Coll, F; Phelan, J; Hill-Cawthorne, GA; Nair, MB; Mallard, K; Ali, S; Abdallah, AM; Alghamdi, S; Alsomali, M; Ahmed, AO; +41 more... Portelli, S; Oppong, Y; Alves, A; Bessa, TB; Campino, S; Caws, M; Chatterjee, A; Crampin, AC; Dheda, K; Furnham, N; Glynn, JR; Grandjean, L; Minh Ha, D; Hasan, R; Hasan, Z; Hibberd, ML; Joloba, M; Jones-López, EC; Matsumoto, T; Miranda, A; Moore, DJ; Mocillo, N; Panaiotov, S; Parkhill, J; Penha, C; Perdigão, J; Portugal, I; Rchiad, Z; Robledo, J; Sheen, P; Shesha, NT; Sirgel, FA; Sola, C; Oliveira Sousa, E; Streicher, EM; Helden, PV; Viveiros, M; Warren, RM; McNerney, R; Pain, A; Clark, TG; (2018) Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature genetics. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-017-0029-0

Phelan, J; de Sessions, PF; Tientcheu, L; Perdigao, J; Machado, D; Hasan, R; Hasan, Z; Bergval, IL; Anthony, R; McNerney, R; +6 more... Antonio, M; Portugal, I; Viveiros, M; Campino, S; Hibberd, ML; Clark, TG; (2018) Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. Scientific reports, 8 (1). p. 160. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-017-18188-y

Ali, A; Hasan, Z; McNerney, R; Mallard, K; Hill-Cawthorne, G; Coll, F; Nair, M; Pain, A; Clark, TG; Hasan, R; (2015) Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan. PloS one, 10 (2). e0117771. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0117771

Coll, F; McNerney, R; Preston, MD; Guerra-Assunção, JA; Warry, A; Hill-Cawthorne, G; Mallard, K; Nair, M; Miranda, A; Alves, A; +9 more... Perdigão, J; Viveiros, M; Portugal, I; Hasan, Z; Hasan, R; Glynn, JR; Martin, N; Pain, A; Clark, TG; (2015) Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome medicine, 7 (1). p. 51. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-015-0164-0

Dalla Costa, ER; Vasconcelos, SE; Esteves, LS; Gomes, HM; Gomes, LL; da Silva, PA; Perdigão, J; Portugal, I; Viveiros, M; McNerney, R; +6 more... Pain, A; Clark, TG; Rastogi, N; Unis, G; Rossetti, ML; Suffys, PN; (2015) Multidrug resistant Mycobacterium tuberculosis of the Latin American Mediteranean lineage wrongly identified as Mycobacterium pinnipedii (ST863) causing active tuberculosis in south Brazil. Journal of clinical microbiology, 53 (12). pp. 3805-11. ISSN 0095-1137 DOI: https://doi.org/10.1128/JCM.02012-15 Full text not available from this repository.

Glynn, JR; Guerra-Assunção, JA; Houben, RM; Sichali, L; Mzembe, T; Mwaungulu, LK; Mwaungulu, JN; McNerney, R; Khan, P; Parkhill, J; +2 more... Crampin, AC; Clark, TG; (2015) Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi. PloS one, 10 (7). e0132840. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0132840

Guerra-Assunção, J; Crampin, A; Houben, R; Mzembe, T; Mallard, K; Coll, F; Khan, P; Banda, L; Chiwaya, A; Pereira, R; +5 more... McNerney, R; Fine, P; Parkhill, J; Clark, T; Glynn, J; (2015) Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife, 4. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.05166

Hernández, P; Punchak, M; Camacho, M; Hepple, P; McNerney, R; (2015) Investigating the quality of expectorated sputum for tuberculosis diagnosis in Bolivia. The international journal of tuberculosis and lung disease, 19 (9). pp. 1065-7. ISSN 1027-3719 DOI: https://doi.org/10.5588/ijtld.14.0700 Full text not available from this repository.

Kanji, A; Hasan, Z; Ali, A; McNerney, R; Mallard, K; Coll, F; Hill-Cawthorne, G; Nair, M; Clark, TG; Zaver, A; +2 more... Jafri, S; Hasan, R; (2015) Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan. International journal of mycobacteriology, 4 (1). pp. 73-9. ISSN 2212-5531 DOI: https://doi.org/10.1016/j.ijmyco.2014.11.049

McNerney, R; Cunningham, J; Hepple, P; Zumla, A; (2015) New tuberculosis diagnostics and rollout. International journal of infectious diseases, 32. pp. 81-86. ISSN 1201-9712 DOI: https://doi.org/10.1016/j.ijid.2015.01.012

McNerney, R; Peeling, RW; (2015) Regulatory In Vitro Diagnostics Landscape in Africa: Update on Regional Activities. Clinical infectious diseases, 61 (suppl 3). S135-S140. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/civ553 Full text not available from this repository.

McNerney, R; Zumla, A; (2015) Impact of the Xpert MTB/RIF diagnostic test for tuberculosis in countries with a high burden of disease. Current opinion in pulmonary medicine, 21 (3). pp. 304-8. ISSN 1070-5287 DOI: https://doi.org/10.1097/MCP.0000000000000161 Full text not available from this repository.

Nicoara, SC; Turner, NW; Minnikin, DE; Lee, OY; O'Sullivan, DM; McNerney, R; Mutetwa, R; Corbett, LE; Morgan, GH; (2015) Development of sample clean up methods for the analysis of Mycobacterium tuberculosis methyl mycocerosate biomarkers in sputum extracts by gas chromatography-mass spectrometry. Journal of chromatography B, Analytical technologies in the biomedical and life sciences, 986-987C. pp. 135-142. ISSN 1570-0232 DOI: https://doi.org/10.1016/j.jchromb.2015.02.010

Senthilingam, M; Pietersen, E; McNerney, R; Te Riele, J; Sedres, P; Wilson, R; Dheda, K; (2015) Lifestyle, attitudes and needs of uncured XDR-TB patients living in the communities of South Africa: A qualitative study. Tropical medicine & international health, 20 (9). pp. 1155-1161. ISSN 1360-2276 DOI: https://doi.org/10.1111/tmi.12532 Full text not available from this repository.

Bergval, I; Coll, F; Schuitema, A; de Ronde, H; Mallard, K; Pain, A; McNerney, R; Clark, TG; Anthony, RM; (2014) A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture. FEMS microbiology letters, 362 (2). pp. 1-7. ISSN 0378-1097 DOI: https://doi.org/10.1093/femsle/fnu037

Boyle, DS; McNerney, R; Teng Low, H; Leader, BT; Pérez-Osorio, AC; Meyer, JC; O'Sullivan, DM; Brooks, DG; Piepenburg, O; Forrest, MS; (2014) Rapid Detection of Mycobacterium tuberculosis by Recombinase Polymerase Amplification. PloS one, 9 (8). e103091. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0103091

Coll, F; McNerney, R; Guerra-Assunção, JA; Glynn, JR; Perdigão, J; Viveiros, M; Portugal, I; Pain, A; Martin, N; Clark, TG; (2014) A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature communications, 5. p. 4812. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms5812

Coll, F; Preston, M; Guerra-Assunção, JA; Hill-Cawthorn, G; Harris, D; Perdigão, J; Viveiros, M; Portugal, I; Drobniewski, F; Gagneux, S; +6 more... Glynn, JR; Pain, A; Parkhill, J; McNerney, R; Martin, N; Clark, TG; (2014) PolyTB: A genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland), 94 (3). pp. 346-54. ISSN 1472-9792 DOI: https://doi.org/10.1016/j.tube.2014.02.005

Guerra-Assunção, JA; Houben, RM; Crampin, AC; Mzembe, T; Mallard, K; Coll, F; Khan, P; Banda, L; Chiwaya, A; Pereira, RP; +5 more... McNerney, R; Harris, D; Parkhill, J; Clark, TG; Glynn, JR; (2014) Relapse or reinfection with tuberculosis: a whole genome sequencing approach in a large population-based cohort with high HIV prevalence and active follow-up. The Journal of infectious diseases, 211 (7). pp. 1154-63. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiu574

Kirenga, BJ; Levin, J; Ayakaka, I; Worodria, W; Reilly, N; Mumbowa, F; Nabanjja, H; Nyakoojo, G; Fennelly, K; Nakubulwa, S; +9 more... Joloba, M; Okwera, A; Eisenach, KD; McNerney, R; Elliott, AM; Mugerwa, RD; Smith, PG; Ellner, JJ; Jones-López, EC; (2014) Treatment outcomes of new tuberculosis patients hospitalized in kampala, Uganda: a prospective cohort study. PloS one, 9 (3). e90614. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0090614

McNerney, R; Sollis, K; Peeling, R; (2014) Improving access to new diagnostics through harmonised regulation: priorities for action. Afr J Lab Med, 3 (1). http://researchonline.lshtm.ac.uk/id/eprint/1649067 Full text not available from this repository.

McNerney, R; Sollis, K; Peeling, RW; (2014) Improving access to new diagnostics through harmonised regulation: priorities for action. African journal of laboratory medicine, 3 (1). p. 123. ISSN 2225-2002 DOI: https://doi.org/10.4102/ajlm.v3i1.123

Peeling, RW; McNerney, R; (2014) Emerging technologies in point-of-care molecular diagnostics for resource-limited settings. Expert review of molecular diagnostics, 14 (5). pp. 525-34. ISSN 1473-7159 DOI: https://doi.org/10.1586/14737159.2014.915748 Full text not available from this repository.

Perdigão, J; Silva, H; Machado, D; Macedo, R; Maltez, F; Silva, C; Jordao, L; Couto, I; Mallard, K; Coll, F; +6 more... Hill-Cawthorne, GA; McNerney, R; Pain, A; Clark, TG; Viveiros, M; Portugal, I; (2014) Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC genomics, 15. p. 991. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-15-991

Rugera, SP; McNerney, R; Poon, AK; Akimana, G; Mariki, RF; Kajumbula, H; Kamau, E; Mpawenimana, S; Said, SY; Toroitich, A; +4 more... Ronoh, W; Sollis, KA; Sonoiya, S; Peeling, RW; (2014) Regulation of medical diagnostics and medical devices in the East African community partner states. BMC health services research, 14. p. 524. ISSN 1472-6963 DOI: https://doi.org/10.1186/s12913-014-0524-2

Abubakar, I; Zignol, M; Falzon, D; Raviglione, M; Ditiu, L; Masham, S; Adetifa, I; Ford, N; Cox, H; Lawn, SD; +21 more... Marais, BJ; McHugh, TD; Mwaba, P; Bates, M; Lipman, M; Zijenah, L; Logan, S; McNerney, R; Zumla, A; Sarda, K; Nahid, P; Hoelscher, M; Pletschette, M; Memish, ZA; Kim, P; Hafner, R; Cole, S; Migliori, GB; Maeurer, M; Schito, M; Zumla, A; (2013) Drug-resistant tuberculosis: time for visionary political leadership. The Lancet infectious diseases. ISSN 1473-3099 DOI: https://doi.org/10.1016/S1473-3099(13)70030-6

Clark, TG; Mallard, K; Coll, F; Preston, M; Assefa, S; Harris, D; Ogwang, S; Mumbowa, F; Kirenga, B; O'Sullivan, DM; +8 more... Okwera, A; Eisenach, KD; Joloba, M; Bentley, SD; Ellner, JJ; Parkhill, J; Jones-López, EC; McNerney, R; (2013) Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PloS one, 8 (12). e83012. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0083012

Coll, F; Mallard, K; Preston, MD; Bentley, S; Parkhill, J; McNerney, R; Martin, N; Clark, TG; (2012) SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics (Oxford, England), 28 (22). pp. 2991-3. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bts544

Hepple, P; Ford, N; McNerney, R; (2012) Microscopy compared to culture for the diagnosis of tuberculosis in induced sputum samples: a systematic review. The international journal of tuberculosis and lung disease, 16 (5). pp. 579-88. ISSN 1027-3719 DOI: https://doi.org/10.5588/ijtld.11.0617 Full text not available from this repository.

Jones-López, EC; Ayakaka, I; Levin, J; Reilly, N; Mumbowa, F; Dryden-Peterson, S; Nyakoojo, G; Fennelly, K; Temple, B; Nakubulwa, S; +8 more... Joloba, ML; Okwera, A; Eisenach, KD; McNerney, R; Elliott, AM; Ellner, JJ; Smith, PG; Mugerwa, RD; (2011) Effectiveness of the Standard WHO Recommended Retreatment Regimen (Category II) for Tuberculosis in Kampala, Uganda: A Prospective Cohort Study. PLoS medicine, 8 (3). e1000427. ISSN 1549-1277 DOI: https://doi.org/10.1371/journal.pmed.1000427

McNerney, R; (2002) Workplace protection from tuberculosis. Africa health, 24 (6). pp. 15-16. ISSN 0141-9536 http://researchonline.lshtm.ac.uk/id/eprint/15545 Full text not available from this repository.

McNerney, R; (2002) Mutagens in the medical laboratory: what can be done? Africa health, 25 (1). pp. 14-15. ISSN 0141-9536 http://researchonline.lshtm.ac.uk/id/eprint/15546 Full text not available from this repository.