Gomez-Gonzalez, Paula J; Andreu, Nuria; Phelan, Jody E; de Sessions, Paola Florez; Glynn, Judith R; Crampin, Amelia C; Campino, Susana; Butcher, Philip D; Hibberd, Martin L; Clark, Taane G; (2019) An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome. SCIENTIFIC REPORTS, 9 (1). ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-41692-2

Campos, MC; Dombrowski, JG; Phelan, J; Marinho, CRF; Hibberd, M; Clark, TG; Campino, S; (2018) Zika might not be acting alone: Using an ecological study approach to investigate potential co-acting risk factors for an unusual pattern of microcephaly in Brazil. PloS one, 13 (8). e0201452. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0201452

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

Herman, LS; Fornace, K; Phelan, J; Grigg, MJ; Anstey, NM; William, T; Moon, RW; Blackman, MJ; Drakeley, CJ; Tetteh, KKA; (2018) Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure. PLoS neglected tropical diseases, 12 (6). e0006457. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0006457

Higgins, M; Ravenhall, M; Ward, D; Phelan, J; Ibrahim, A; Forrest, MS; Clark, TG; Campino, S; (2018) PrimedRPA: Primer design for Recombinase polymerase amplification assays. Bioinformatics (Oxford, England). ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bty701

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

Palittapongarnpim, P; Ajawatanawong, P; Viratyosin, W; Smittipat, N; Disratthakit, A; Mahasirimongkol, S; Yanai, H; Yamada, N; Nedsuwan, S; Imasanguan, W; +13 more... Kantipong, P; Chaiyasirinroje, B; Wongyai, J; Toyo-Oka, L; Phelan, J; Parkhill, J; Clark, TG; Hibberd, ML; Ruengchai, W; Palittapongarnpim, P; Juthayothin, T; Tongsima, S; Tokunaga, K; (2018) Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. Scientific reports, 8 (1). p. 11597. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-29986-3

Phelan, J; (2018) A bioinformatic analysis of Mycobacterium tuberculosis and host genomic data. PhD (research paper style) thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04646310

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

Portelli, S; Phelan, JE; Ascher, DB; Clark, TG; Furnham, N; (2018) Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Scientific reports, 8 (1). p. 15356. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-33370-6

Sepúlveda, N; Phelan, J; Diez-Benavente, E; Campino, S; Clark, TG; Hopkins, H; Sutherland, C; Drakeley, CJ; Beshir, KB; (2018) Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. Infection, genetics and evolution. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2018.04.039

Sobkowiak, B; Glynn, JR; Houben, RMGJ; Mallard, K; Phelan, JE; Guerra-Assunção, JA; Banda, L; Mzembe, T; Viveiros, M; McNerney, R; +3 more... Parkhill, J; Crampin, AC; Clark, TG; (2018) Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC genomics, 19 (1). p. 613. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-018-4988-z

C de Oliveira, T; Rodrigues, PT; Menezes, MJ; Gonçalves-Lopes, RM; Bastos, MS; Lima, NF; Barbosa, S; Gerber, AL; Loss de Morais, G; Berná, L; +5 more... Phelan, J; Robello, C; de Vasconcelos, ATR; Alves, JMP; Ferreira, MU; (2017) Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax. PLoS neglected tropical diseases, 11 (7). e0005824. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0005824

Campos, MC; Phelan, J; Francisco, AF; Taylor, MC; Lewis, MD; Pain, A; Clark, TG; Kelly, JM; (2017) Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole. Scientific reports, 7 (1). p. 14407. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-017-14986-6

Kanji, A; Hasan, R; Ali, A; Zaver, A; Zhang, Y; Imtiaz, K; Shi, W; Clark, TG; McNerney, R; Phelan, J; +3 more... Rao, S; Shafiq, S; Hasan, Z; (2017) Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan. Tuberculosis (Edinburgh, Scotland), 107 (Supple). pp. 20-30. ISSN 1472-9792 DOI: https://doi.org/10.1016/j.tube.2017.07.012 Full text not available from this repository.

Kanji, A; Hasan, R; Ali, A; Zaver, A; Zhang, Y; Imtiaz, K; Shi, W; Clark, TG; McNerney, R; Phelan, J; +3 more... Rao, S; Shafiq, S; Hasan, Z; (2017) Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan. Tuberculosis (Edinburgh, Scotland), 107. pp. 20-30. ISSN 1472-9792 DOI: https://doi.org/10.1016/j.tube.2017.07.012

Sengstake, S; Bergval, IL; Schuitema, AR; de Beer, JL; Phelan, J; de Zwaan, R; Clark, TG; van Soolingen, D; Anthony, RM; (2017) Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia. BMC infectious diseases, 17. ISSN 1471-2334 DOI: https://doi.org/10.1186/s12879-017-2594-3