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; Ha, DM; 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; Sousa, EO; Streicher, EM; Van Helden, P; Viveiros, M; Warren, RM; McNerney, R; Pain, A; Clark, TG; (2018) Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature genetics. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-018-0074-3 Full text not available from this repository.

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

Last, AR; Pickering, H; Roberts, CH; Coll, F; Phelan, J; Burr, SE; Cassama, E; Nabicassa, M; Seth-Smith, HMB; Hadfield, J; +7 more... Cutcliffe, LT; Clarke, IN; Mabey, DCW; Bailey, RL; Clark, TG; Thomson, NR; Holland, MJ; (2018) Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity. Genome medicine, 10 (1). p. 15. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-018-0521-x

Ajileye, A; Alvarez, N; Merker, M; Walker, TM; Akter, S; Brown, K; Moradigaravand, D; Schön, T; Andres, S; Schleusener, V; +14 more... Omar, SV; Coll, F; Huang, H; Diel, R; Ismail, N; Parkhill, J; de Jong, BC; Peto, TE; Crook, DW; Niemann, S; Robledo, J; Smith, EG; Peacock, SJ; Köser, CU; (2017) Some synonymous and non-synonymous gyrA mutations in Mycobacterium tuberculosis lead to systematic false-resistance results to fluoroquinolones with the Hain GenoType MTBDRsl assays. Antimicrobial agents and chemotherapy. ISSN 0066-4804 DOI: https://doi.org/10.1128/AAC.02169-16

Coll, F; Harrison, EM; Toleman, MS; Reuter, S; Raven, KE; Blane, B; Palmer, B; Kappeler, ARM; Brown, NM; Török, ME; +2 more... Parkhill, J; Peacock, SJ; (2017) Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Science translational medicine, 9 (413). ISSN 1946-6234 DOI: https://doi.org/10.1126/scitranslmed.aak9745

Harrison, EM; Coll, F; Toleman, MS; Blane, B; Brown, NM; Török, ME; Parkhill, J; Peacock, SJ; (2017) Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England. Scientific reports, 7 (1). p. 7406. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-017-07662-2

Jamrozy, D; Coll, F; Mather, AE; Harris, SR; Harrison, EM; MacGowan, A; Karas, A; Elston, T; Estée Török, M; Parkhill, J; +1 more... Peacock, SJ; (2017) Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events. BMC genomics, 18 (1). p. 684. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-017-4065-z

Ludden, C; Reuter, S; Judge, K; Gouliouris, T; Blane, B; Coll, F; Naydenova, P; Hunt, M; Tracey, A; Hopkins, KL; +4 more... Brown, NM; Woodford, N; Parkhill, J; Peacock, SJ; (2017) Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. Microbial genomics, 3 (7). e000114. ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000114

Nakatani, Y; Opel-Reading, HK; Merker, M; Machado, D; Andres, S; Kumar, SS; Moradigaravand, D; Coll, F; Perdigão, J; Portugal, I; +19 more... Schön, T; Nair, D; Devi, KRU; Kohl, TA; Beckert, P; Clark, TG; Maphalala, G; Khumalo, D; Diel, R; Klaos, K; Aung, HL; Cook, GM; Parkhill, J; Peacock, SJ; Swaminathan, S; Viveiros, M; Niemann, S; Krause, KL; Köser, CU; (2017) Role of alanine racemase mutations in Mycobacterium tuberculosis D-cycloserine resistance. Antimicrobial agents and chemotherapy. ISSN 0066-4804 DOI: https://doi.org/10.1128/AAC.01575-17

Raven, KE; Gouliouris, T; Brodrick, H; Coll, F; Brown, NM; Reynolds, R; Reuter, S; Török, ME; Parkhill, J; Peacock, SJ; (2017) Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing. Clinical infectious diseases, 64 (7). pp. 886-893. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciw872

Toleman, MS; Watkins, ER; Williams, T; Blane, B; Sadler, B; Harrison, EM; Coll, F; Parkhill, J; Nazareth, B; Brown, NM; +1 more... Peacock, SJ; (2017) Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting. Clinical infectious diseases. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/cix539

Harrison, EM; Ludden, C; Brodrick, HJ; Blane, B; Brennan, G; Morris, D; Coll, F; Reuter, S; Brown, NM; Holmes, MA; +5 more... O'Connell, B; Parkhill, J; Török, ME; Cormican, M; Peacock, SJ; (2016) Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks. Genome medicine, 8 (1). p. 102. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-016-0353-5

Phelan, J; Coll, F; McNerney, R; Ascher, DB; Pires, DE; Furnham, N; Coeck, N; Hill-Cawthorne, GA; Nair, MB; Mallard, K; +6 more... Ramsay, A; Campino, S; Hibberd, ML; Pain, A; Rigouts, L; Clark, TG; (2016) Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC medicine, 14 (1). p. 31. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-016-0575-9

Phelan, JE; Coll, F; Bergval, I; Anthony, RM; Warren, R; Sampson, SL; Gey van Pittius, NC; Glynn, JR; Crampin, AC; Alves, A; +20 more... Bessa, TB; Campino, S; Dheda, K; Grandjean, L; Hasan, R; Hasan, Z; Miranda, A; Moore, D; Panaiotov, S; Perdigao, J; Portugal, I; Sheen, P; de Oliveira Sousa, E; Streicher, EM; van Helden, PD; Viveiros, M; Hibberd, ML; Pain, A; McNerney, R; Clark, TG; (2016) Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC genomics, 17 (1). p. 151. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-016-2467-y

Refrégier, G; Abadia, E; Matsumoto, T; Ano, H; Takashima, T; Tsuyuguchi, I; Aktas, E; Cömert, F; Gomgnimbou, MK; Panaiotov, S; +6 more... Phelan, J; Coll, F; McNerney, R; Pain, A; Clark, TG; Sola, C; (2016) Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. Infection, genetics and evolution, 45. pp. 461-473. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2016.10.009

Toleman, MS; Reuter, S; Coll, F; Harrison, EM; Blane, B; Brown, NM; Török, ME; Parkhill, J; Peacock, SJ; (2016) Systematic surveillance detects multiple silent introductions and household transmission of methicillin-resistant Staphylococcus aureus USA300 in the east of England. The Journal of infectious diseases. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiw166

Toleman, MS; Reuter, S; Coll, F; Harrison, EM; Peacock, SJ; (2016) Local Persistence of Novel MRSA Lineage after Hospital Ward Outbreak, Cambridge, UK, 2011-2013. Emerging infectious diseases, 22 (9). pp. 1658-9. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2209.151100

Abdallah, AM; Hill-Cawthorne, GA; Otto, TD; Coll, F; Guerra-Assunção, JA; Gao, G; Naeem, R; Ansari, H; Malas, TB; Adroub, SA; +10 more... Verboom, T; Ummels, R; Zhang, H; Panigrahi, AK; McNerney, R; Brosch, R; Clark, TG; Behr, MA; Bitter, W; Pain, A; (2015) Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific reports, 5. p. 15443. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep15443

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

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

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

Phelan, J; Maitra, A; McNerney, R; Nair, M; Gupta, A; Coll, F; Pain, A; Bhakta, S; Clark, TG; (2015) The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae. International journal of mycobacteriology, 4 (3). pp. 207-16. ISSN 2212-5531 DOI: https://doi.org/10.1016/j.ijmyco.2015.05.001

Samad, H; Coll, F; Preston, MD; Ocholla, H; Fairhurst, RM; Clark, TG; (2015) Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites. PLoS genetics, 11 (4). e1005131. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1005131

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

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

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

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