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Refrégier, G., Abadia, E., Matsumoto, T., Ano, H., Takashima, T., Tsuyuguchi, I., Aktas, E., Cömert, F., Gomgnimbou, M. K., Panaiotov, S., Phelan, J., Coll, F., McNerney, R., Pain, A., Clark, T. G., & Sola, C. (2016). Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. Infection, Genetics and Evolution, 45, 461–473. https://doi.org/10.1016/j.meegid.2016.10.009

Harrison, E. M., Ludden, C., Brodrick, H. J., Blane, B., Brennan, G., Morris, D., Coll, F., Reuter, S., Brown, N. M., Holmes, M. A., O’Connell, B., Parkhill, J., Török, M. E., Cormican, M., & Peacock, S. J. (2016). Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks. Genome Medicine, 8(1). https://doi.org/10.1186/s13073-016-0353-5

Toleman, M. S., Reuter, S., Coll, F., Harrison, E. M., Blane, B., Brown, N. M., Török, M. E., Parkhill, J., & Peacock, S. J. (2016). Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-ResistantStaphylococcus aureusUSA300 in the East of England. Journal of Infectious Diseases, 214(3), 447–453. https://doi.org/10.1093/infdis/jiw166

Phelan, J. E., Coll, F., Bergval, I., Anthony, R. M., Warren, R., Sampson, S. L., Gey van Pittius, N. C., Glynn, J. R., Crampin, A. C., Alves, A., Bessa, T. B., Campino, S., Dheda, K., Grandjean, L., Hasan, R., Hasan, Z., Miranda, A., Moore, D., Panaiotov, S., … Clark, T. G. (2016). Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC Genomics, 17(1). https://doi.org/10.1186/s12864-016-2467-y

Last, A., Roberts, C., Coll, F., Burr, S., Clarke, I., Mabey, D., Bailey, R., Clark, T., Thomson, N., & Holland, M. (2016). Ocular chlamydial genomic variants and disease severity in trachoma: a cross-sectional population-based genome-wide association study. The Lancet, 387, S63. https://doi.org/10.1016/s0140-6736(16)00450-5

Phelan, J., Coll, F., McNerney, R., Ascher, D. B., Pires, D. E. V., Furnham, N., Coeck, N., Hill-Cawthorne, G. A., Nair, M. B., Mallard, K., Ramsay, A., Campino, S., Hibberd, M. L., Pain, A., Rigouts, L., & Clark, T. G. (2016). Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Medicine, 14(1). https://doi.org/10.1186/s12916-016-0575-9

Toleman, M. S., Reuter, S., Coll, F., Harrison, E. M., & Peacock, S. J. (2016). Local Persistence of Novel MRSA Lineage after Hospital Ward Outbreak, Cambridge, UK, 2011–2013. Emerging Infectious Diseases, 22(9), 1658–1659. https://doi.org/10.3201/eid2209.151100

(2016). Correction: Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites. PLOS Genetics, 12(8), e1006300. https://doi.org/10.1371/journal.pgen.1006300

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

Phelan, J., Maitra, A., McNerney, R., Nair, M., Gupta, A., Coll, F., Pain, A., Bhakta, S., & Clark, T. G. (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), 207–216. https://doi.org/10.1016/j.ijmyco.2015.05.001

Coll, F., McNerney, R., Preston, M. D., Guerra-Assunção, J. A., Warry, A., Hill-Cawthorne, G., Mallard, K., Nair, M., Miranda, A., Alves, A., Perdigão, J., Viveiros, M., Portugal, I., Hasan, Z., Hasan, R., Glynn, J. R., Martin, N., Pain, A., & Clark, T. G. (2015). Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Medicine, 7(1). https://doi.org/10.1186/s13073-015-0164-0

Benavente, E. D., Coll, F., Furnham, N., McNerney, R., Glynn, J. R., Campino, S., Pain, A., Mohareb, F. R., & Clark, T. G. (2015). PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics, 16(1). https://doi.org/10.1186/s12859-015-0603-3

Guerra-Assunção, J., Crampin, A., Houben, R., Mzembe, T., Mallard, K., Coll, F., Khan, P., Banda, L., Chiwaya, A., Pereira, R., 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. CLOCKSS. https://doi.org/10.7554/elife.05166

Samad, H., Coll, F., Preston, M. D., Ocholla, H., Fairhurst, R. M., & Clark, T. G. (2015). Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites. PLOS Genetics, 11(4), e1005131. https://doi.org/10.1371/journal.pgen.1005131

Abdallah, A. M., Hill-Cawthorne, G. A., Otto, T. D., Coll, F., Guerra-Assunção, J. A., Gao, G., Naeem, R., Ansari, H., Malas, T. B., Adroub, S. A., Verboom, T., Ummels, R., Zhang, H., Panigrahi, A. K., McNerney, R., Brosch, R., Clark, T. G., Behr, M. A., 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(1). https://doi.org/10.1038/srep15443

Kanji, A., Hasan, Z., Ali, A., McNerney, R., Mallard, K., Coll, F., Hill-Cawthorne, G., Nair, M., Clark, T. G., Zaver, A., 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), 73–79. https://doi.org/10.1016/j.ijmyco.2014.11.049

Perdigão, J., Silva, H., Machado, D., Macedo, R., Maltez, F., Silva, C., Jordao, L., Couto, I., Mallard, K., Coll, F., Hill-Cawthorne, G. A., McNerney, R., Pain, A., Clark, T. G., Viveiros, M., & Portugal, I. (2014). Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-991

Coll, F., Preston, M., Guerra-Assunção, J. A., Hill-Cawthorn, G., Harris, D., Perdigão, J., Viveiros, M., Portugal, I., Drobniewski, F., Gagneux, S., Glynn, J. R., Pain, A., Parkhill, J., McNerney, R., Martin, N., & Clark, T. G. (2014). PolyTB: A genomic variation map for Mycobacterium tuberculosis. Tuberculosis, 94(3), 346–354. https://doi.org/10.1016/j.tube.2014.02.005

Coll, F., McNerney, R., Guerra-Assunção, J. A., Glynn, J. R., Perdigão, J., Viveiros, M., Portugal, I., Pain, A., Martin, N., & Clark, T. G. (2014). A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications, 5(1). https://doi.org/10.1038/ncomms5812

Guerra-Assunção, J. A., Houben, R. M. G. J., Crampin, A. C., Mzembe, T., Mallard, K., Coll, F., Khan, P., Banda, L., Chiwaya, A., Pereira, R. P. A., McNerney, R., Harris, D., Parkhill, J., Clark, T. G., & Glynn, J. R. (2014). Recurrence due to Relapse or Reinfection WithMycobacterium tuberculosis: A Whole-Genome Sequencing Approach in a Large, Population-Based Cohort With a High HIV Infection Prevalence and Active Follow-up. Journal of Infectious Diseases, 211(7), 1154–1163. https://doi.org/10.1093/infdis/jiu574

Bergval, I., Coll, F., Schuitema, A., de Ronde, H., Mallard, K., Pain, A., McNerney, R., Clark, T. G., & Anthony, R. M. (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), 1–7. https://doi.org/10.1093/femsle/fnu037

Clark, T. G., Mallard, K., Coll, F., Preston, M., Assefa, S., Harris, D., Ogwang, S., Mumbowa, F., Kirenga, B., O’Sullivan, D. M., Okwera, A., Eisenach, K. D., Joloba, M., Bentley, S. D., Ellner, J. J., Parkhill, J., Jones-López, E. C., & McNerney, R. (2013). Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing. PLoS ONE, 8(12), e83012. https://doi.org/10.1371/journal.pone.0083012

Coll, F., Mallard, K., Preston, M. D., Bentley, S., Parkhill, J., McNerney, R., Martin, N., & Clark, T. G. (2012). SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics, 28(22), 2991–2993. https://doi.org/10.1093/bioinformatics/bts544