao, Wei-Wei and Kalon, Stobdan and Kohl, Thomas A. and Kontsevaya, Irina and Lillebæk, Troels and Maeda, Shinji and Nikolayevskyy, Vladyslav and Rasmussen, Michael and Rastogi, Nalin and Samper, Sofia and Sanchez-Padilla, Elisabeth and Savic, Branislava and Shamputa, Isdore Chola and Shen, Adong and Sng, Li-Hwei and Stakenas, Petras and Toit, Kadri and Varaine, Francis and Vukovic, Dragana and Wahl, Céline and Warren, Robin and Supply, Philip and Niemann, Stefan and Wirth, Thierry. (2015) Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nature genetics, Vol. 47, H. 3. pp. 242-249.

Mhalu, Grace and Hella, Jerry and Doulla, Basra and Mhimbira, Francis and Mtutu, Hawa and Hiza, Helen and Sasamalo, Mohamed and Rutaihwa, Liliana and Rieder, Hans L. and Seimon, Tamsyn and Mutayoba, Beatrice and Weiss, Mitchell G. and Fenner, Lukas. (2015) Do instructional videos on sputum submission result in increased tuberculosis case detection? : a randomized controlled trial. PLoS one, Vol. 10, H. 9 , e0138413.

Molefi, Mooketsi and Chofle, Awilly A. and Molloy, Síle F. and Kalluvya, Samuel and Changalucha, John M. and Cainelli, Francesca and Leeme, Tshepo and Lekwape, Nametso and Goldberg, Drew W. and Haverkamp, Miriam and Bisson, Gregory P. and Perfect, John R. and Letang, Emili and Fenner, Lukas and Meintjes, Graeme and Burton, Rosie and Makadzange, Tariro and Ndhlovu, Chiratidzo E. and Hope, William and Harrison, Thomas S. and Jarvis, Joseph N.. (2015) AMBITION-cm : intermittent high dose AmBisome on a high dose fluconazole backbone for cryptococcal meningitis induction therapy in sub-Saharan Africa : study protocol for a randomized controlled trial. Trials, Vol. 16. p. 276.

Nicol, Mark Patrick and Gnanashanmugam, Devasena and Browning, Renee and Click, Eleanor S. and Cuevas, Luis E. and Detjen, Anne and Graham, Steve M. and Levin, Michael and Makhene, Mamodikoe and Nahid, Payam and Perez-Velez, Carlos M. and Reither, Klaus and Song, Rinn and Spiegel, Hans M. L. and Worrell, Carol and Zar, Heather J. and Walzl, Gerhard. (2015) A blueprint to address research gaps in the development of biomarkers for pediatric tuberculosis. Clinical Infectious Diseases, Vol. 61, H. Suppl. 3 , S164-S172.

Olaru, I. D. and Rachow, A. and Lange, C. and Ntinginya, N. E. and Reither, K. and Hoelscher, M. and Vollrath, O. and Niemann, S.. (2015) Ascertaining in vivo virulence of Mycobacterium tuberculosis lineages in patients in Mbeya, Tanzania. The international journal of tuberculosis and lung disease, Vol. 19, H. 1. pp. 70-73.

Petrone, Linda and Cannas, Angela and Aloi, Francesco and Nsubuga, Martin and Sserumkuma, Joseph and Nazziwa, Ritah Angella and Jugheli, Levan and Lukindo, Tedson and Girardi, Enrico and Reither, Klaus and Goletti, Delia. (2015) Blood or urine IP-10 cannot discriminate between active tuberculosis and respiratory diseases different from tuberculosis in children. BioMed research international, 2015. ID589471.

Reither, Klaus and Jugheli, Levan and Glass, Tracy R. and Sasamalo, Mohamed and Mhimbira, Francis A. and Weetjens, Bart J. and Cox, Christophe and Edwards, Timothy L. and Mulder, Christiaan and Beyene, Negussie W. and Mahoney, Amanda. (2015) Evaluation of giant african pouched rats for detection of pulmonary tuberculosis in patients from a high-endemic setting. PLoS one, Vol. 10, H. 10 , e0135877.

Reither, Klaus and Manyama, Christina and Clowes, Petra and Rachow, Andrea and Mapamba, Daniel and Steiner, Andreas and Ross, Amanda and Mfinanga, Elirehema and Sasamalo, Mohamed and Nsubuga, Martin and Aloi, Francesco and Cirillo, Daniela and Jugheli, Levan and Lwilla, Fred. (2015) Xpert MTB/RIF assay for diagnosis of pulmonary tuberculosis in children : a prospective, multi-centre evaluation. The journal of infection, Vol. 70, H. 4. pp. 392-399.

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.

Steiner, A. and Mangu, C. and van den Hombergh, J. and van Deutekom, H. and van Ginneken, B. and Clowes, P. and Mhimbira, F. and Mfinanga, S. and Rachow, A. and Reither, K. and Hoelscher, M.. (2015) Screening for pulmonary tuberculosis in a Tanzanian prison and computer-aided interpretation of chest X-rays. Public health action, 5 (4). pp. 249-254.

Stucki, David. Transmission and evolution of "Mycobacterium tuberculosis" studied by whole genome sequencing and single nucleotide polymorphism-typing. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

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. The Journal of Infectious Diseases, Vol. 211, H. 8. pp. 1306-1316.

Sánchez-Busó, Leonor and Coscollà, Mireia and Palero, Ferran and Camaró, María Luisa and Gimeno, Ana and Moreno, Pilar and Escribano, Isabel and López Perezagua, María Mar and Colomina, Javier and Vanaclocha, Herme and González-Candelas, Fernando. (2015) Geographical and temporal structures of Legionella pneumophila sequence types in comunitat Valenciana (Spain), 1998 to 2013. Applied and Environmental Microbiology, 81 (20). pp. 7106-7113.

Wampande, 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.

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.

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.

Zumla, A. and Chakaya, J. and Hoelscher, M. and Ntoumi, F. and Rustomjee, R. and Vilaplana, C. and Yeboah-Manu, D. and Rasolof, V. and Munderi, P. and Singh, N. and Aklillu, E. and Padayatchi, N. and Macete, E. and Kapata, N. and Mulenga, M. and Kibiki, G. and Mfinanga, S. and Nyirenda, T. and Maboko, L. and Garcia-Basteiro, A. and Rakotosamimanana, N. and Bates, M. and Mwaba, P. and Reither, K. and Gagneux, S. and Edwards, S. and Mfinanga, E. and Abdulla, S. and Cardona, P. J. and Russell, J. B. and Gant, V. and Noursadeghi, M. and Elkington, P. and Bonnet, M. and Menendez, C. and Dieye, T. N. and Diarra, B. and Maiga, A. and Aseffa, A. and Parida, S. and Wejse, C. and Petersen, E. and Kaleebu, P. and Oliver, M. and Craig, G. and Corrah, T. and Tientcheu, L. and Antonio, M. and Rao, M. and McHugh, T. D. and Sheikh, A. and Ippolito, G. and Ramjee, G. and Kaufmann, S. H. and Churchyard, G. and Steyn, A. and Grobusch, M. and Sanne, I. and Martinson, N. and Madansein, R. and Wilkinson, R. J. and Mayosi, B. and Schito, M. and Wallis, R. S. and Maeurer, M.. (2015) Towards host-directed therapies for tuberculosis. Nature reviews. Drug discovery, 14 (8). pp. 511-512.

Zumla, Alimuddin and Maeurer, Markus and Host-Directed Therapies Network Consortium, . (2015) Host-directed therapies for tackling multi-drug resistant tuberculosis : learning from the pasteur-bechamp debates. Clinical infectious diseases, 61 (9). pp. 1432-1438.

2014

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.

Ballif, M. and Nhandu, V. and Wood, R. and Dusingize, J. C. and Carter, E. J. and Cortes, C. P. and McGowan, C. C. and Diero, L. and Graber, C. and Renner, L. and Hawerlander, D. and Kiertiburanakul, S. and Du, Q. T. and Sterling, T. R. and Egger, M. and Fenner, L. and International epidemiological Databases to Evaluate Aids, . (2014) Detection and management of drug-resistant tuberculosis in HIV-infected patients in lower-income countries. The international journal of tuberculosis and lung disease, Vol. 18, H. 11. pp. 1327-1336.

Bos, K. I. and Harkins, K. M. and Herbig, A. and Coscolla, M. and Weber, N. and Comas, I. and Forrest, S. A. and Bryant, J. M. and Harris, S. R. and Schuenemann, V. J. and Campbell, T. J. and Majander, K. and Wilbur, A. K. and Guichon, R. A. and Wolfe Steadman, D. L. and Cook, D. C. and Niemann, S. and Behr, M. A. and Zumarraga, M. and Bastida, R. and Huson, D. and Nieselt, K. and Young, D. and Parkhill, J. and Buikstra, J. E. and Gagneux, S. and Stone, A. C. and Krause, J.. (2014) Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature, Vol. 514, H. 7523. pp. 494-497.

Chipman, Ariel D. and Ferrier, David E. K. and Brena, Carlo and Qu, Jiaxin and Hughes, Daniel S. T. and Schröder, Reinhard and Torres-Oliva, Montserrat and Znassi, Nadia and Jiang, Huaiyang and Almeida, Francisca C. and Alonso, Claudio R. and Apostolou, Zivkos and Aqrawi, Peshtewani and Arthur, Wallace and Barna, Jennifer C. J. and Blankenburg, Kerstin P. and Brites, Daniela and Capella-Gutiérrez, Salvador and Coyle, Marcus and Dearden, Peter K. and Du Pasquier, Louis and Duncan, Elizabeth J. and Ebert, Dieter and Eibner, Cornelius and Erikson, Galina and Evans, Peter D. and Extavour, Cassandra G. and Francisco, Liezl and Gabaldón, Toni and Gillis, William J. and Goodwin-Horn, Elizabeth A. and Green, Jack E. and Griffiths-Jones, Sam and Grimmelikhuijzen, Cornelis J. P. and Gubbala, Sai and Guigó, Roderic and Han, Yi and Hauser, Frank and Havlak, Paul and Hayden, Luke and Helbing, Sophie and Holder, Michael and Hui, Jerome H. L. and Hunn, Julia P. and Hunnekuhl, Vera S. and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N. and Jiggins, Francis M. and Jones, Tamsin E. and Kaiser, Tobias S. and Kalra, Divya and Kenny, Nathan J. and Korchina, Viktoriya and Kovar, Christie L. and Kraus, F. Bernhard and Lapraz, François and Lee, Sandra L. and Lv, Jie and Mandapat, Christigale and Manning, Gerard and Mariotti, Marco and Mata, Robert and Mathew, Tittu and Neumann, Tobias and Newsham, Irene and Ngo, Dinh N. and Ninova, Maria and Okwuonu, Geoffrey and Ongeri, Fiona and Palmer, William J. and Patil, Shobha and Patraquim, Pedro and Pham, Christopher and Pu, Ling-Ling and Putman, Nicholas H. and Rabouille, Catherine and Ramos, Olivia Mendivil and Rhodes, Adelaide C. and Robertson, Helen E. and Robertson, Hugh M. and Ronshaugen, Matthew and Rozas, Julio and Saada, Nehad and Sánchez-Gracia, Alejandro and Scherer, Steven E. and Schurko, Andrew M. and Siggens, Kenneth W. and Simmons, DeNard and Stief, Anna and Stolle, Eckart and Telford, Maximilian J. and Tessmar-Raible, Kristin and Thornton, Rebecca and van der Zee, Maurijn and von Haeseler, Arndt and Williams, James M. and Willis, Judith H. and Wu, Yuanqing and Zou, Xiaoyan and Lawson, Daniel and Muzny, Donna M. and Worley, Kim C. and Gibbs, Richard A. and Akam, Michael and Richards, Stephen. (2014) The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede strigamia maritima. PLoS biology, 12 (11). e1002005.

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.

Coscolla, Mireia and Gagneux, Sebastien. (2014) Consequences of genomic diversity in Mycobacterium tuberculosis. Seminars in immunology, Vol. 26, H. 6. pp. 431-444.

Coscollá, Mireia and Fernández, Carmen and Colomina, Javier and Sánchez-Busó, Leonor and González-Candelas, Fernando. (2014) Mixed infection by Legionella pneumophila in outbreak patients. Zentralblatt für Bakteriologie = International journal of medical microbiology, Vol. 304, H. 3/4. pp. 307-313.

Gagneux, S.. (2014) Interactions between mycobacterial and human genetic diversity and implications for new TB vaccines. In: The art & science of Tuberculosis vaccine development. - 2nd ed.. Shah Alam, pp. 337-349.

Kroidl, Inge and Clowes, Petra and Mwakyelu, Joshua and Maboko, Leonard and Kiangi, Abubakary and Rachow, Andrea and Reither, Klaus and Jung, Jutta and Nsojo, Anthony and Saathoff, Elmar and Hoelscher, Michael. (2014) Reasons for false-positive lipoarabinomannan ELISA results in a Tanzanian population. Scandinavian journal of infectious diseases, Vol. 46, H. 2. pp. 144-148.

Köser, C. U. and Bryant, J. M. and Comas, I. and Feuerriegel, S. and Niemann, S. and Gagneux, S. and Parkhill, J. and Peacock, S. J.. (2014) Comment on: Characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array. Journal of Antimicrobial Chemotherapy, Vol. 69, H. 8. pp. 2298-2299.

Köser, C. U. and Bryant, J. M. and Comas, I. and Feuerriegel, S. and Niemann, S. and Gagneux, S. and Parkhill, J. and Peacock, S. J.. (2014) Genetic diversity within Mycobacterium tuberculosis complex impacts on the accuracy of genotypic pyrazinamide drug-susceptibility assay. Tuberculosis, Vol. 94. pp. 451-453.

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.

Narayanaswamy, Pradeep and Shinde, Sudhirkumar and Sulc, Robert and Kraut, Rachel and Staples, Gregory and Thiam, Chung Hwee and Grimm, Rudolf and Sellergren, Börje and Torta, Federico and Wenk, Markus R.. (2014) Lipidomic "deep profiling" : an enhanced workflow to reveal new molecular species of signaling lipids. Analytical chemistry, Vol. 86, H. 6. pp. 3043-3047.

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.

Reither, Klaus and Katsoulis, Lynn and Beattie, Trevor and Gardiner, Nicolene and Lenz, Nicole and Said, Khadija and Mfinanga, Elirehema and Pohl, Christian and Fielding, Katherine L. and Jeffery, Hannah and Kagina, Benjamin M. and Hughes, Elisabeth J. and Scriba, Thomas J. and Hanekom, Willem A. and Hoff, Søren T. and Bang, Peter and Kromann, Ingrid and Daubenberger, Claudia and Andersen, Peter and Churchyard, Gavin J.. (2014) Safety and immunogenicity of H1/IC31®, an adjuvanted TB subunit vaccine, in HIV-infected adults with CD4+ lymphocyte counts greater than 350 cells/mm3 : a phase II, multi-centre, double-blind, randomized, placebo-controlled trial. PLoS one, Vol. 9, H. 12 , e114602.

Seguín-Estévez, Queralt and Dunand-Sauthier, Isabelle and Lemeille, Sylvain and Iseli, Christian and Ibberson, Mark and Ioannidis, Vassilios and Schmid, Christoph D. and Rousseau, Philippe and Barras, Emmanuèle and Geinoz, Antoine and Xenarios, Ioannis and Acha-Orbea, Hans and Reith, Walter. (2014) Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing. Nucleic Acids Research, Vol. 42, H. 15. pp. 9641-9655.

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.

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.

2013

Aseffa, A. and Mihret, A. and Habte, A. and Abebe, M. and Wassie, L. and Tschopp, R. and Beyene, D. and Ameni, G. and Berg, S. and Doherty, T. M. and Gagneux, S. and Young, D. and Howe, R.. (2013) Advances in tuberculosis. African journal of microbiology research, Vol. 7, H. 2. pp. 73-81.

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.

Brites, D. and Brena, C. and Ebert, D. and Du Pasquier, L.. (2013) More than one way to produce protein diversity: duplication and limited alternative splicing of an adhesion molecule gene in basal arthropods. Evolution, 67 (10). pp. 2999-3011.

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.

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.

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 Ballif, Marie and Graber, Claire and Nhandu, Venerandah and Dusingize, Jean Claude and Cortes, Claudia P. and Carriquiry, Gabriela and Anastos, Kathryn and Garone, Daniela and Jong, Eefje and Gnokoro, Joachim Charles and Sued, Omar and Ajayi, Samuel and Diero, Lameck and Wools-Kaloustian, Kara and Kiertiburanakul, Sasisopin and Castelnuovo, Barbara and Lewden, Charlotte and Durier, Nicolas and Sterling, Timothy R. and Egger, Matthias and International epidemiological Databases to Evaluate Aids, . (2013) Tuberculosis in antiretroviral treatment programs in lower income countries: availability and use of diagnostics and screening. PloS one, Vol. 8, H. 10 , e77697.

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.

Firdessa, R. and Berg, S. and Hailu, E. and Schelling, E. and Gumi, B. and Erenso, G. and Gadisa, E. and Kiros, T. and Habtamu, M. and Hussein, J. and Zinsstag, J. and Robertson, B. D. and Ameni, G. and Lohan, A. J. and Loftus, B. and Comas, I. and Gagneux, S. and Tschopp, R. and Yamuah, L. and Hewinson, G. and Gordon, S. V. and Young, D. B. and Aseffa, A.. (2013) Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerging infectious diseases, Vol. 19, H. 3. pp. 460-463.

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.

Gagneux, Sebastien. (2013) Genetic diversity in Mycobacterium tuberculosis. Current topics in microbiology and immunology, Vol. 374. pp. 1-25.

Garcia-Garcerà, Marc and Garcia-Etxebarria, Koldo and Coscollà, Mireia and Latorre, Amparo and Calafell, Francesca. (2013) A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin. PloS one, Vol. 8, H. 9 , e74914.

Hella, J. J. and Hiza, H. C. and Mfinanga, E. and Reither, K.. (2013) Paraspinal abscess secondary to tuberculous spondylitis diagnosed by Xpert MTB/RIF assay in rural Tanzania. BMJ case reports, 2013, Apr 10. pp. 1-3.

Kato-Maeda, M. and Ho, C. and Passarelli, B. and Banaei, N. and Grinsdale, J. and Flores, L. and Anderson, J. and Murray, M. and Rose, G. and Kawamura, L. M. and Pourmand, N. and Tariq, M. A. and Gagneux, S. and Hopewell, P. C.. (2013) Use of whole genome sequencing to determine the microevolution of Mycobacterium tuberculosis during an outbreak. PLoS one, Vol. 8, H. 3 , e58235.

Klopper, M. and Warren, R. M. and Hayes, C. and van Pittius, N. C. G. and Streicher, E. M. and Müller, B. and Sirgel, F. A. and Chabula-Nxiweni, M. and Hoosain, E. and Coetzee, G. and van Helden, P. D. and Victor, T. C. and Trollip, A. P.. (2013) Emergence and spread of extensively and totally drug-resistant tuberculosis, South Africa. Emerging infectious diseases, Vol. 19, H. 3. pp. 449-455.

Malla, Bijaya. Molecular epidemiology of "mycobacterium tuberculosis" in Nepal. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

Miotto, Paolo and Mwangoka, Grace and Valente, Ilaria C. and Norbis, Luca and Sotgiu, Giovanni and Bosu, Roberta and Ambrosi, Alessandro and Codecasa, Luigi R. and Goletti, Delia and Matteelli, Alberto and Ntinginya, Elias N. and Aloi, Francesco and Heinrich, Norbert and Reither, Klaus and Cirillo, Daniela M.. (2013) miRNA signatures in Sera of patients with active pulmonary tuberculosis. PloS one, Vol. 8, H. 11 , e80149.

Müller, B. and Borrell, S. and Rose, G. and Gagneux, S.. (2013) The heterogeneous evolution of multidrug-resistant Mycobacterium tuberculosis. Trends in genetics : DNA, differentiation and development, Vol. 29, H. 3. pp. 160-169.

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.

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.

Pohl, Christian and Jugheli, Levan and Haraka, Fredrick and Mfinanga, Elirehema and Said, Khadija and Reither, Klaus. (2013) Pulmonary aspergilloma : a treatment challenge in sub-Saharan Africa. PLoS neglected tropical diseases, Vol. 7, H. 10 , e2352.

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.

Said, Khadija and Mkopi, Abdallah and Verver, Suzanne and Lwilla, Fred and Churchyard, Gavin and Shekalaghe, Seif and Battegay, Manuel and Reither, Klaus. (2013) Improved services to enrollees into an HIV rural care and treatment center in Tanzania. Pan African medical journal, Vol. 16 , 34.

Schomaker, Michael and Egger, Matthias and Maskew, Mhairi and Garone, Daniela and Prozesky, Hans and Hoffmann, Christopher J. and Boulle, Andrew and Fenner, Lukas. (2013) Immune recovery after starting ART in HIV-infected patients presenting and not presenting with Tuberculosis in south Africa. JAIDS : journal of acquired immune deficiency syndromes : official publication of the International Retrovirology Association, Vol. 63, H. 1. pp. 142-145.

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.

Sánchez-Busó, Leonor and Coscollá, Mireia and Pinto-Carbó, Marta and Catalán, Vicente and González-Candelas, Fernando. (2013) Genetic characterization of Legionella pneumophila isolated from a common watershed in comunidad Valenciana, Spain. PloS one, Vol. 8, H. 4 , e61564.

Via, 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.

Wampande, Eddie M. and Mupere, Ezekiel and Debanne, Sara M. and Asiimwe, Benon B. and Nsereko, Mary and Mayanja, Harriet and Eisenach, Kathleen and Kaplan, Gilla and Boom, Henry W. and Sebastien, Gagneux and Joloba, Moses L.. (2013) Long-term dominance of Mycobacterium tuberculosis Uganda family in peri-urban Kampala-Uganda is not associated with cavitary disease. BMC infectious diseases, Vol. 13 , 484.

de Vos, M. and Müller, B. and Borrell, S. and Black, P. and van Helden, P. and Warren, R. and Gagneux, S. and Victor, T.. (2013) Putative compensatory mutations in the rpoC gene of rifampicin-resistant Mycobacterium tuberculosis are associated with ongoing transmission. Antimicrobial agents and chemotherapy : AAC, Vol. 57, H. 2. pp. 827-832.

2012

Bentley, S. D. and Comas, I. and Bryant, J. M. and Walker, D. and Smith, N. H. and Harris, S. R. and Thurston, S. and Gagneux, S. and Wood, J. and Antonio, M. and Quail, M. A. and Gehre, F. and Adegbola, R. A. and Parkhill, J. and de Jong, B. C.. (2012) The genome of Mycobacterium africanum west African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. PLoS neglected tropical diseases, Vol. 6, H. 2 , e1552.

Beyene, N. and Mahoney, A. and Cox, C. and Weetjens, B. and Makingi, G. and Mgode, G. and Durgin, A. and Kuipers, D. and Jubitana, M. and Egwaga, S. and Kamara, D. and Lwilla, F. and Mfinanga, S. G. and Kahwa, A. and Machang'u, R. and Kazwala, R. and Reither, K. and Kaufmann, S. H. E. and Poling, A.. (2012) APOPO's tuberculosis research agenda : achievements, challenges and prospects. Tanzania journal of health research, Vol. 14, H. 2. pp. 1-13.

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.

Fenner, L. and Egger, M. and Bodmer, T. and Altpeter, E. and Zwahlen, M. and Jaton, K. and Pfyffer, G. E. and Borrell, S. and Dubuis, O. and Bruderer, T. and Siegrist, H. H. and Furrer, H. and Calmy, A. and Fehr, J. and Stalder, J. M. and Ninet, B. and Bottger, E. C. and Gagneux, S.. (2012) Effect of mutation and genetic background on drug resistance in Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy, Vol. 56, H. 6. pp. 3047-3053.

Fenner, L. and Gagneux, S. and Helbling, P. and Battegay, M. and Rieder, H. L. and Pfyffer, G. E. and Zwahlen, M. and Furrer, H. and Siegrist, H. H. and Fehr, J. and Dolina, M. and Calmy, A. and Stucki, D. and Jaton, K. and Janssens, J. P. and Stalder, J. M. and Bodmer, T. and Ninet, B. and Böttger, E. C. and Egger, M.. (2012) Mycobacterium tuberculosis transmission in a country with low tuberculosis incidence : role of immigration and HIV infection. Journal of clinical microbiology, Vol. 50, H. 2. pp. 388-395.

Fenner, L. and Gagneux, S. and Janssens, J. P. and Fehr, J. and Cavassini, M. and Hoffmann, M. and Bernasconi, E. and Schrenzel, J. and Bodmer, T. and Bottger, E. C. and Helbling, P. and Egger, M.. (2012) Tuberculosis in HIV-negative and HIV-infected patients in a low-incidence country : clinical characteristics and treatment outcomes. PLoS one, Vol. 7, H. 3 , e34186.

Gagneux, S.. (2012) Host-pathogen coevolution in human tuberculosis. Philosophical transactions / The Royal Society of London. Biological sciences, Vol. 367, H. 1590. pp. 850-859.

Haraka, F. and Rutaihwa, L. K. and Battegay, M. and Reither, K.. (2012) Mycobacterium intracellulare infection in non-HIV infected patient in a region with a high burden of tuberculosis. BMJ case reports, 8 May 2012. p. 3.

Kato-Maeda, M. and Shanley, C. A. and Ackart, D. and Jarlsberg, L. G. and Shang, S. and Obregon-Henao, A. and Harton, M. and Basaraba, R. J. and Henao-Tamayo, M. and Barrozo, J. C. and Rose, J. and Kawamura, L. M. and Coscolla, M. and Fofanov, V. Y. and Koshinsky, H. and Gagneux, S. and Hopewell, P. C. and Ordway, D. J. and Orme, I. M.. (2012) Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the Guinea pig. Clinical and vaccine immunology, Vol. 19, H. 8. pp. 1227-1237.

Luo, 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.

Mahoney, Amanda and Weetjens, Bart J. and Cox, Christophe and Beyene, Negussie and Reither, Klaus and Makingi, George and Jubitana, Maureen and Kazwala, Rudovick and Mfinanga, Godfrey S. and Kahwa, Amos and Durgin, Amy and Poling, Alan. (2012) Pouched rats' detection of tuberculosis in human sputum : comparison to culturing and polymerase chain reaction. Tuberculosis research and treatment, Vol. 2012 , 716989.

Malla, B. and Stucki, D. and Borrell, S. and Feldmann, J. and Maharjan, B. and Shrestha, B. and Fenner, L. and Gagneux, S.. (2012) First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Nepal. PLoS one, Vol. 7, H. 12 , e52297.

McEvoy, C. R. and Cloete, R. and Müller, B. and Schurch, A. C. and van Helden, P. D. and Gagneux, S. and Warren, R. M. and Gey van Pittius, N. C.. (2012) Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PLoS one, Vol. 7, H. 4 , e30593.

Ntinginya, E. N. and Squire, S. B. and Millington, K. A. and Mtafya, B. and Saathoff, E. and Heinrich, N. and Rojas-Ponce, G. and Kowuor, D. and Maboko, L. and Reither, K. and Clowes, P. and Hoelscher, M. and Rachow, A.. (2012) Performance of the Xpert® MTB/RIF assay in an active case-finding strategy : a pilot study from Tanzania. The international journal of tuberculosis and lung disease : the official journal of the International Union Against Tuberculosis and Lung Disease, Vol. 16, H. 11. pp. 1468-1470.

Rachow, A. and Clowes, P. and Saathoff, E. and Mtafya, B. and Michael, E. and Ntinginya, E. N. and Kowour, D. and Rojas-Ponce, G. and Kroidl, A. and Maboko, L. and Heinrich, N. and Reither, K. and Hoelscher, M.. (2012) Increased and expedited case detection by Xpert MTB/RIF assay in childhood tuberculosis : a prospective cohort study. Clinical Infectious Diseases, Vol. 54, H. 10. pp. 1388-1396.

Stucki, D. and Malla, B. and Hostettler, S. and Huna, T. and Feldmann, J. and Yeboah-Manu, D. and Borrell, S. and Fenner, L. and Comas, I. and Coscolla, M. and Gagneux, S.. (2012) Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages. PLoS one, Vol. 7, H. 7 , e41253.

Weiner, B. and Gomez, J. and Victor, T. C. and Warren, R. M. and Sloutsky, A. and Plikaytis, B. B. and Posey, J. E. and van Helden, P. D. and Gey van Pittius, N. C. and Koehrsen, M. and Sisk, P. and Stolte, C. and White, J. and Gagneux, S. and Birren, B. and Hung, D. and Murray, M. and Galagan, J.. (2012) Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region. PLoS one, Vol. 7, H. 2 , e26038.

2011

Borrell, S. and Gagneux, S.. (2011) Strain diversity, epistasis and the evolution of drug resistance in Mycobacterium tuberculosis. Clinical microbiology and infection : CMI : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, Vol. 17, H. 6. pp. 815-820.

Comas, I. and Gagneux, S.. (2011) A role for systems epidemiology in tuberculosis research. Trends in microbiology : virulence, infection and pathogenesis, Vol. 19, H. 10. pp. 492-500.

Coscolla, M. and Comas, I. and Gonzalez-Candelas, F.. (2011) Quantifying nonvertical inheritance in the evolution of Legionella pneumophila. Molecular biology and evolution, 28 (2). pp. 985-1001.

Fenner, 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.

Kato-Maeda M., and Gagneux, S. and Flores, L. L. and Kim, E. Y. and Small, P. M. and Desmond, E. P. and Hopewell, P. C.. (2011) Strain classification of Mycobacterium tuberculosis : congruence between large sequence polymorphisms and spoligotypes. The international journal of tuberculosis and lung disease : the official journal of the International Union Against Tuberculosis and Lung Disease, Vol. 15, H. 1. pp. 131-133.

Portevin, Damien and Gagneux, Sébastien and Comas, Iñaki and Young, Douglas. (2011) Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages. PLoS Pathogens, Vol. 7, H. 3 , e1001307.

Rachow, A. and Zumla, A. and Heinrich, N. and Rojas-Ponce G., and Mtafya, B. and Reither, K. and Ntinginya, E. N. and O'Grady J., and Huggett, J. and Dheda, K. and Boehme, C. and Perkins, M. and Saathoff, E. and Hoelscher, M.. (2011) Rapid and accurate detection of Mycobacterium tuberculosis in sputum samples by Cepheid Xpert MTB/RIF assay : a clinical validation study. PLoS one, Vol. 6, H. 6 , e20458.

Rey-Jurado, Emma and Tudó, Griselda and Borrell, Sònia and Alcaide, Fernando and Coll, Pere and Español, Montserrat and Martín-Casabona, Núria and Mick, Virginie and Montemayor, Michel and Moure, Raquel and Salvadó, Margarita and Vicente, Eva and González-Martín, Julià. (2011) Impaired fitness of Mycobacterium tuberculosis resistant isolates in a cell culture model of murine macrophages. The journal of antimicrobial chemotherapy, 66 (10). pp. 2277-2280.

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.

Yeboah-Manu D., and Asante-Poku A., and Bodmer, T. and Stucki, D. and Koram, K. and Bonsu, F. and Pluschke, G. and Gagneux, S.. (2011) Genotypic diversity and drug susceptibility patterns among M. tuberculosis complex isolates from South-Western Ghana. PLoS one, Vol. 6, H. 7 , e21906.

2010

Comas, Iñaki and Chakravartti, Jaidip and Small, Peter M. and Galagan, James and Niemann, Stefan and Kremer, Kristin and Ernst, Joel D. and Gagneux, Sébastien. (2010) Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nature genetics, 42 (6). pp. 498-503.

Coscolla, M. and Gagneux, S.. (2010) Does M. tuberculosis genomic diversity explain disease diversity? Drug discovery today. Disease mechanisms, Vol. 7, H. 1 , e43-e59.

Gagneux, S. and Brennan, M.. (2010) Strain and antigen variation in Mycobacterium tuberculosis : implications for the development of new tools for tuberculosis. In: >>The<< art and science of tuberculosis vaccine development. Shah Alam, pp. 130-147.

Nahid, P. and Bliven, E. E. and Kim, E. Y. and Mac Kenzie W. R., and Stout, J. E. and Diem, L. and Johnson, J. L. and Gagneux, S. and Hopewell, P. C. and Kato-Maeda M., . (2010) Influence of M. tuberculosis lineage variability within a clinical trial for pulmonary tuberculosis. PLoS one, Vol. 5, H. 5 , e10753.

de Jong B. C., and Antonio, M. and Gagneux, S.. (2010) Mycobacterium africanum : review of an important cause of human tuberculosis in West Africa. PLoS neglected tropical diseases, Vol. 4, H. 9 , e744.

2009

Borrell, S. and Gagneux, S.. (2009) Infectiousness, reproductive fitness and evolution of drug-resistant Mycobacterium tuberculosis. The international journal of tuberculosis and lung disease, 13 (12). pp. 1456-1466.

2007

Leimkugel, 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.

Leimkugel, Julia and Hodgson, Abraham and Forgor, Abudulai Adams and Pflüger, Valentin and Dangy, Jean-Pierre and Smith, Tom and Achtman, Mark and Gagneux, Sébastien and Pluschke, Gerd. (2007) Clonal waves of Neisseria colonisation and disease in the African meningitis belt : eight- year longitudinal study in northern Ghana. PLoS medicine, Vol. 4, H. 3 , e101.

2005

Forgor, Abdulai Adams and Leimkugel, Julia and Hodgson, Abraham and Bugri, Akalifa and Dangy, Jean-Pierre and Gagneux, Sébastien and Smith, Tom and Pluschke, Gerd. (2005) Emergence of W135 meningococcal meningitis in Ghana. Tropical medicine and international health : TM & IH : a European journal, 10 (12). pp. 1229-1234.

Leimkugel, Julia and Adams Forgor, Abudulai and Gagneux, Sébastien and Pflüger, Valentin and Flierl, Christian and Awine, Elizabeth and Naegeli, Martin and Dangy, Jean-Pierre and Smith, Tom and Hodgson, Abraham and Pluschke, Gerd. (2005) An outbreak of serotype 1 Streptococcus pneumoniae meningitis in northern Ghana with features that are characteristic of Neisseria meningitidis meningitis epidemics. The Journal of Infectious Diseases, Vol. 192, H. 2. pp. 192-199.

2002

Gagneux, Sébastien and Wirth, Thierry and Hodgson, Abraham and Ehrhard, Ingrid and Morelli, Giovanna and Kriz, Paula and Genton, Blaise and Smith, Tom and Binka, Fred and Pluschke, Gerd and Achtman, Mark. (2002) Clonal groupings in serogroup X Neisseria meningitidis. Emerging Infectious Diseases, Vol. 8, H. 5. pp. 462-466.

Gagneux, Sébastien P. and Hodgson, Abraham and Smith, Tom A. and Wirth, Thierry and Ehrhard, Ingrid and Morelli, Giovanna and Genton, Blaise and Binka, Fred N. and Achtman, Mark and Pluschke, Gerd. (2002) Prospective study of a serogroup X Neisseria meningitidis outbreak in northern Ghana. The Journal of Infectious Diseases, Vol. 185, H. 5. pp. 618-626.

2001

Hodgson, A. and Smith, T. and Gagneux, S. and Adjuik, M. and Pluschke, G. and Mensah, N. K. and Binka, F. and Genton, B.. (2001) Risk factors for meningococcal meningitis in northern Ghana. Transactions of The Royal Society of Tropical Medicine and Hygiene, Vol. 95, H. 5. pp. 477-480.

Hodgson, A. and Smith, T. and Gagneux, S. and Akumah, I. and Adjuik, M. and Pluschke, G. and Binka, F. and Genton, B.. (2001) Survival and sequelae of meningococcal meningitis in Ghana. International Journal of Epidemiology, Vol. 30, H. 6. pp. 1440-1446.

Zhu, P. and van der Ende, A. and Falush, D. and Brieske, N. and Morelli, G. and Linz, B. and Popovic, T. and Schuurman, I. G. and Adegbola, R. A. and Zurth, K. and Gagneux, S. and Platonov, A. E. and Riou, J. Y. and Caugant, D. A. and Nicolas, P. and Achtman, M.. (2001) Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, H. 9. pp. 5234-5239.

2000

Gagneux, S. and Hodgson, A. and Ehrhard, I. and Morelli, G. and Genton, B. and Smith, T. and Tanner, M. and Binka, F. and Achtman, M. and Pluschke, G.. (2000) Microheterogeneity of serogroup A (subgroup III) Neisseria meningitidis during an outbreak in northern Ghana. Tropical medicine and international health : TM & IH : a European journal, 5 (4). pp. 280-287.