Abdallah, Abdallah M; Hill-Cawthorne, Grant A; Otto, Thomas D; Coll, Francesc; Guerra-Assunção, José Afonso; Gao, Ge; Naeem, Raeece; Ansari, Hifzur; Malas, Tareq B; Adroub, Sabir A; +10 more... Verboom, Theo; Ummels, Roy; Zhang, Huoming; Panigrahi, Aswini Kumar; McNerney, Ruth; Brosch, Roland; Clark, Taane G; Behr, Marcel A; Bitter, Wilbert; Pain, Arnab; (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). 15443-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep15443

Ajawatanawong, Pravech; Yanai, Hideki; Smittipat, Nat; Disratthakit, Areeya; Yamada, Norio; Miyahara, Reiko; Nedsuwan, Supalert; Imasanguan, Worarat; Kantipong, Pacharee; Chaiyasirinroje, Boonchai; +16 more... Wongyai, Jiraporn; Plitphonganphim, Supada; Tantivitayakul, Pornpen; Phelan, Jody; Parkhill, Julian; Clark, Taane G; Hibberd, Martin L; Ruangchai, Wuthiwat; Palittapongarnpim, Panawun; Juthayothin, Tada; Thawornwattana, Yuttapong; Viratyosin, Wasna; Tongsima, Sissades; Mahasirimongkol, Surakameth; Tokunaga, Katsushi; Palittapongarnpim, Prasit; (2019) A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages. Scientific reports, 9 (1). 13718-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-50078-3

Ali, Asho; Hasan, Zahra; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant; Coll, Francesc; Nair, Mridul; Pain, Arnab; Clark, Taane G; Hasan, Rumina; (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

Almagro-Garcia, Jacob; Manske, Magnus; Carret, Celine; Campino, Susana; Auburn, Sarah; Macinnis, Bronwyn L; Maslen, Gareth; Pain, Arnab; Newbold, Christopher I; Kwiatkowski, Dominic P; +1 more... Clark, Taane G; (2009) SnoopCGH: software for visualizing comparative genomic hybridization data. Bioinformatics (Oxford, England), 25 (20). pp. 2732-2733. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btp488

Alsford, Sam; Currier, Rachel B; Guerra-Assunção, José Afonso; Clark, Taane G; Horn, David; (2014) Cathepsin-L can resist lysis by human serum in Trypanosoma brucei brucei. PLoS pathogens, 10 (5). e1004130-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1004130

Andreu, Nuria; Phelan, Jody; de Sessions, Paola F; Cliff, Jacqueline M; Clark, Taane G; Hibberd, Martin L; (2017) Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. Scientific reports, 7 (1). 42225-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep42225

Ansari, Hifzur Rahman; Templeton, Thomas J; Subudhi, Amit Kumar; Ramaprasad, Abhinay; Tang, Jianxia; Lu, Feng; Naeem, Raeece; Hashish, Yasmeen; Oguike, Mary C; Benavente, Ernest Diez; +6 more... Clark, Taane G; Sutherland, Colin J; Barnwell, John W; Culleton, Richard; Cao, Jun; Pain, Arnab; (2016) Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species. International journal for parasitology, 46 (11). pp. 685-696. ISSN 0020-7519 DOI: https://doi.org/10.1016/j.ijpara.2016.05.009

Assefa, Samuel A; Preston, Mark D; Campino, Susana; Ocholla, Harold; Sutherland, Colin J; Clark, Taane G; (2014) estMOI: estimating multiplicity of infection using parasite deep sequencing data. Bioinformatics (Oxford, England), 30 (9). pp. 1292-1294. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btu005

Assefa, Samuel; Lim, Caeul; Preston, Mark D; Duffy, Craig W; Nair, Mridul B; Adroub, Sabir A; Kadir, Khamisah A; Goldberg, Jonathan M; Neafsey, Daniel E; Divis, Paul; +5 more... Clark, Taane G; Duraisingh, Manoj T; Conway, David J; Pain, Arnab; Singh, Balbir; (2015) Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi. Proceedings of the National Academy of Sciences of the United States of America, 112 (42). pp. 13027-13032. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1509534112

Attia, Itzhak Zachi; Tseng, Andrew S; Benavente, Ernest Diez; Medina-Inojosa, Jose R; Clark, Taane G; Malyutina, Sofia; Kapa, Suraj; Schirmer, Henrik; Kudryavtsev, Alexander V; Noseworthy, Peter A; +6 more... Carter, Rickey E; Ryabikov, Andrew; Perel, Pablo; Friedman, Paul A; Leon, David A; Lopez-Jimenez, Francisco; (2021) External validation of a deep learning electrocardiogram algorithm to detect ventricular dysfunction. International journal of cardiology, 329. pp. 130-135. ISSN 0167-5273 DOI: https://doi.org/10.1016/j.ijcard.2020.12.065

Auburn, Sarah; Benavente, Ernest D; Miotto, Olivo; Pearson, Richard D; Amato, Roberto; Grigg, Matthew J; Barber, Bridget E; William, Timothy; Handayuni, Irene; Marfurt, Jutta; +9 more... Trimarsanto, Hidayat; Noviyanti, Rintis; Sriprawat, Kanlaya; Nosten, Francois; Campino, Susana; Clark, Taane G; Anstey, Nicholas M; Kwiatkowski, Dominic P; Price, Ric N; (2018) Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics. Nature communications, 9 (1). 2585-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-018-04965-4

Auburn, Sarah; Campino, Susana; Clark, Taane G; Djimde, Abdoulaye A; Zongo, Issaka; Pinches, Robert; Manske, Magnus; Mangano, Valentina; Alcock, Daniel; Anastasi, Elisa; +8 more... Maslen, Gareth; Macinnis, Bronwyn; Rockett, Kirk; Modiano, David; Newbold, Christopher I; Doumbo, Ogobara K; Ouédraogo, Jean Bosco; Kwiatkowski, Dominic P; (2011) An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing. PLOS ONE, 6 (7). e22213-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0022213

Auburn, Sarah; Campino, Susana; Miotto, Olivo; Djimde, Abdoulaye A; Zongo, Issaka; Manske, Magnus; Maslen, Gareth; Mangano, Valentina; Alcock, Daniel; MacInnis, Bronwyn; +5 more... Rockett, Kirk A; Clark, Taane G; Doumbo, Ogobara K; Ouédraogo, Jean Bosco; Kwiatkowski, Dominic P; (2012) Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. PloS one, 7 (2). e32891-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0032891

Auburn, Sarah; Fry, Andrew E; Clark, Taane G; Campino, Susana; Diakite, Mahamadou; Green, Angela; Richardson, Anna; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; +5 more... Molyneux, Malcolm E; Taylor, Terrie E; Haldar, Kasturi; Rockett, Kirk A; Kwiatkowski, Dominic P; (2010) Further evidence supporting a role for gs signal transduction in severe malaria pathogenesis. PloS one, 5 (4). e10017-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0010017

Auburn, Sarah; Marfurt, Jutta; Maslen, Gareth; Campino, Susana; Ruano Rubio, Valentin; Manske, Magnus; Machunter, Barbara; Kenangalem, Enny; Noviyanti, Rintis; Trianty, Leily; +12 more... Sebayang, Boni; Wirjanata, Grennady; Sriprawat, Kanlaya; Alcock, Daniel; Macinnis, Bronwyn; Miotto, Olivo; Clark, Taane G; Russell, Bruce; Anstey, Nicholas M; Nosten, François; Kwiatkowski, Dominic P; Price, Ric N; (2013) Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing. PloS one, 8 (1). e53160-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0053160

Band, Gavin; Le, Quang Si; Jostins, Luke; Pirinen, Matti; Kivinen, Katja; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bojang, Kalifa; Pinder, Margaret; Sirugo, Giorgio; +25 more... Conway, David J; Nyirongo, Vysaul; Kachala, David; Molyneux, Malcolm; Taylor, Terrie; Ndila, Carolyne; Peshu, Norbert; Marsh, Kevin; Williams, Thomas N; Alcock, Daniel; Andrews, Robert; Edkins, Sarah; Gray, Emma; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Schuldt, Kathrin; Clark, Taane G; Small, Kerrin S; Teo, Yik Ying; Kwiatkowski, Dominic P; Rockett, Kirk A; Barrett, Jeffrey C; Spencer, Chris CA; Malaria Genomic Epidemiology Network; (2013) Imputation-based meta-analysis of severe malaria in three African populations. PLoS genetics, 9 (5). e1003509-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1003509

Benavente, Ernest D; Coll, Francesc; Furnham, Nick; McNerney, Ruth; Glynn, Judith R; Campino, Susana; Pain, Arnab; Mohareb, Fady R; Clark, Taane G; (2015) PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics, 16 (1). 155-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-015-0603-3

Benavente, Ernest Diez; Gomes, Ana Rita; De Silva, Jeremy Ryan; Grigg, Matthew; Walker, Harriet; Barber, Bridget E; William, Timothy; Yeo, Tsin Wen; de Sessions, Paola Florez; Ramaprasad, Abhinay; +10 more... Ibrahim, Amy; Charleston, James; Hibberd, Martin L; Pain, Arnab; Moon, Robert W; Auburn, Sarah; Ling, Lau Yee; Anstey, Nicholas M; Clark, Taane G; Campino, Susana; (2019) Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations. Scientific reports, 9 (1). 9873-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-46398-z

Benavente, Ernest Diez; Manko, Emilia; Phelan, Jody; Campos, Monica; Nolder, Debbie; Fernandez, Diana; Velez-Tobon, Gabriel; Castaño, Alberto Tobón; Dombrowski, Jamille G; Marinho, Claudio RF; +8 more... Aguiar, Anna Caroline C; Pereira, Dhelio Batista; Sriprawat, Kanlaya; Nosten, Francois; Moon, Robert; Sutherland, Colin J; Campino, Susana; Clark, Taane G; (2021) Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa. Nature communications, 12 (1). p. 3160. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-021-23422-3

Benavente, Ernest Diez; Oresegun, Damilola R; de Sessions, Paola Florez; Walker, Eloise M; Roper, Cally; Dombrowski, Jamille G; de Souza, Rodrigo M; Marinho, Claudio RF; Sutherland, Colin J; Hibberd, Martin L; +4 more... Mohareb, Fady; Baker, David A; Clark, Taane G; Campino, Susana; (2018) Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development. Scientific reports, 8 (1). 15429-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-33767-3

Benavente, Ernest Diez; de Sessions, Paola Florez; Moon, Robert W; Grainger, Munira; Holder, Anthony A; Blackman, Michael J; Roper, Cally; Drakeley, Christopher J; Pain, Arnab; Sutherland, Colin J; +3 more... Hibberd, Martin L; Campino, Susana; Clark, Taane G; (2017) A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line. International journal for parasitology, 48 (3-4). pp. 191-196. ISSN 0020-7519 DOI: https://doi.org/10.1016/j.ijpara.2017.09.008

Bergval, Indra; Coll, Francesc; Schuitema, Anja; de Ronde, Hans; Mallard, Kim; Pain, Arnab; McNerney, Ruth; Clark, Taane G; Anthony, Richard 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). pp. 1-7. ISSN 0378-1097 DOI: https://doi.org/10.1093/femsle/fnu037

Bhatia, M; Howard, SC; Clark, TG; Neale, R; Qizilbash, N; Murphy, MFG; Rothwell, PM; (2006) Apolipoproteins as predictors of ischaemic stroke in patients with a previous transient ischaemic attack. Cerebrovascular diseases (Basel, Switzerland), 21 (5-6). pp. 323-328. ISSN 1015-9770 DOI: https://doi.org/10.1159/000091537 Full text not available from this repository.

Borley, Neil R; Mortensen, Neil J McC; Chaudry, Mohammed A; Mohammed, Said; Warren, Bryan F; George, Bruce D; Clark, Taane; Jewell, Derek P; Kettlewell, Michael GW; (2002) Recurrence after abdominal surgery for Crohn's disease: relationship to disease site and surgical procedure. Diseases of the colon and rectum, 45 (3). pp. 377-383. ISSN 0012-3706 DOI: https://doi.org/10.1007/s10350-004-6186-0 Full text not available from this repository.

Borrmann, Steffen; Straimer, Judith; Mwai, Leah; Abdi, Abdirahman; Rippert, Anja; Okombo, John; Muriithi, Steven; Sasi, Philip; Kortok, Moses Mosobo; Lowe, Brett; +10 more... Campino, Susana; Assefa, Samuel; Auburn, Sarah; Manske, Magnus; Maslen, Gareth; Peshu, Norbert; Kwiatkowski, Dominic P; Marsh, Kevin; Nzila, Alexis; Clark, Taane G; (2013) Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya. SCIENTIFIC REPORTS, 3 (1). 3318-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep03318

Bradburn, MJ; Clark, TG; Love, SB; Altman, DG; (2003) Survival analysis part II: multivariate data analysis--an introduction to concepts and methods. British journal of cancer, 89 (3). pp. 431-436. ISSN 0007-0920 DOI: https://doi.org/10.1038/sj.bjc.6601119

Bradburn, MJ; Clark, TG; Love, SB; Altman, DG; (2003) Survival analysis Part III: multivariate data analysis -- choosing a model and assessing its adequacy and fit. British journal of cancer, 89 (4). pp. 605-611. ISSN 0007-0920 DOI: https://doi.org/10.1038/sj.bjc.6601120

Briggs, Andrew; Clark, Taane; Wolstenholme, Jane; Clarke, Philip; (2003) Missing... presumed at random: cost-analysis of incomplete data. Health economics, 12 (5). pp. 377-392. ISSN 1057-9230 DOI: https://doi.org/10.1002/hec.766 Full text not available from this repository.

Brynildsrud, Ola B; Pepperell, Caitlin S; Suffys, Philip; Grandjean, Louis; Monteserin, Johana; Debech, Nadia; Bohlin, Jon; Alfsnes, Kristian; Pettersson, John O-H; Kirkeleite, Ingerid; +20 more... Fandinho, Fatima; da Silva, Marcia Aparecida; Perdigao, Joao; Portugal, Isabel; Viveiros, Miguel; Clark, Taane; Caws, Maxine; Dunstan, Sarah; Thai, Phan Vuong Khac; Lopez, Beatriz; Ritacco, Viviana; Kitchen, Andrew; Brown, Tyler S; van Soolingen, Dick; O'Neill, Mary B; Holt, Kathryn E; Feil, Edward J; Mathema, Barun; Balloux, Francois; Eldholm, Vegard; (2018) Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. SCIENCE ADVANCES, 4 (10). eaat5869-. ISSN 2375-2548 DOI: https://doi.org/10.1126/sciadv.aat5869

Cairns, MD; Preston, MD; Lawley, TD; Clark, TG; Stabler, RA; Wren, BW; (2015) Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England. Journal of clinical microbiology, 53 (10). pp. 3141-3147. ISSN 0095-1137 DOI: https://doi.org/10.1128/JCM.00648-15

Campino, Susana; Auburn, Sarah; Kivinen, Katja; Zongo, Issaka; Ouedraogo, Jean-Bosco; Mangano, Valentina; Djimde, Abdoulaye; Doumbo, Ogobara K; Kiara, Steven M; Nzila, Alexis; +21 more... Borrmann, Steffen; Marsh, Kevin; Michon, Pascal; Mueller, Ivo; Siba, Peter; Jiang, Hongying; Su, Xin-Zhuan; Amaratunga, Chanaki; Socheat, Duong; Fairhurst, Rick M; Imwong, Mallika; Anderson, Timothy; Nosten, François; White, Nicholas J; Gwilliam, Rhian; Deloukas, Panos; MacInnis, Bronwyn; Newbold, Christopher I; Rockett, Kirk; Clark, Taane G; Kwiatkowski, Dominic P; (2011) Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay. PloS one, 6 (6). e20251-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0020251

Campino, Susana; Benavente, Ernest Diez; Assefa, Samuel; Thompson, Eloise; Drought, Laura G; Taylor, Catherine J; Gorvett, Zaria; Carret, Celine K; Flueck, Christian; Ivens, Al C; +4 more... Kwiatkowski, Dominic P; Alano, Pietro; Baker, David A; Clark, Taane G; (2016) Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines. Malaria journal, 15 (1). 229-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-016-1254-1

Campino, Susana; Forton, Julian; Auburn, Sarah; Fry, Andrew; Diakite, Mahamadou; Richardson, Anna; Hull, Jeremy; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; +5 more... Molyneux, Malcolm E; Taylor, Terrie E; Rockett, Kirk; Clark, Taane G; Kwiatkowski, Dominic P; (2009) TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expression. Malaria journal, 8 (1). 44-. ISSN 1475-2875 DOI: https://doi.org/10.1186/1475-2875-8-44

Campino, Susana; Forton, Julian; Raj, Srilakshmi; Mohr, Bert; Auburn, Sarah; Fry, Andrew; Mangano, Valentina D; Vandiedonck, Claire; Richardson, Anna; Rockett, Kirk; +2 more... Clark, Taane G; Kwiatkowski, Dominic P; (2008) Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations. PloS one, 3 (12). e4105-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0004105

Campino, Susana; Marin-Menendez, Alejandro; Kemp, Alison; Cross, Nadia; Drought, Laura; Otto, Thomas D; Benavente, Ernest Diez; Ravenhall, Matt; Schwach, Frank; Girling, Gareth; +8 more... Manske, Magnus; Theron, Michel; Gould, Kelda; Drury, Eleanor; Clark, Taane G; Kwiatkowski, Dominic P; Pance, Alena; Rayner, Julian C; (2018) A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways. PLoS pathogens, 14 (11). e1007436-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1007436

Campos, Monica C; Dombrowski, Jamille G; Phelan, Jody; Marinho, Claudio RF; Hibberd, Martin; Clark, Taane G; Campino, Susana; (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

Campos, Monica; Ward, Daniel; Morales, Raika Francesca; Gomes, Ana Rita; Silva, Keily; Sepúlveda, Nuno; Gomez, Lara Ferrero; Clark, Taane G; Campino, Susana; (2020) Surveillance of Aedes aegypti populations in the city of Praia, Cape Verde: Zika virus infection, insecticide resistance and genetic diversity. PARASITES & VECTORS, 13 (1). 481-. ISSN 1756-3305 DOI: https://doi.org/10.1186/s13071-020-04356-z

Campos, Mônica C; Phelan, Jody; Francisco, Amanda F; Taylor, Martin C; Lewis, Michael D; Pain, Arnab; Clark, Taane G; Kelly, John M; (2017) Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole. Scientific reports, 7 (1). 14407-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-017-14986-6

Carroll, Robert P; Segundo, David San; Hollowood, Kevin; Marafioti, Teresa; Clark, Taane G; Harden, Paul N; Wood, Kathryn J; (2010) Immune phenotype predicts risk for posttransplantation squamous cell carcinoma. Journal of the American Society of Nephrology, 21 (4). pp. 713-722. ISSN 1046-6673 DOI: https://doi.org/10.1681/ASN.2009060669 Full text not available from this repository.

Clark, TG; Bradburn, MJ; Love, SB; Altman, DG; (2003) Survival analysis part I: basic concepts and first analyses. British journal of cancer, 89 (2). pp. 232-238. ISSN 0007-0920 DOI: https://doi.org/10.1038/sj.bjc.6601118

Clark, TG; Bradburn, MJ; Love, SB; Altman, DG; (2003) Survival analysis part IV: further concepts and methods in survival analysis. British journal of cancer, 89 (5). pp. 781-786. ISSN 0007-0920 DOI: https://doi.org/10.1038/sj.bjc.6601117

Clark, TG; Murphy, MFG; Rothwell, PM; (2003) Long term risks of stroke, myocardial infarction, and vascular death in "low risk" patients with a non-recent transient ischaemic attack. Journal of neurology, neurosurgery, and psychiatry, 74 (5). pp. 577-580. ISSN 0022-3050 DOI: https://doi.org/10.1136/jnnp.74.5.577 Full text not available from this repository.

Clark, TG; Stewart, ME; Altman, DG; Gabra, H; Smyth, JF; (2001) A prognostic model for ovarian cancer. British journal of cancer, 85 (7). pp. 944-952. ISSN 0007-0920 DOI: https://doi.org/10.1054/bjoc.2001.2030

Clark, Taane G; Altman, Douglas G; (2003) Developing a prognostic model in the presence of missing data: an ovarian cancer case study. Journal of clinical epidemiology, 56 (1). pp. 28-37. ISSN 0895-4356 DOI: https://doi.org/10.1016/s0895-4356(02)00539-5 Full text not available from this repository.

Clark, Taane G; Altman, Douglas G; De Stavola, Bianca L; (2002) Quantification of the completeness of follow-up. Lancet, 359 (9314). pp. 1309-1310. ISSN 0140-6736 DOI: https://doi.org/10.1016/s0140-6736(02)08272-7 Full text not available from this repository.

Clark, Taane G; Andrew, Toby; Cooper, Gregory M; Margulies, Elliott H; Mullikin, James C; Balding, David J; (2007) Functional constraint and small insertions and deletions in the ENCODE regions of the human genome. Genome biology, 8 (9). R180-. ISSN 1465-6906 DOI: https://doi.org/10.1186/gb-2007-8-9-r180

Clark, Taane G; Campino, Susana G; Anastasi, Elisa; Auburn, Sarah; Teo, Yik Y; Small, Kerrin; Rockett, Kirk A; Kwiatkowski, Dominic P; Holmes, Christopher C; (2010) A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals. Bioinformatics (Oxford, England), 26 (16). pp. 1999-2003. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btq327 Full text not available from this repository.

Clark, Taane G; De Iorio, Maria; Griffiths, Robert C; (2007) Bayesian logistic regression using a perfect phylogeny. Biostatistics (Oxford, England), 8 (1). pp. 32-52. ISSN 1465-4644 DOI: https://doi.org/10.1093/biostatistics/kxj030 Full text not available from this repository.

Clark, Taane G; De Iorio, Maria; Griffiths, Robert C; Farrall, Martin; (2005) Finding associations in dense genetic maps: a genetic algorithm approach. Human heredity, 60 (2). pp. 97-108. ISSN 0001-5652 DOI: https://doi.org/10.1159/000088845 Full text not available from this repository.

Clark, Taane G; De Iorio, Maria; Griffths, Robert C; (2008) An Evolutionary Algorithm to Find Associations in Dense Genetic Maps. Ieee Transactions on Evolutionary Computation, 12 (3). pp. 297-306. ISSN 1089-778X DOI: https://doi.org/10.1109/tevc.2007.900984 Full text not available from this repository.

Clark, Taane G; Diakite, Mahamadou; Auburn, Sarah; Campino, Susana; Fry, Andrew E; Green, Angela; Richardson, Anna; Small, Kerrin; Teo, Yik Y; Wilson, Jonathan; +11 more... Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Griffiths, Michael J; Peshu, Norbert; Williams, Thomas N; Marsh, Kevin; Molyneux, Malcolm E; Taylor, Terrie E; Rockett, Kirk A; Kwiatkowski, Dominic P; (2009) Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populations. The Journal of infectious diseases, 199 (4). pp. 569-575. ISSN 0022-1899 DOI: https://doi.org/10.1086/596320 Full text not available from this repository.

Clark, Taane G; Fry, Andrew E; Auburn, Sarah; Campino, Susana; Diakite, Mahamadou; Green, Angela; Richardson, Anna; Teo, Yik Y; Small, Kerrin; Wilson, Jonathan; +6 more... Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Sabeti, Pardis; Kwiatkowski, Dominic P; Rockett, Kirk A; (2009) Allelic heterogeneity of G6PD deficiency in West Africa and severe malaria susceptibility. European journal of human genetics, 17 (8). pp. 1080-1085. ISSN 1018-4813 DOI: https://doi.org/10.1038/ejhg.2009.8 Full text not available from this repository.

Clark, Taane G; Mallard, Kim; Coll, Francesc; Preston, Mark; Assefa, Samuel; Harris, David; Ogwang, Sam; Mumbowa, Francis; Kirenga, Bruce; O'Sullivan, Denise M; +8 more... Okwera, Alphonse; Eisenach, Kathleen D; Joloba, Moses; Bentley, Stephen D; Ellner, Jerrold J; Parkhill, Julian; Jones-López, Edward C; McNerney, Ruth; (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

Clark, Taane G; Murphy, Michael FG; Hey, Kate; Drury, Mark; Cheng, KK; Aveyard, Paul; (2006) Does smoking influence survival in cancer patients through effects on respiratory and vascular disease? European journal of cancer prevention, 15 (1). pp. 87-90. ISSN 0959-8278 DOI: https://doi.org/10.1097/01.cej.0000186634.81753.45 Full text not available from this repository.

Clark, Taane G; Stewart, Moira; Rye, Tzyvia; Smyth, John F; Gourley, Charlie; (2007) Validation of a new prognostic index for advanced epithelial ovarian cancer: results from its application to a UK-based cohort. Journal of clinical oncology, 25 (35). pp. 5669-5670. ISSN 0732-183X DOI: https://doi.org/10.1200/JCO.2007.14.2976 Full text not available from this repository.

Clarke, Geraldine M; Rockett, Kirk; Kivinen, Katja; Hubbart, Christina; Jeffreys, Anna E; Rowlands, Kate; Jallow, Muminatou; Conway, David J; Bojang, Kalifa A; Pinder, Margaret; +68 more... Usen, Stanley; Sisay-Joof, Fatoumatta; Sirugo, Giorgio; Toure, Ousmane; Thera, Mahamadou A; Konate, Salimata; Sissoko, Sibiry; Niangaly, Amadou; Poudiougou, Belco; Mangano, Valentina D; Bougouma, Edith C; Sirima, Sodiomon B; Modiano, David; Amenga-Etego, Lucas N; Ghansah, Anita; Koram, Kwadwo A; Wilson, Michael D; Enimil, Anthony; Evans, Jennifer; Amodu, Olukemi K; Olaniyan, Subulade; Apinjoh, Tobias; Mugri, Regina; Ndi, Andre; Ndila, Carolyne M; Uyoga, Sophie; Macharia, Alexander; Peshu, Norbert; Williams, Thomas N; Manjurano, Alphaxard; Sepúlveda, Nuno; Clark, Taane G; Riley, Eleanor; Drakeley, Chris; Reyburn, Hugh; Nyirongo, Vysaul; Kachala, David; Molyneux, Malcolm; Dunstan, Sarah J; Phu, Nguyen Hoan; Quyen, Nguyen Ngoc; Thai, Cao Quang; Hien, Tran Tinh; Manning, Laurens; Laman, Moses; Siba, Peter; Karunajeewa, Harin; Allen, Steve; Allen, Angela; Davis, Timothy Me; Michon, Pascal; Mueller, Ivo; Molloy, Síle F; Campino, Susana; Kerasidou, Angeliki; Cornelius, Victoria J; Hart, Lee; Shah, Shivang S; Band, Gavin; Spencer, Chris Ca; Agbenyega, Tsiri; Achidi, Eric; Doumbo, Ogobara K; Farrar, Jeremy; Marsh, Kevin; Taylor, Terrie; Kwiatkowski, Dominic P; MalariaGEN Consortium; (2017) Characterisation of the opposing effects of G6PD deficiency on cerebral malaria and severe malarial anaemia. eLife, 6. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.15085

Cliff, Jacqueline M; Lee, Ji-Sook; Constantinou, Nicholas; Cho, Jang-Eun; Clark, Taane G; Ronacher, Katharina; King, Elizabeth C; Lukey, Pauline T; Duncan, Ken; Van Helden, Paul D; +2 more... Walzl, Gerhard; Dockrell, Hazel M; (2012) Distinct phases of blood gene expression pattern through tuberculosis treatment reflect modulation of the humoral immune response. The Journal of infectious diseases, 207 (1). pp. 18-29. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jis499 Full text not available from this repository.

Coker, Olabisi Oluwabukola; Chaiprasert, Angkana; Ngamphiw, Chumpol; Tongsima, Sissades; Regmi, Sanjib Mani; Clark, Taane G; Ong, Rick Twee Hee; Teo, Yik-Ying; Prammananan, Therdsak; Palittapongarnpim, Prasit; (2016) Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand. PeerJ, 4 (4). e1905-. ISSN 2167-8359 DOI: https://doi.org/10.7717/peerj.1905

Coll, Francesc; Mallard, Kim; Preston, Mark D; Bentley, Stephen; Parkhill, Julian; McNerney, Ruth; Martin, Nigel; Clark, Taane G; (2012) SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics (Oxford, England), 28 (22). pp. 2991-2993. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bts544

Coll, Francesc; McNerney, Ruth; Guerra-Assunção, José Afonso; Glynn, Judith R; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Pain, Arnab; Martin, Nigel; Clark, Taane G; (2014) A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature communications, 5 (1). 4812-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms5812

Coll, Francesc; McNerney, Ruth; Preston, Mark D; Guerra-Assunção, José Afonso; Warry, Andrew; Hill-Cawthorne, Grant; Mallard, Kim; Nair, Mridul; Miranda, Anabela; Alves, Adriana; +9 more... Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Hasan, Zahra; Hasan, Rumina; Glynn, Judith R; Martin, Nigel; Pain, Arnab; Clark, Taane G; (2015) Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome medicine, 7 (1). 51-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-015-0164-0

Coll, Francesc; Phelan, Jody; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; Ali, Shahjahan; Abdallah, Abdallah M; Alghamdi, Saad; Alsomali, Mona; Ahmed, Abdallah O; +41 more... Portelli, Stephanie; Oppong, Yaa; Alves, Adriana; Bessa, Theolis Barbosa; Campino, Susana; Caws, Maxine; Chatterjee, Anirvan; Crampin, Amelia C; Dheda, Keertan; Furnham, Nicholas; Glynn, Judith R; Grandjean, Louis; Minh Ha, Dang; Hasan, Rumina; Hasan, Zahra; Hibberd, Martin L; Joloba, Moses; Jones-López, Edward C; Matsumoto, Tomoshige; Miranda, Anabela; Moore, David J; Mocillo, Nora; Panaiotov, Stefan; Parkhill, Julian; Penha, Carlos; Perdigão, João; Portugal, Isabel; Rchiad, Zineb; Robledo, Jaime; Sheen, Patricia; Shesha, Nashwa Talaat; Sirgel, Frik A; Sola, Christophe; Oliveira Sousa, Erivelton; Streicher, Elizabeth M; Helden, Paul Van; Viveiros, Miguel; Warren, Robert M; McNerney, Ruth; Pain, Arnab; Clark, Taane G; (2018) Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature genetics, 50 (2). pp. 307-316. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-017-0029-0

Coll, Francesc; Phelan, Jody; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; Ali, Shahjahan; Abdallah, Abdallah M; Alghamdi, Saad; Alsomali, Mona; Ahmed, Abdallah O; +41 more... Portelli, Stephanie; Oppong, Yaa; Alves, Adriana; Bessa, Theolis Barbosa; Campino, Susana; Caws, Maxine; Chatterjee, Anirvan; Crampin, Amelia C; Dheda, Keertan; Furnham, Nicholas; Glynn, Judith R; Grandjean, Louis; Ha, Dang Minh; Hasan, Rumina; Hasan, Zahra; Hibberd, Martin L; Joloba, Moses; Jones-López, Edward C; Matsumoto, Tomoshige; Miranda, Anabela; Moore, David J; Mocillo, Nora; Panaiotov, Stefan; Parkhill, Julian; Penha, Carlos; Perdigão, João; Portugal, Isabel; Rchiad, Zineb; Robledo, Jaime; Sheen, Patricia; Shesha, Nashwa Talaat; Sirgel, Frik A; Sola, Christophe; Sousa, Erivelton Oliveira; Streicher, Elizabeth M; Van Helden, Paul; Viveiros, Miguel; Warren, Robert M; McNerney, Ruth; Pain, Arnab; Clark, Taane G; (2018) Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature genetics, 50 (5). 764-. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-018-0074-3 Full text not available from this repository.

Coll, Francesc; Preston, Mark; Guerra-Assunção, José Afonso; Hill-Cawthorn, Grant; Harris, David; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Drobniewski, Francis; Gagneux, Sebastien; +6 more... Glynn, Judith R; Pain, Arnab; Parkhill, Julian; McNerney, Ruth; Martin, Nigel; Clark, Taane G; (2014) PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland), 94 (3). pp. 346-354. ISSN 1472-9792 DOI: https://doi.org/10.1016/j.tube.2014.02.005

Cook, Sarah; Malyutina, Sofia; Kudryavtsev, Alexander V; Averina, Maria; Bobrova, Natalia; Boytsov, Sergey; Brage, Soren; Clark, Taane G; Diez Benavente, Ernest; Eggen, Anne Elise; +26 more... Hopstock, Laila A; Hughes, Alun; Johansen, Heidi; Kholmatova, Kamila; Kichigina, Anastasiya; Kontsevaya, Anna; Kornev, Michael; Leong, Darryl; Magnus, Per; Mathiesen, Ellisiv; McKee, Martin; Morgan, Katy; Nilssen, Odd; Plakhov, Ilya; Quint, Jennifer K; Rapala, Alicja; Ryabikov, Andrey; Saburova, Lyudmila; Schirmer, Henrik; Shapkina, Marina; Shiekh, Suhail; Shkolnikov, Vladimir M; Stylidis, Michael; Voevoda, Michael; Westgate, Kate; Leon, David A; (2018) Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18. Wellcome open research, 3. 67-. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.14619.3

Cook, Sarah; Malyutina, Sofia; Kudryavtsev, Alexander V; Averina, Maria; Bobrova, Natalia; Boytsov, Sergey; Brage, Soren; Clark, Taane G; Diez Benavente, Ernest; Eggen, Anne Elise; +26 more... Hopstock, Laila A; Hughes, Alun; Johansen, Heidi; Kholmatova, Kamila; Kichigina, Anastasiya; Kontsevaya, Anna; Kornev, Michael; Leong, Darryl; Magnus, Per; Mathiesen, Ellisiv; McKee, Martin; Morgan, Katy; Nilssen, Odd; Plakhov, Ilya; Quint, Jennifer K; Rapala, Alicja; Ryabikov, Andrey; Saburova, Lyudmila; Schirmer, Henrik; Shapkina, Marina; Shiekh, Suhail; Shkolnikov, Vladimir M; Stylidis, Michael; Voevoda, Michael; Westgate, Kate; Leon, David A; (2018) Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18. Wellcome Open Research, 3. 67-. DOI: https://doi.org/10.12688/wellcomeopenres.14619.3

Cook, Sarah; Malyutina, Sofia; Kudryavtsev, Alexander; Averina, Maria; Bobrova, Natalia; Boytsov, Sergey; Brage, Soren; Clark, Taane; Diez Benavente, Ernest; Eggen, Anne Elise; +26 more... Hopstock, Laila; Hughes, Alun; Johansen, Heidi; Kholmatova, Kamila; Kichigina, Anastasiya; Kontsevaya, Anna; Kornev, Michael; Leong, Darryl; Magnus, Per; Mathiesen, Ellisiv; McKee, Martin; Morgan, Katy; Nilssen, Odd; Plakhov, Ilya; Quint, Jennifer; Rapala, Alicja; Ryabikov, Andrey; Saburova, Lyudmila; Schirmer, Henrik; Shapkina, Marina; Shiekh, Suhail; Shkolnikov, Vladimir; Stylidis, Michael; Voevoda, Michael; Westgate, Kate; Leon, David; (2018) Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18. Wellcome Open Research. ISSN 2398-502X DOI: https://doi.org/10.12688/wellcomeopenres.14619.3

Cook, Sarah; Malyutina, Sofia; Kudryavtsev, Alexander; Averina, Maria; Bobrova, Natalia; Boytsov, Sergey; Brage, Soren; Clark, Taane; Diez Benavente, Ernest; Eggen, Anne Elise; +26 more... Hopstock, Laila; Hughes, Alun; Johansen, Heidi; Kholmatova, Kamila; Kichigina, Anastasiya; Kontsevaya, Anna; Kornev, Michael; Leong, Darryl; Magnus, Per; Mathiesen, Ellisiv; McKee, Martin; Morgan, Katy; Nilssen, Odd; Plakhov, Ilya; Quint, Jennifer; Rapala, Alicja; Ryabikov, Andrey; Saburova, Lyudmila; Schirmer, Henrik; Shapkina, Marina; Shiekh, Suhail; Shkolnikov, Vladimir; Stylidis, Michael; Voevoda, Michael; Westgate, Kate; Leon, David; (2018) Know Your Heart: Rationale, design and conduct of a cross-sectional study of cardiovascular structure, function and risk factors in 4500 men and women aged 35-69 years from two Russian cities, 2015-18. Wellcome Open Research, 3. 67-67-. DOI: https://doi.org/10.12688/wellcomeopenres.14619.1

Costa, Sofia Santos; Sobkowiak, Benjamin; Parreira, Ricardo; Edgeworth, Jonathan D; Viveiros, Miguel; Clark, Taane G; Couto, Isabel; (2019) Genetic Diversity of norA, Coding for a Main Efflux Pump of Staphylococcus aureus. Frontiers in Genetics, 9 (JAN). 710-. ISSN 1664-8021 DOI: https://doi.org/10.3389/fgene.2018.00710

Da Veiga Leal, Silvania; Ward, Daniel; Campino, Susana; Benavente, Ernest Diez; Ibrahim, Amy; Claret, Tânia; Isaías, Varela; Monteiro, Davidson; Clark, Taane G; Gonçalves, Luzia; +4 more... Valdez, Tomas; da Luz Lima Mendonça, Maria; Silveira, Henrique; Nogueira, Fatima; (2021) Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: the 2017 malaria outbreak. Malaria journal, 20 (1). 172-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-021-03708-z

Daelemans, Caroline; Ritchie, Matthew E; Smits, Guillaume; Abu-Amero, Sayeda; Sudbery, Ian M; Forrest, Matthew S; Campino, Susana; Clark, Taane G; Stanier, Philip; Kwiatkowski, Dominic; +5 more... Deloukas, Panos; Dermitzakis, Emmanouil T; Tavaré, Simon; Moore, Gudrun E; Dunham, Ian; (2010) High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC genetics, 11 (1). 25-. ISSN 1471-2156 DOI: https://doi.org/10.1186/1471-2156-11-25

Dalla Costa, Elis R; Vasconcelos, Sidra EG; Esteves, Leonardo S; Gomes, Harrison M; Gomes, Lia L; da Silva, Pedro Almeida; Perdigão, João; Portugal, Isabel; Viveiros, Miguel; McNerney, Ruth; +6 more... Pain, Arnab; Clark, Taane G; Rastogi, Nalin; Unis, Gisela; Rossetti, Maria Lucia R; Suffys, Philip Noel; (2015) Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil. Journal of clinical microbiology, 53 (12). pp. 3805-3811. ISSN 0095-1137 DOI: https://doi.org/10.1128/JCM.02012-15 Full text not available from this repository.

Deelder, Wouter; Benavente, Ernest Diez; Phelan, Jody; Manko, Emilia; Campino, Susana; Palla, Luigi; Clark, Taane G; (2021) Using deep learning to identify recent positive selection in malaria parasite sequence data. Malaria journal, 20 (1). p. 270. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-021-03788-x

Deelder, Wouter; Christakoudi, Sofia; Phelan, Jody; Benavente, Ernest Diez; Campino, Susana; McNerney, Ruth; Palla, Luigi; Clark, Taane G; (2019) Machine Learning Predicts Accurately Mycobacterium tuberculosis Drug Resistance From Whole Genome Sequencing Data. Frontiers in Genetics, 10 (SEP). 922-. DOI: https://doi.org/10.3389/fgene.2019.00922

Dheda, Keertan; Gumbo, Tawanda; Maartens, Gary; Dooley, Kelly E; McNerney, Ruth; Murray, Megan; Furin, Jennifer; Nardell, Edward A; London, Leslie; Lessem, Erica; +32 more... Theron, Grant; van Helden, Paul; Niemann, Stefan; Merker, Matthias; Dowdy, David; Van Rie, Annelies; Siu, Gilman KH; Pasipanodya, Jotam G; Rodrigues, Camilla; Clark, Taane G; Sirgel, Frik A; Esmail, Aliasgar; Lin, Hsien-Ho; Atre, Sachin R; Schaaf, H Simon; Chang, Kwok Chiu; Lange, Christoph; Nahid, Payam; Udwadia, Zarir F; Horsburgh, C Robert; Churchyard, Gavin J; Menzies, Dick; Hesseling, Anneke C; Nuermberger, Eric; McIlleron, Helen; Fennelly, Kevin P; Goemaere, Eric; Jaramillo, Ernesto; Low, Marcus; Jara, Carolina Morán; Padayatchi, Nesri; Warren, Robin M; (2017) The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. The lancet Respiratory medicine, 5 (4). pp. 291-360. ISSN 2213-2600 DOI: https://doi.org/10.1016/S2213-2600(17)30079-6 Full text not available from this repository.

Dheda, Keertan; Limberis, Jason D; Pietersen, Elize; Phelan, Jody; Esmail, Aliasgar; Lesosky, Maia; Fennelly, Kevin P; Te Riele, Julian; Mastrapa, Barbara; Streicher, Elizabeth M; +13 more... Dolby, Tania; Abdallah, Abdallah M; Ben-Rached, Fathia; Simpson, John; Smith, Liezel; Gumbo, Tawanda; van Helden, Paul; Sirgel, Frederick A; McNerney, Ruth; Theron, Grant; Pain, Arnab; Clark, Taane G; Warren, Robin M; (2017) Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study. The lancet Respiratory medicine, 5 (4). pp. 269-281. ISSN 2213-2600 DOI: https://doi.org/10.1016/S2213-2600(16)30433-7 Full text not available from this repository.

Diakite, Mahamadou; Clark, Taane G; Auburn, Sarah; Campino, Susana; Fry, Andrew E; Green, Angela; Morris, Andrew P; Richardson, Anna; Jallow, Muminatou; Sisay-Joof, Fatou; +3 more... Pinder, Margaret; Kwiatkowski, Dominic P; Rockett, Kirk A; (2009) A genetic association study in the Gambia using tagging polymorphisms in the major histocompatibility complex class III region implicates a HLA-B associated transcript 2 polymorphism in severe malaria susceptibility. Human genetics, 125 (1). pp. 105-109. ISSN 0340-6717 DOI: https://doi.org/10.1007/s00439-008-0597-2 Full text not available from this repository.

Diakité, Seidina AS; Traoré, Karim; Sanogo, Ibrahim; Clark, Taane G; Campino, Susana; Sangaré, Modibo; Dabitao, Djeneba; Dara, Antoine; Konaté, Drissa S; Doucouré, Fousseyni; +9 more... Cissé, Amadou; Keita, Bourama; Doumbouya, Mory; Guindo, Merepen A; Toure, Mahamoudou B; Sogoba, Nafomon; Doumbia, Seydou; Awandare, Gordon A; Diakité, Mahamadou; (2019) A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali. Malaria journal, 18 (1). 361-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-019-2986-5

Diez Benavente, Ernest; Campos, Monica; Phelan, Jody; Nolder, Debbie; Dombrowski, Jamille G; Marinho, Claudio RF; Sriprawat, Kanlaya; Taylor, Aimee R; Watson, James; Roper, Cally; +4 more... Nosten, Francois; Sutherland, Colin J; Campino, Susana; Clark, Taane G; (2020) A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria. PLoS genetics, 16 (2). e1008576-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1008576

Diez Benavente, Ernest; Florez de Sessions, Paola; Moon, Robert W; Holder, Anthony A; Blackman, Michael J; Roper, Cally; Drakeley, Christopher J; Pain, Arnab; Sutherland, Colin J; Hibberd, Martin L; +2 more... Campino, Susana; Clark, Taane G; (2017) Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations. PLoS genetics, 13 (9). e1007008-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1007008

Diez Benavente, Ernest; Jimenez-Lopez, Francisco; Attia, Zachi I; Malyutina, Sofia; Kudryavtsev, Alexander; Ryabikov, Andrew; Friedman, Paul A; Kapa, Suraj; Voevoda, Michael; Perel, Pablo; +4 more... Schirmer, Henrik; Hughes, Alun D; Clark, Taane G; Leon, David A; (2021) Studying accelerated cardiovascular ageing in Russian adults through a novel deep-learning ECG biomarker. Wellcome Open Research, 6. p. 12. DOI: https://doi.org/10.12688/wellcomeopenres.16499.1

Diez Benavente, Ernest; Ward, Zoe; Chan, Wilson; Mohareb, Fady R; Sutherland, Colin J; Roper, Cally; Campino, Susana; Clark, Taane G; (2017) Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure. PloS one, 12 (5). e0177134-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0177134

Dombrowski, Jamille G; Souza, Rodrigo M; Curry, Jonathan; Hinton, Laura; Silva, Natercia RM; Grignard, Lynn; Gonçalves, Ligia A; Gomes, Ana Rita; Epiphanio, Sabrina; Drakeley, Chris; +4 more... Huggett, Jim; Clark, Taane G; Campino, Susana; Marinho, Claudio RF; (2017) G6PD deficiency alleles in a malaria-endemic region in the Western Brazilian Amazon. Malaria journal, 16 (1). 253-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-017-1889-6

Dombrowski, Jamille Gregório; Barateiro, André; Peixoto, Erika Paula Machado; Barros, André Boler Cláudio da Silva; Souza, Rodrigo Medeiros de; Clark, Taane Gregory; Campino, Susana; Wrenger, Carsten; Wunderlich, Gerhard; Palmisano, Giuseppe; +3 more... Epiphanio, Sabrina; Gonçalves, Lígia Antunes; Marinho, Claudio Romero Farias; (2021) Adverse pregnancy outcomes are associated with Plasmodium vivax malaria in a prospective cohort of women from the Brazilian Amazon. PLoS neglected tropical diseases, 15 (4). e0009390. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0009390

Dombrowski, Jamille Gregório; Souza, Rodrigo Medeiros de; Lima, Flávia Afonso; Bandeira, Carla Letícia; Murillo, Oscar; Costa, Douglas de Sousa; Peixoto, Erika Paula Machado; Cunha, Marielton Dos Passos; Zanotto, Paolo Marinho de Andrade; Bevilacqua, Estela; +8 more... Grisotto, Marcos Augusto Grigolin; Pedroso de Lima, Antonio Carlos; Singer, Julio da Motta; Campino, Susana; Clark, Taane Gregory; Epiphanio, Sabrina; Gonçalves, Lígia Antunes; Marinho, Cláudio Romero Farias; (2019) Association of Malaria Infection During Pregnancy With Head Circumference of Newborns in the Brazilian Amazon. JAMA network open, 2 (5). e193300-. ISSN 2574-3805 DOI: https://doi.org/10.1001/jamanetworkopen.2019.3300

Downing, Tim; Imamura, Hideo; Decuypere, Saskia; Clark, Taane G; Coombs, Graham H; Cotton, James A; Hilley, James D; de Doncker, Simonne; Maes, Ilse; Mottram, Jeremy C; +10 more... Quail, Mike A; Rijal, Suman; Sanders, Mandy; Schönian, Gabriele; Stark, Olivia; Sundar, Shyam; Vanaerschot, Manu; Hertz-Fowler, Christiane; Dujardin, Jean-Claude; Berriman, Matthew; (2011) Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome research, 21 (12). pp. 2143-2156. ISSN 1088-9051 DOI: https://doi.org/10.1101/gr.123430.111 Full text not available from this repository.

Doyle, Ronan M; O'Sullivan, Denise M; Aller, Sean D; Bruchmann, Sebastian; Clark, Taane; Coello Pelegrin, Andreu; Cormican, Martin; Diez Benavente, Ernest; Ellington, Matthew J; McGrath, Elaine; +11 more... Motro, Yair; Phuong Thuy Nguyen, Thi; Phelan, Jody; Shaw, Liam P; Stabler, Richard A; van Belkum, Alex; van Dorp, Lucy; Woodford, Neil; Moran-Gilad, Jacob; Huggett, Jim F; Harris, Kathryn A; (2020) Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. Microbial Genomics, 6 (2). DOI: https://doi.org/10.1099/mgen.0.000335

Doyle, Ronan M; O’Sullivan, Denise M; Aller, Sean D; Bruchmann, Sebastian; Clark, Taane; Pelegrin, Andreu Coello; Cormican, Martin; Benavente, Ernest Diez; Ellington, Matthew J; McGrath, Elaine; +11 more... Motro, Yair; Thuy Nguyen, Thi Phuong; Phelan, Jody; Shaw, Liam P; Stabler, Richard A; van Belkum, Alex; van Dorp, Lucy; Woodford, Neil; Moran-Gilad, Jacob; Huggett, Jim F; Harris, Kathryn A; (2019) Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study. BioRxiv. DOI: https://doi.org/10.1101/793885

Dunstan, SJ; Rockett, KA; Quyen, NTN; Teo, YY; Thai, CQ; Hang, NT; Jeffreys, A; Clark, TG; Small, KS; Simmons, CP; +7 more... Day, N; O'Riordan, SE; Kwiatkowski, DP; Farrar, J; Phu, NH; Hien, TT; MalariaGEN Consortium; (2012) Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese. Genes and immunity, 13 (6). pp. 503-508. ISSN 1466-4879 DOI: https://doi.org/10.1038/gene.2012.25 Full text not available from this repository.

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Hill-Cawthorne, Grant A; Hudson, Lyndsey O; El Ghany, Moataz Fouad Abd; Piepenburg, Olaf; Nair, Mridul; Dodgson, Andrew; Forrest, Matthew S; Clark, Taane G; Pain, Arnab; (2014) Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus. PloS one, 9 (6). e101419-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0101419

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Jabbar, Abdul; Phelan, Jody E; de Sessions, Paola Florez; Khan, Taj Ali; Rahman, Hazir; Khan, Sadiq Noor; Cantillon, Daire M; Wildner, Leticia Muraro; Ali, Sajid; Campino, Susana; +2 more... Waddell, Simon J; Clark, Taane G; (2019) Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan. Scientific reports, 9 (1). 14996-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-51562-6

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Johnstone, Elaine C; Clark, Taane G; Griffiths, Siân-Elin; Murphy, Michael F; Walton, Robert T; (2002) Polymorphisms in dopamine metabolic enzymes and tobacco consumption in smokers: seeking confirmation of the association in a follow-up study. Pharmacogenetics, 12 (7). pp. 585-587. ISSN 0960-314X DOI: https://doi.org/10.1097/00008571-200210000-00012 Full text not available from this repository.

Kafsack, BF; Rovira-Graells, N; Clark, TG; Bancells, C; Crowley, VM; Campino, SG; Williams, AE; Drought, LG; Kwiatkowski, DP; Baker, DA; +2 more... Cortés, A; Llinás, M; (2014) A transcriptional switch underlies commitment tosexual development in malaria parasites. Nature, 507 (7491). pp. 248-52. ISSN 0028-0836 DOI: https://doi.org/10.1038/nature12920

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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

Kanji, Akbar; Hasan, Rumina; Ali, Asho; Zaver, Ambreen; Zhang, Ying; Imtiaz, Kehkashan; Shi, Wanliang; Clark, Taane G; McNerney, Ruth; Phelan, Jody; +3 more... Rao, Shoaib; Shafiq, Samreen; Hasan, Zahra; (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, Akbar; Hasan, Rumina; Zaver, Ambreen; Ali, Asho; Imtiaz, Kehkashan; Ashraf, Mussarat; Clark, Taane G; McNerney, Ruth; Shafiq, Samreen; Hasan, Zahra; (2016) Alternate efflux pump mechanism may contribute to drug resistance in extensively drug-resistant isolates of Mycobacterium tuberculosis. International journal of mycobacteriology, 5 Supp. S97-S98. ISSN 2212-5531 DOI: https://doi.org/10.1016/j.ijmyco.2016.09.064

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Kariuki, Symon M; Rockett, Kirk; Clark, Taane G; Reyburn, Hugh; Agbenyega, Tsiri; Taylor, Terrie E; Birbeck, Gretchen L; Williams, Thomas N; Newton, Charles RJC; (2013) The genetic risk of acute seizures in African children with falciparum malaria. Epilepsia, 54 (6). pp. 990-1001. ISSN 0013-9580 DOI: https://doi.org/10.1111/epi.12173

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Keays, David A; Clark, Taane G; Campbell, Thomas G; Broxholme, John; Valdar, William; (2007) Estimating the number of coding mutations in genotypic and phenotypic driven N-ethyl-N-nitrosourea (ENU) screens: revisited. Mammalian genome, 18 (2). pp. 123-124. ISSN 0938-8990 DOI: https://doi.org/10.1007/s00335-006-0065-z Full text not available from this repository.

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Khan, Anwar Sheed; Phelan, Jody E; Khan, Muhammad Tahir; Ali, Sajid; Qasim, Muhammad; Napier, Gary; Campino, Susana; Ahmad, Sajjad; Cabral-Marques, Otavio; Zhang, Shulin; +4 more... Rahman, Hazir; Wei, Dong-Qing; Clark, Taane G; Khan, Taj Ali; (2021) Author Correction: Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan. Scientific reports, 11 (1). p. 15100. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-94687-3

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Perdigão, João; Caneiras, Cátia; Elias, Rita; Modesto, Ana; Spadar, Anton; Phelan, Jody; Campino, Susana; Clark, Taane G; Costa, Eliana; Saavedra, Maria José; +1 more... Duarte, Aida; (2020) Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain. MICROORGANISMS, 8 (12). p. 1986. ISSN 2076-2607 DOI: https://doi.org/10.3390/microorganisms8121986

Perdigão, João; Gomes, Pedro; Miranda, Anabela; Maltez, Fernando; Machado, Diana; Silva, Carla; Phelan, Jody E; Brum, Laura; Campino, Susana; Couto, Isabel; +3 more... Viveiros, Miguel; Clark, Taane G; Portugal, Isabel; (2020) Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal. Scientific reports, 10 (1). 2600-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-020-59558-3

Perdigão, João; Modesto, Ana; Pereira, AL; Neto, O; Matos, V; Godinho, A; Phelan, Jody; Charleston, James; Spadar, Anton; de Sessions, Paola Florez; +9 more... Hibberd, Martin; Campino, Susana; Costa, A; Fernandes, F; Ferreira, F; Correia, AB; Gonçalves, Luisa; Clark, Taane G; Duarte, Aida; (2020) Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital. Microbial genomics, 7 (6). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000349

Perdigão, João; Silva, Carla; Diniz, Jaciara; Pereira, Catarina; Machado, Diana; Ramos, Jorge; Silva, Hugo; Abilleira, Fernanda; Brum, Clarice; Reis, Ana J; +28 more... Macedo, Maíra; Scaini, João L; Silva, Ana B; Esteves, Leonardo; Macedo, Rita; Maltez, Fernando; Clemente, Sofia; Coelho, Elizabeth; Viegas, Sofia; Rabna, Paulo; Rodrigues, Amabélia; Taveira, Nuno; Jordao, Luísa; Kritski, Afrânio; Lapa E Silva, José R; Mokrousov, Igor; Couvin, David; Rastogi, Nalin; Couto, Isabel; Pain, Arnab; McNerney, Ruth; Clark, Taane G; von Groll, Andrea; Dalla-Costa, Elis R; Rossetti, Maria Lúcia; Silva, Pedro EA; Viveiros, Miguel; Portugal, Isabel; (2018) Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries. Infection, genetics and evolution, 72. pp. 44-58. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2018.03.011

Perdigão, João; Silva, Carla; Maltez, Fernando; Machado, Diana; Miranda, Anabela; Couto, Isabel; Rabna, Paulo; Florez de Sessions, Paola; Phelan, Jody; Pain, Arnab; +6 more... McNerney, Ruth; Hibberd, Martin L; Mokrousov, Igor; Clark, Taane G; Viveiros, Miguel; Portugal, Isabel; (2020) Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing. EMERGING MICROBES & INFECTIONS, 9 (1). pp. 1342-1353. ISSN 2222-1751 DOI: https://doi.org/10.1080/22221751.2020.1774425

Perdigão, João; Silva, Hugo; Machado, Diana; Macedo, Rita; Maltez, Fernando; Silva, Carla; Jordao, Luisa; Couto, Isabel; Mallard, Kim; Coll, Francesc; +6 more... Hill-Cawthorne, Grant A; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Viveiros, Miguel; Portugal, Isabel; (2014) Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. BMC genomics, 15 (1). 991-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-15-991

Phelan, Jody E; Coll, Francesc; Bergval, Indra; Anthony, Richard M; Warren, Rob; Sampson, Samantha L; Gey van Pittius, Nicolaas C; Glynn, Judith R; Crampin, Amelia C; Alves, Adriana; +20 more... Bessa, Theolis Barbosa; Campino, Susana; Dheda, Keertan; Grandjean, Louis; Hasan, Rumina; Hasan, Zahra; Miranda, Anabela; Moore, David; Panaiotov, Stefan; Perdigao, Joao; Portugal, Isabel; Sheen, Patricia; de Oliveira Sousa, Erivelton; Streicher, Elizabeth M; van Helden, Paul D; Viveiros, Miguel; Hibberd, Martin L; Pain, Arnab; McNerney, Ruth; Clark, Taane G; (2016) Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. BMC genomics, 17 (1). 151-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-016-2467-y

Phelan, Jody E; Lim, Dodge R; Mitarai, Satoshi; de Sessions, Paola Florez; Tujan, Ma Angelica A; Reyes, Lorenzo T; Medado, Inez Andrea P; Palparan, Alma G; Naim, Ahmad Nazri Mohamed; Jie, Song; +10 more... Segubre-Mercado, Edelwisa; Simoes, Beatriz; Campino, Susana; Hafalla, Julius C; Murase, Yoshiro; Morishige, Yuta; Hibberd, Martin L; Kato, Seiya; Ama, Ma Cecilia G; Clark, Taane G; (2019) Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines. Scientific reports, 9 (1). 9305-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-45566-5

Phelan, Jody E; O'Sullivan, Denise M; Machado, Diana; Ramos, Jorge; Oppong, Yaa EA; Campino, Susana; O'Grady, Justin; McNerney, Ruth; Hibberd, Martin L; Viveiros, Miguel; +2 more... Huggett, Jim F; Clark, Taane G; (2019) Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome medicine, 11 (1). 41-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-019-0650-x

Phelan, Jody; Coll, Francesc; McNerney, Ruth; Ascher, David B; Pires, Douglas EV; Furnham, Nick; Coeck, Nele; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; +6 more... Ramsay, Andrew; Campino, Susana; Hibberd, Martin L; Pain, Arnab; Rigouts, Leen; Clark, Taane G; (2016) Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC medicine, 14 (1). 31-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-016-0575-9

Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane 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). pp. 207-216. ISSN 2212-5531 DOI: https://doi.org/10.1016/j.ijmyco.2015.05.001

Phelan, Jody; O'Sullivan, Denise M; Machado, Diana; Ramos, Jorge; Whale, Alexandra S; O'Grady, Justin; Dheda, Keertan; Campino, Susana; McNerney, Ruth; Viveiros, Miguel; +2 more... Huggett, Jim F; Clark, Taane G; (2016) The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs. Genome medicine, 8 (1). 132-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-016-0385-x

Phelan, Jody; de Sessions, Paola Florez; Tientcheu, Leopold; Perdigao, Joao; Machado, Diana; Hasan, Rumina; Hasan, Zahra; Bergval, Indra L; Anthony, Richard; McNerney, Ruth; +6 more... Antonio, Martin; Portugal, Isabel; Viveiros, Miguel; Campino, Susana; Hibberd, Martin L; Clark, Taane G; (2018) Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. Scientific reports, 8 (1). 160-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-017-18188-y

Portelli, Stephanie; Phelan, Jody E; Ascher, David B; Clark, Taane G; Furnham, Nicholas; (2018) Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Scientific reports, 8 (1). 15356-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-33370-6

Preston, Mark D; Assefa, Samuel A; Ocholla, Harold; Sutherland, Colin J; Borrmann, Steffen; Nzila, Alexis; Michon, Pascal; Hien, Tran Tinh; Bousema, Teun; Drakeley, Christopher J; +9 more... Zongo, Issaka; Ouédraogo, Jean-Bosco; Djimde, Abdoulaye A; Doumbo, Ogobara K; Nosten, Francois; Fairhurst, Rick M; Conway, David J; Roper, Cally; Clark, Taane G; (2013) PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation. The Journal of infectious diseases, 209 (11). pp. 1808-1815. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jit812

Preston, Mark D; Campino, Susana; Assefa, Samuel A; Echeverry, Diego F; Ocholla, Harold; Amambua-Ngwa, Alfred; Stewart, Lindsay B; Conway, David J; Borrmann, Steffen; Michon, Pascal; +12 more... Zongo, Issaka; Ouédraogo, Jean-Bosco; Djimde, Abdoulaye A; Doumbo, Ogobara K; Nosten, Francois; Pain, Arnab; Bousema, Teun; Drakeley, Chris J; Fairhurst, Rick M; Sutherland, Colin J; Roper, Cally; Clark, Taane G; (2014) A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. Nature communications, 5 (1). 4052-. ISSN 2041-1723 DOI: https://doi.org/10.1038/ncomms5052

Preston, Mark D; Manske, Magnus; Horner, Neil; Assefa, Samuel; Campino, Susana; Auburn, Sarah; Zongo, Issaka; Ouedraogo, Jean-Bosco; Nosten, Francois; Anderson, Tim; +1 more... Clark, Taane G; (2012) VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data. Bioinformatics (Oxford, England), 28 (22). pp. 2983-2985. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bts557

Ravenhall, Matt; Benavente, Ernest Diez; Mipando, Mwapatsa; Jensen, Anja TR; Sutherland, Colin J; Roper, Cally; Sepúlveda, Nuno; Kwiatkowski, Dominic P; Montgomery, Jacqui; Phiri, Kamija S; +5 more... Terlouw, Anja; Craig, Alister; Campino, Susana; Ocholla, Harold; Clark, Taane G; (2016) Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi. Malaria journal, 15 (1). 575-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-016-1634-6

Ravenhall, Matt; Benavente, Ernest Diez; Sutherland, Colin J; Baker, David A; Campino, Susana; Clark, Taane G; (2019) An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene. Scientific reports, 9 (1). 8287-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-44599-0

Ravenhall, Matt; Campino, Susana; Clark, Taane G; (2019) SV-Pop: population-based structural variant analysis and visualization. BMC bioinformatics, 20 (1). 136-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-019-2718-4

Ravenhall, Matt; Campino, Susana; Sepúlveda, Nuno; Manjurano, Alphaxard; Nadjm, Behzad; Mtove, George; Wangai, Hannah; Maxwell, Caroline; Olomi, Raimos; Reyburn, Hugh; +4 more... Drakeley, Christopher J; Riley, Eleanor M; Clark, Taane G; MalariaGEN; (2018) Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania. PLoS genetics, 14 (1). e1007172-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1007172

Refrégier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cömert, Füsun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; +6 more... Phelan, Jody; Coll, Francesc; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Sola, Christophe; (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

Roberts, Chrissy H; Franklin, Christopher S; Makalo, Pateh; Joof, Hassan; Sarr, Isatou; Mahdi, Olaimatu S; Sillah, Ansumana; Bah, Momodou; Payne, Felicity; Jeffreys, Anna E; +13 more... Bottomley, William; Natividad, Angels; Molina-Gonzalez, Sandra; Burr, Sarah E; Preston, Mark; Kwiatkowski, Dominic; Rockett, Kirk A; Clark, Taane G; Burton, Matthew J; Mabey, David CW; Bailey, Robin; Barroso, Inês; Holland, Martin J; (2015) Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study. Scientific reports, 5 (1). 17447-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep17447

Robinson, Timothy; Campino, Susana G; Auburn, Sarah; Assefa, Samuel A; Polley, Spencer D; Manske, Magnus; MacInnis, Bronwyn; Rockett, Kirk A; Maslen, Gareth L; Sanders, Mandy; +5 more... Quail, Michael A; Chiodini, Peter L; Kwiatkowski, Dominic P; Clark, Taane G; Sutherland, Colin J; (2011) Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients. PloS one, 6 (8). e23204-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0023204

Rothwell, Peter M; Howard, Sally C; Power, Dermot A; Gutnikov, Sergei A; Algra, Ale; van Gijn, Jan; Clark, Tanne G; Murphy, Michael FG; Warlow, Charles P; (2004) Fibrinogen concentration and risk of ischemic stroke and acute coronary events in 5113 patients with transient ischemic attack and minor ischemic stroke. Stroke; a journal of cerebral circulation, 35 (10). pp. 2300-2305. ISSN 0039-2499 DOI: https://doi.org/10.1161/01.STR.0000141701.36371.d1 Full text not available from this repository.

Samad, Hanif; Coll, Francesc; Preston, Mark D; Ocholla, Harold; Fairhurst, Rick M; Clark, Taane G; (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

Sambo, Maria Rosário; Trovoada, Maria Jesus; Benchimol, Carla; Quinhentos, Vatúsia; Gonçalves, Lígia; Velosa, Rute; Marques, Maria Isabel; Sepúlveda, Nuno; Clark, Taane G; Mustafa, Stefan; +3 more... Wagner, Oswald; Coutinho, António; Penha-Gonçalves, Carlos; (2010) Transforming growth factor beta 2 and heme oxygenase 1 genes are risk factors for the cerebral malaria syndrome in Angolan children. PloS one, 5 (6). e11141-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0011141

Sawyer, Elizabeth B; Phelan, Jody E; Clark, Taane G; Cortes, Teresa; (2021) A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling. Cell Reports, 34 (5). 108695-. ISSN 2211-1247 DOI: https://doi.org/10.1016/j.celrep.2021.108695

Sawyer, Elizabeth B; Phelan, Jody E; Clark, Taane G; Cortes, Teresa; (2020) Ribosome profiling inMycobacterium tuberculosisreveals robust leaderless translation. BioRxiv. DOI: https://doi.org/10.1101/2020.04.22.055855 Item availability may be restricted.

Sengstake, Sarah; Bergval, Indra L; Schuitema, Anja R; de Beer, Jessica L; Phelan, Jody; de Zwaan, Rina; Clark, Taane G; van Soolingen, Dick; Anthony, Richard M; (2017) Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia. BMC infectious diseases, 17 (1). 491-. ISSN 1471-2334 DOI: https://doi.org/10.1186/s12879-017-2594-3

Sepúlveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G; (2013) A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data. BMC genomics, 14 (1). 128-. ISSN 1471-2164 DOI: https://doi.org/10.1186/1471-2164-14-128

Sepúlveda, Nuno; Grignard, Lynn; Curry, Jonathan; Mahey, Laleta; Bastiaens, Guido JH; Tiono, Alfred B; Okebe, Joseph; Coulibaly, Sam A; Gonçalves, Bronner P; Affara, Muna; +15 more... Ouédraogo, Alphonse; Bougouma, Edith C; Sanou, Guillaume S; Nébié, Issa; Lanke, Kjerstin; Sirima, Sodiomon B; Dicko, Alassane; d'Alessandro, Umberto; Clark, Taane G; Campino, Susana; Chen, Ingrid; Eziefula, Alice C; Gosling, Roly; Bousema, Teun; Drakeley, Chris; (2021) G6PD Polymorphisms and Hemolysis After Antimalarial Treatment With Low Single-Dose Primaquine: A Pooled Analysis of Six African Clinical Trials. Frontiers in genetics, 12. 645688-. DOI: https://doi.org/10.3389/fgene.2021.645688

Sepúlveda, Nuno; Manjurano, Alphaxard; Campino, Susana G; Lemnge, Martha; Lusingu, John; Olomi, Raimos; Rockett, Kirk A; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; +4 more... Clark, Taane G; Riley, Eleanor M; Drakeley, Chris J; MalariaGEN Consortium; (2017) Malaria Host Candidate Genes Validated by Association With Current, Recent, and Historical Measures of Transmission Intensity. The Journal of infectious diseases, 216 (1). pp. 45-54. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jix250

Sepúlveda, Nuno; Manjurano, Alphaxard; Drakeley, Chris; Clark, Taane G; (2014) On the performance of multiple imputation based on chained equations in tackling missing data of the African α3.7 -globin deletion in a malaria association study. Annals of human genetics, 78 (4). pp. 277-289. ISSN 0003-4800 DOI: https://doi.org/10.1111/ahg.12065

Sepúlveda, Nuno; Phelan, Jody; Diez-Benavente, Ernest; Campino, Susana; Clark, Taane G; Hopkins, Heidi; Sutherland, Colin; Drakeley, Chris J; Beshir, Khalid B; (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, 62. pp. 211-219. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2018.04.039

Sheen, Patricia; Requena, David; Gushiken, Eduardo; Gilman, Robert H; Antiparra, Ricardo; Lucero, Bryan; Lizárraga, Pilar; Cieza, Basilio; Roncal, Elisa; Grandjean, Louis; +5 more... Pain, Arnab; McNerney, Ruth; Clark, Taane G; Moore, David; Zimic, Mirko; (2017) A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. BMC genomics, 18 (1). 769-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-017-4146-z

Shelton, Jennifer MG; Corran, Patrick; Risley, Paul; Silva, Nilupa; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Craik, Rachel; Cornelius, Victoria; Hensmann, Meike; +48 more... Molloy, Sile; Sepulveda, Nuno; Clark, Taane G; Band, Gavin; Clarke, Geraldine M; Spencer, Christopher CA; Kerasidou, Angeliki; Campino, Susana; Auburn, Sarah; Tall, Adama; Ly, Alioune Badara; Mercereau-Puijalon, Odile; Sakuntabhai, Anavaj; Djimdé, Abdoulaye; Maiga, Boubacar; Touré, Ousmane; Doumbo, Ogobara K; Dolo, Amagana; Troye-Blomberg, Marita; Mangano, Valentina D; Verra, Frederica; Modiano, David; Bougouma, Edith; Sirima, Sodiomon B; Ibrahim, Muntaser; Hussain, Ayman; Eid, Nahid; Elzein, Abier; Mohammed, Hiba; Elhassan, Ahmed; Elhassan, Ibrahim; Williams, Thomas N; Ndila, Carolyne; Macharia, Alexander; Marsh, Kevin; Manjurano, Alphaxard; Reyburn, Hugh; Lemnge, Martha; Ishengoma, Deus; Carter, Richard; Karunaweera, Nadira; Fernando, Deepika; Dewasurendra, Rajika; Drakeley, Christopher J; Riley, Eleanor M; Kwiatkowski, Dominic P; Rockett, Kirk A; MalariaGEN Consortium; (2015) Genetic determinants of anti-malarial acquired immunity in a large multi-centre study. Malaria journal, 14 (1). 333-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-015-0833-x

Sindato, Calvin; Mboera, Leonard EG; Katale, Bugwesa Z; Frumence, Gasto; Kimera, Sharadhuli; Clark, Taane G; Legido-Quigley, Helena; Mshana, Stephen E; Rweyemamu, Mark M; Matee, Mecky; (2020) Knowledge, attitudes and practices regarding antimicrobial use and resistance among communities of Ilala, Kilosa and Kibaha districts of Tanzania. ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL, 9 (1). 194-. ISSN 2047-2994 DOI: https://doi.org/10.1186/s13756-020-00862-y

Smith, Miriam; Campino, Susana; Gu, Yong; Clark, Taane G; Otto, Thomas D; Maslen, Gareth; Manske, Magnus; Imwong, Mallika; Dondorp, Arjen M; Kwiatkowski, Dominic P; +2 more... Quail, Michael A; Swerdlow, Harold; (2012) An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS. The Open Genomics Journal, 5 (1). pp. 18-29. DOI: https://doi.org/10.2174/1875693X01205010018

Sobkowiak, Benjamin; Banda, Louis; Mzembe, Themba; Crampin, Amelia C; Glynn, Judith R; Clark, Taane G; (2020) Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants. MICROBIAL GENOMICS, 6 (4). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.000361

Sobkowiak, Benjamin; Glynn, Judith R; Houben, Rein MGJ; Mallard, Kim; Phelan, Jody E; Guerra-Assunção, José Afonso; Banda, Louis; Mzembe, Themba; Viveiros, Miguel; McNerney, Ruth; +3 more... Parkhill, Julian; Crampin, Amelia C; Clark, Taane G; (2018) Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC genomics, 19 (1). 613-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-018-4988-z

Sousa, Inês; Clark, Taane G; Holt, Richard; Pagnamenta, Alistair T; Mulder, Erik J; Minderaa, Ruud B; Bailey, Anthony J; Battaglia, Agatino; Klauck, Sabine M; Poustka, Fritz; +2 more... Monaco, Anthony P; International Molecular Genetic Study of Autism Consortium (IMGS; (2010) Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry. Molecular autism, 1 (1). 7-. ISSN 2040-2392 DOI: https://doi.org/10.1186/2040-2392-1-7

Sousa, Inês; Clark, Taane G; Toma, Claudio; Kobayashi, Kazuhiro; Choma, Maja; Holt, Richard; Sykes, Nuala H; Lamb, Janine A; Bailey, Anthony J; Battaglia, Agatino; +3 more... Maestrini, Elena; Monaco, Anthony P; International Molecular Genetic Study of Autism Consortium (IMGS; (2009) MET and autism susceptibility: family and case-control studies. European journal of human genetics, 17 (6). pp. 749-758. ISSN 1018-4813 DOI: https://doi.org/10.1038/ejhg.2008.215 Full text not available from this repository.

Spadar, Anton; Perdigão, João; Phelan, Jody; Charleston, James; Modesto, Ana; Elias, Rita; de Sessions, Paola Florez; Hibberd, Martin L; Campino, Susana; Duarte, Aida; +1 more... Clark, Taane G; (2021) Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals. Scientific reports, 11 (1). p. 6491. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-85724-2

Spadar, Anton; Phelan, Jody E; Benavente, Ernest Diez; Campos, Monica; Gomez, Lara Ferrero; Mohareb, Fady; Clark, Taane G; Campino, Susana; (2021) Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus. Parasites & vectors, 14 (1). p. 332. ISSN 1756-3305 DOI: https://doi.org/10.1186/s13071-021-04828-w

Srilohasin, Prapaporn; Prammananan, Therdsak; Faksri, Kiatichai; Phelan, Jody E; Suriyaphol, Prapat; Kamolwat, Phalin; Smithtikarn, Saijai; Disratthakit, Areeya; Regmi, Sanjib Mani; Leechawengwongs, Manoon; +5 more... Twee-Hee Ong, Rick; Teo, Yik Ying; Tongsima, Sissades; Clark, Taane G; Chaiprasert, Angkana; (2020) Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype. EMERGING MICROBES & INFECTIONS, 9 (1). pp. 2632-2641. ISSN 2222-1751 DOI: https://doi.org/10.1080/22221751.2020.1852891

Takala-Harrison, Shannon; Clark, Taane G; Jacob, Christopher G; Cummings, Michael P; Miotto, Olivo; Dondorp, Arjen M; Fukuda, Mark M; Nosten, Francois; Noedl, Harald; Imwong, Mallika; +29 more... Bethell, Delia; Se, Youry; Lon, Chanthap; Tyner, Stuart D; Saunders, David L; Socheat, Duong; Ariey, Frederic; Phyo, Aung Pyae; Starzengruber, Peter; Fuehrer, Hans-Peter; Swoboda, Paul; Stepniewska, Kasia; Flegg, Jennifer; Arze, Cesar; Cerqueira, Gustavo C; Silva, Joana C; Ricklefs, Stacy M; Porcella, Stephen F; Stephens, Robert M; Adams, Matthew; Kenefic, Leo J; Campino, Susana; Auburn, Sarah; MacInnis, Bronwyn; Kwiatkowski, Dominic P; Su, Xin-zhuan; White, Nicholas J; Ringwald, Pascal; Plowe, Christopher V; (2013) Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proceedings of the National Academy of Sciences of the United States of America, 110 (1). pp. 240-245. ISSN 0027-8424 DOI: https://doi.org/10.1073/pnas.1211205110 Item availability may be restricted.

Takala-Harrison, Shannon; Jacob, Christopher G; Arze, Cesar; Cummings, Michael P; Silva, Joana C; Dondorp, Arjen M; Fukuda, Mark M; Hien, Tran Tinh; Mayxay, Mayfong; Noedl, Harald; +35 more... Nosten, Francois; Kyaw, Myat P; Nhien, Nguyen Thanh Thuy; Imwong, Mallika; Bethell, Delia; Se, Youry; Lon, Chanthap; Tyner, Stuart D; Saunders, David L; Ariey, Frederic; Mercereau-Puijalon, Odile; Menard, Didier; Newton, Paul N; Khanthavong, Maniphone; Hongvanthong, Bouasy; Starzengruber, Peter; Fuehrer, Hans-Peter; Swoboda, Paul; Khan, Wasif A; Phyo, Aung Pyae; Nyunt, Myaing M; Nyunt, Myat H; Brown, Tyler S; Adams, Matthew; Pepin, Christopher S; Bailey, Jason; Tan, John C; Ferdig, Michael T; Clark, Taane G; Miotto, Olivo; MacInnis, Bronwyn; Kwiatkowski, Dominic P; White, Nicholas J; Ringwald, Pascal; Plowe, Christopher V; (2014) Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia. The Journal of infectious diseases, 211 (5). pp. 670-679. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiu491 Full text not available from this repository.

Teo, YY; Small, KS; Clark, TG; Kwiatkowski, DP; (2008) Perturbation analysis: a simple method for filtering SNPs with erroneous genotyping in genome-wide association studies. Annals of human genetics, 72 (Pt 3). pp. 368-374. ISSN 0003-4800 DOI: https://doi.org/10.1111/j.1469-1809.2007.00422.x Full text not available from this repository.

Teo, Yik Y; Fry, Andrew E; Bhattacharya, Kanishka; Small, Kerrin S; Kwiatkowski, Dominic P; Clark, Taane G; (2009) Genome-wide comparisons of variation in linkage disequilibrium. Genome research, 19 (10). pp. 1849-1860. ISSN 1088-9051 DOI: https://doi.org/10.1101/gr.092189.109 Full text not available from this repository.

Teo, Yik Y; Fry, Andrew E; Clark, Taane G; Tai, ES; Seielstad, Mark; (2007) On the usage of HWE for identifying genotyping errors. Annals of human genetics, 71 (Pt 5). pp. 701-703. ISSN 0003-4800 DOI: https://doi.org/10.1111/j.1469-1809.2007.00356.x Full text not available from this repository.

Teo, Yik Y; Fry, Andrew E; Sanjoaquin, Miguel A; Pederson, Bonnie; Small, Kerrin S; Rockett, Kirk A; Kwiatkowski, Dominic P; Clark, Taane G; (2009) Assessing genuine parents-offspring trios for genetic association studies. Human heredity, 67 (1). pp. 26-37. ISSN 0001-5652 DOI: https://doi.org/10.1159/000164396 Full text not available from this repository.

Teo, Yik Y; Inouye, Michael; Small, Kerrin S; Gwilliam, Rhian; Deloukas, Panagiotis; Kwiatkowski, Dominic P; Clark, Taane G; (2007) A genotype calling algorithm for the Illumina BeadArray platform. Bioinformatics (Oxford, England), 23 (20). pp. 2741-2746. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btm443 Full text not available from this repository.

Teo, Yik Y; Small, Kerrin S; Fry, Andrew E; Wu, Yumeng; Kwiatkowski, Dominic P; Clark, Taane G; (2009) Power consequences of linkage disequilibrium variation between populations. Genetic epidemiology, 33 (2). pp. 128-135. ISSN 0741-0395 DOI: https://doi.org/10.1002/gepi.20366 Full text not available from this repository.

Tosas Auguet, Olga; Stabler, Richard A; Betley, Jason; Preston, Mark D; Dhaliwal, Mandeep; Gaunt, Michael; Ioannou, Avgousta; Desai, Nergish; Karadag, Tacim; Batra, Rahul; +4 more... Otter, Jonathan A; Marbach, Helene; Clark, Taane G; Edgeworth, Jonathan D; (2017) Frequent Undetected Ward-Based Methicillin-Resistant Staphylococcus aureus Transmission Linked to Patient Sharing Between Hospitals. Clinical infectious diseases, 66 (6). pp. 840-848. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/cix901

Toure, Ousmane; Konate, Salimata; Sissoko, Sibiri; Niangaly, Amadou; Barry, Abdoulaye; Sall, Abdourahmane H; Diarra, Elisabeth; Poudiougou, Belco; Sepulveda, Nuno; Campino, Susana; +5 more... Rockett, Kirk A; Clark, Taane G; Thera, Mahamadou A; Doumbo, Ogobara; Collaboration with The MalariaGEN Consortium; (2012) Candidate polymorphisms and severe malaria in a Malian population. PloS one, 7 (9). e43987-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0043987

Trimarsanto, Hidayat; Benavente, Ernest D; Noviyanti, Rintis; Utami, Retno Ayu Setya; Trianty, Leily; Pava, Zuleima; Getachew, Sisay; Kim, Jung-Yeon; Goo, Youn-Kyoung; Wangchuck, Sonam; +7 more... Liu, Yaobao; Gao, Qi; Dowd, Simone; Cheng, Qin; Clark, Taane G; Price, Ric N; Auburn, Sarah; (2017) VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations. PLoS neglected tropical diseases, 11 (3). e0005465-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0005465

Tunstall, Tanushree; Phelan, Jody; Eccleston, Charlotte; Clark, Taane G; Furnham, Nicholas; (2021) Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages. Frontiers in molecular biosciences, 8. p. 619403. ISSN 2296-889X DOI: https://doi.org/10.3389/fmolb.2021.619403

Tunstall, Tanushree; Portelli, Stephanie; Phelan, Jody; Clark, Taane G; Ascher, David B; Furnham, Nicholas; (2020) Combining structure and genomics to understand antimicrobial resistance. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18. pp. 3377-3394. ISSN 2001-0370 DOI: https://doi.org/10.1016/j.csbj.2020.10.017

Turkiewicz, Anna; Manko, Emilia; Sutherland, Colin J; Diez Benavente, Ernest; Campino, Susana; Clark, Taane G; (2020) Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance. PLOS GENETICS, 16 (12). e1009268-. ISSN 1553-7404 DOI: https://doi.org/10.1371/journal.pgen.1009268

Walk, Jona; Reuling, Isaie J; Behet, Marije C; Meerstein-Kessel, Lisette; Graumans, Wouter; van Gemert, Geert-Jan; Siebelink-Stoter, Rianne; van de Vegte-Bolmer, Marga; Janssen, Thorsten; Teelen, Karina; +11 more... de Wilt, Johannes HW; de Mast, Quirijn; van der Ven, André J; Diez Benavente, Ernest; Campino, Susana; Clark, Taane G; Huynen, Martijn A; Hermsen, Cornelus C; Bijker, Else M; Scholzen, Anja; Sauerwein, Robert W; (2017) Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial. BMC medicine, 15 (1). 168-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-017-0923-4

Ward, Daniel; Higgins, Matthew; Phelan, Jody E; Hibberd, Martin L; Campino, Susana; Clark, Taane G; (2021) An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. GENOME MEDICINE, 13 (1). 4-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-020-00822-6

Whitlock, G; Clark, T; Vander Hoorn, S; Rodgers, A; Jackson, R; Norton, R; MacMahon, S; (2001) Random errors in the measurement of 10 cardiovascular risk factors. European journal of epidemiology, 17 (10). pp. 907-909. ISSN 0393-2990 DOI: https://doi.org/10.1023/a:1016228410194 Full text not available from this repository.

Whitlock, G; Norton, R; Clark, T; Jackson, R; MacMahon, S; (2004) Motor vehicle driver injury and marital status: a cohort study with prospective and retrospective driver injuries. Injury prevention, 10 (1). pp. 33-36. ISSN 1353-8047 DOI: https://doi.org/10.1136/ip.2003.003020 Full text not available from this repository.

Whitlock, G; Norton, R; Clark, T; Pledger, M; Jackson, R; MacMahon, S; (2003) Motor vehicle driver injury and socioeconomic status: a cohort study with prospective and retrospective driver injuries. Journal of epidemiology and community health, 57 (7). pp. 512-516. ISSN 0143-005X DOI: https://doi.org/10.1136/jech.57.7.512 Full text not available from this repository.

Whitlock, Gary; Clark, Taane; (2002) The effect of missing values for covariates. Epidemiology (Cambridge, Mass), 13 (1). 113-. ISSN 1044-3983 DOI: https://doi.org/10.1097/00001648-200201000-00019 Full text not available from this repository.

Whitlock, Gary; Norton, Robyn; Clark, Taane; Jackson, Rodney; MacMahon, Stephen; (2003) Is body mass index a risk factor for motor vehicle driver injury? A cohort study with prospective and retrospective outcomes. International journal of epidemiology, 32 (1). pp. 147-149. ISSN 0300-5771 DOI: https://doi.org/10.1093/ije/dyg022 Full text not available from this repository.

Zetteler, Jessica I; Clark, Taane G; Johnstone, Elaine C; Munafò, Marcus R; (2005) Association of the dopamine-β-hydroxylase gene with nicotine dependence: No evidence for mediation by personality. Personality and individual differences, 39 (6). pp. 1113-1122. ISSN 0191-8869 DOI: https://doi.org/10.1016/j.paid.2005.03.021 Full text not available from this repository.

da Silva Santos, Simone; Clark, Taane G; Campino, Susana; Suarez-Mutis, Martha Cecília; Rockett, Kirk A; Kwiatkowski, Dominic P; Fernandes, Octavio; (2012) Investigation of host candidate malaria-associated risk/protective SNPs in a Brazilian Amazonian population. PloS one, 7 (5). e36692-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0036692

Kariuki, SM; Rockett, K; Clark, TG; Reyburn, H; Agbenyega, T; Taylor, TE; Williams, TN; Newton, CR; (2011) HUMAN GENETIC POLYMORPHISMS AND THE RISK OF MALARIA-ASSOCIATED SEIZURES IN AFRICAN POPULATIONS. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/18747 Full text not available from this repository.

Last, A; Cassama, E; Nabicassa, M; Clark, T; Coll, F; Gundogdu, O; Burr, S; Cutcliffe, L; Clarke, I; Thompson, N; +3 more... Mabey, D; Bailey, R; Holland, M; (2013) Genomic diversity in candidate virulence-associated genes in clinical strains of ocular Chlamydia trachomatis from a trachoma-hyperendemic population on the Bijagós Archipelago of Guinea Bissau in West Africa. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/1472196 Full text not available from this repository.

Díez Benavente, E; (2018) Using whole genome sequence data to study genomic diversity and develop molecular barcodes to profile Plasmodium malaria parasites. PhD (research paper style) thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04650892

Oppong, YEA; (2020) Investigating the genomic basis of antimicrobial resistance in Mycobacterium tuberculosis (Mtb) using genome-wide methodologies. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04657715

Ravenhall, M; (2019) A bioinformatic analysis of malaria host and pathogen genomics. PhD (research paper style) thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04653632