Year Item Type Full Text

Article

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. (2015) 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; Verboom, Theo; Ummels, Roy; Zhang, Huoming; Panigrahi, Aswini Kumar; McNerney, Ruth; Brosch, Roland; Clark, Taane G; Behr, Marcel A; Bitter, Wilbert; Pain, Arnab

Application of a targeted amplicon sequencing panel to screen for insecticide resistance mutations in Anopheles darlingi populations from Brazil. (2025) Acford-Palmer, Holly; Andrade, Alice O; Phelan, Jody E; Santana, Rosa A; Lopes, Stefanie CP; Medeiros, Jansen F; Clark, Taane G; Araujo, Maisa S; Campino, Susana

Genome wide population genetics and molecular surveillance of insecticide resistance in Anopheles stephensi mosquitoes from Awash Sebat Kilo in Ethiopia. (2025) Acford-Palmer, Holly; Tadesse, Fitsum G; Manko, Emilia; Phelan, Jody E; Higgins, Matthew; Osborne, Ashley; Kristan, Mojca; Walker, Thomas; Bousema, Teun; Messenger, Louisa A; Clark, Taane G; Campino, Susana

A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages. (2019) Ajawatanawong, Pravech; Yanai, Hideki; Smittipat, Nat; Disratthakit, Areeya; Yamada, Norio; Miyahara, Reiko; Nedsuwan, Supalert; Imasanguan, Worarat; Kantipong, Pacharee; Chaiyasirinroje, Boonchai; 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

Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan. (2015) Ali, Asho; Hasan, Zahra; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant; Coll, Francesc; Nair, Mridul; Pain, Arnab; Clark, Taane G; Hasan, Rumina

SnoopCGH: software for visualizing comparative genomic hybridization data. (2009) Almagro-Garcia, Jacob; Manske, Magnus; Carret, Celine; Campino, Susana; Auburn, Sarah; Macinnis, Bronwyn L; Maslen, Gareth; Pain, Arnab; Newbold, Christopher I; Kwiatkowski, Dominic P; Clark, Taane G

Cathepsin-L can resist lysis by human serum in Trypanosoma brucei brucei. (2014) Alsford, Sam; Currier, Rachel B; Guerra-Assunção, José Afonso; Clark, Taane G; Horn, David

Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. (2017) Andreu, Nuria; Phelan, Jody; de Sessions, Paola F; Cliff, Jacqueline M; Clark, Taane G; Hibberd, Martin L

Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species. (2016) 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; Clark, Taane G; Sutherland, Colin J; Barnwell, John W; Culleton, Richard; Cao, Jun; Pain, Arnab

estMOI: estimating multiplicity of infection using parasite deep sequencing data. (2014) Assefa, Samuel A; Preston, Mark D; Campino, Susana; Ocholla, Harold; Sutherland, Colin J; Clark, Taane G

Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi. (2015) 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; Clark, Taane G; Duraisingh, Manoj T; Conway, David J; Pain, Arnab; Singh, Balbir

External validation of a deep learning electrocardiogram algorithm to detect ventricular dysfunction. (2021) 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; Carter, Rickey E; Ryabikov, Andrew; Perel, Pablo; Friedman, Paul A; Leon, David A; Lopez-Jimenez, Francisco

Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics. (2018) Auburn, Sarah; Benavente, Ernest D; Miotto, Olivo; Pearson, Richard D; Amato, Roberto; Grigg, Matthew J; Barber, Bridget E; William, Timothy; Handayuni, Irene; Marfurt, Jutta; Trimarsanto, Hidayat; Noviyanti, Rintis; Sriprawat, Kanlaya; Nosten, Francois; Campino, Susana; Clark, Taane G; Anstey, Nicholas M; Kwiatkowski, Dominic P; Price, Ric N

An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing. (2011) Auburn, Sarah; Campino, Susana; Clark, Taane G; Djimde, Abdoulaye A; Zongo, Issaka; Pinches, Robert; Manske, Magnus; Mangano, Valentina; Alcock, Daniel; Anastasi, Elisa; Maslen, Gareth; Macinnis, Bronwyn; Rockett, Kirk; Modiano, David; Newbold, Christopher I; Doumbo, Ogobara K; Ouédraogo, Jean Bosco; Kwiatkowski, Dominic P

Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. (2012) Auburn, Sarah; Campino, Susana; Miotto, Olivo; Djimde, Abdoulaye A; Zongo, Issaka; Manske, Magnus; Maslen, Gareth; Mangano, Valentina; Alcock, Daniel; MacInnis, Bronwyn; Rockett, Kirk A; Clark, Taane G; Doumbo, Ogobara K; Ouédraogo, Jean Bosco; Kwiatkowski, Dominic P

Further evidence supporting a role for gs signal transduction in severe malaria pathogenesis. (2010) Auburn, Sarah; Fry, Andrew E; Clark, Taane G; Campino, Susana; Diakite, Mahamadou; Green, Angela; Richardson, Anna; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Molyneux, Malcolm E; Taylor, Terrie E; Haldar, Kasturi; Rockett, Kirk A; Kwiatkowski, Dominic P

Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing. (2013) Auburn, Sarah; Marfurt, Jutta; Maslen, Gareth; Campino, Susana; Ruano Rubio, Valentin; Manske, Magnus; Machunter, Barbara; Kenangalem, Enny; Noviyanti, Rintis; Trianty, Leily; 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

Antibiotic Susceptibility Patterns and Virulence Profiles of Classical and Hypervirulent Klebsiella pneumoniae Strains Isolated from Clinical Samples in Khyber Pakhtunkhwa, Pakistan. (2025) Azra; Khan, Taj Ali; Ul Haq, Ihtisham; Hinthong, Woranich; Campino, Susana; Gohar, Aisha; Khan, Noman; Kashif, Muhammad; Ullah, Ihsan; Clark, Taane G picture_as_pdf

Imputation-based meta-analysis of severe malaria in three African populations. (2013) Band, Gavin; Le, Quang Si; Jostins, Luke; Pirinen, Matti; Kivinen, Katja; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bojang, Kalifa; Pinder, Margaret; Sirugo, Giorgio; 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

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. (2015) Benavente, Ernest D; Coll, Francesc; Furnham, Nick; McNerney, Ruth; Glynn, Judith R; Campino, Susana; Pain, Arnab; Mohareb, Fady R; Clark, Taane G

Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations. (2019) 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; 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 picture_as_pdf

Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa. (2021) 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; Aguiar, Anna Caroline C; Pereira, Dhelio Batista; Sriprawat, Kanlaya; Nosten, Francois; Moon, Robert; Sutherland, Colin J; Campino, Susana; Clark, Taane G

Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development. (2018) 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; Mohareb, Fady; Baker, David A; Clark, Taane G; Campino, Susana

A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line. (2017) 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; Hibberd, Martin L; Campino, Susana; Clark, Taane G

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. (2014) Bergval, Indra; Coll, Francesc; Schuitema, Anja; de Ronde, Hans; Mallard, Kim; Pain, Arnab; McNerney, Ruth; Clark, Taane G; Anthony, Richard M

Apolipoproteins as predictors of ischaemic stroke in patients with a previous transient ischaemic attack. (2006) Bhatia, M; Howard, SC; Clark, TG; Neale, R; Qizilbash, N; Murphy, MFG; Rothwell, PM

Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences. (2023) Billows, Nina; Phelan, Jody E; Xia, Dong; Peng, Yonghong; Clark, Taane G; Chang, Yu-Mei

Large-scale statistical analysis of Mycobacterium tuberculosis genome sequences identifies compensatory mutations associated with multi-drug resistance. (2024) Billows, Nina; Phelan, Jody; Xia, Dong; Peng, Yonghong; Clark, Taane G; Chang, Yu-Mei picture_as_pdf

Recurrence after abdominal surgery for Crohn's disease: relationship to disease site and surgical procedure. (2002) 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

Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya. (2013) Borrmann, Steffen; Straimer, Judith; Mwai, Leah; Abdi, Abdirahman; Rippert, Anja; Okombo, John; Muriithi, Steven; Sasi, Philip; Kortok, Moses Mosobo; Lowe, Brett; Campino, Susana; Assefa, Samuel; Auburn, Sarah; Manske, Magnus; Maslen, Gareth; Peshu, Norbert; Kwiatkowski, Dominic P; Marsh, Kevin; Nzila, Alexis; Clark, Taane G

Survival analysis part II: multivariate data analysis--an introduction to concepts and methods. (2003) Bradburn, MJ; Clark, TG; Love, SB; Altman, DG

Survival analysis Part III: multivariate data analysis -- choosing a model and assessing its adequacy and fit. (2003) Bradburn, MJ; Clark, TG; Love, SB; Altman, DG

Missing... presumed at random: cost-analysis of incomplete data. (2003) Briggs, Andrew; Clark, Taane; Wolstenholme, Jane; Clarke, Philip

Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. (2018) Brynildsrud, Ola B; Pepperell, Caitlin S; Suffys, Philip; Grandjean, Louis; Monteserin, Johana; Debech, Nadia; Bohlin, Jon; Alfsnes, Kristian; Pettersson, John O-H; Kirkeleite, Ingerid; 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

Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England. (2015) Cairns, MD; Preston, MD; Lawley, TD; Clark, TG; Stabler, RA; Wren, BW

Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay. (2011) Campino, Susana; Auburn, Sarah; Kivinen, Katja; Zongo, Issaka; Ouedraogo, Jean-Bosco; Mangano, Valentina; Djimde, Abdoulaye; Doumbo, Ogobara K; Kiara, Steven M; Nzila, Alexis; 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

Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines. (2016) 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; Kwiatkowski, Dominic P; Alano, Pietro; Baker, David A; Clark, Taane G

TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expression. (2009) Campino, Susana; Forton, Julian; Auburn, Sarah; Fry, Andrew; Diakite, Mahamadou; Richardson, Anna; Hull, Jeremy; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Molyneux, Malcolm E; Taylor, Terrie E; Rockett, Kirk; Clark, Taane G; Kwiatkowski, Dominic P

Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations. (2008) Campino, Susana; Forton, Julian; Raj, Srilakshmi; Mohr, Bert; Auburn, Sarah; Fry, Andrew; Mangano, Valentina D; Vandiedonck, Claire; Richardson, Anna; Rockett, Kirk; Clark, Taane G; Kwiatkowski, Dominic P

A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways. (2018) Campino, Susana; Marin-Menendez, Alejandro; Kemp, Alison; Cross, Nadia; Drought, Laura; Otto, Thomas D; Benavente, Ernest Diez; Ravenhall, Matt; Schwach, Frank; Girling, Gareth; Manske, Magnus; Theron, Michel; Gould, Kelda; Drury, Eleanor; Clark, Taane G; Kwiatkowski, Dominic P; Pance, Alena; Rayner, Julian C

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. (2018) Campos, Monica C; Dombrowski, Jamille G; Phelan, Jody; Marinho, Claudio RF; Hibberd, Martin; Clark, Taane G; Campino, Susana

High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors. (2022) Campos, Monica; Phelan, Jody; Spadar, Anton; Collins, Emma; Gonçalves, Adéritow; Pelloquin, Bethanie; Vaselli, Natasha Marcella; Meiwald, Anne; Clark, Emma; Stica, Caleb; Orsborne, James; Sylla, Moussa; Edi, Constant; Camara, Denka; Mohammed, Abdul Rahim; Afrane, Yaw Asare; Kristan, Mojca; Walker, Thomas; Gomez, Lara Ferrero; Messenger, Louisa A; Clark, Taane G; Campino, Susana

Surveillance of Aedes aegypti populations in the city of Praia, Cape Verde: Zika virus infection, insecticide resistance and genetic diversity. (2020) Campos, Monica; Ward, Daniel; Morales, Raika Francesca; Gomes, Ana Rita; Silva, Keily; Sepúlveda, Nuno; Gomez, Lara Ferrero; Clark, Taane G; Campino, Susana

Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole. (2017) Campos, Mônica C; Phelan, Jody; Francisco, Amanda F; Taylor, Martin C; Lewis, Michael D; Pain, Arnab; Clark, Taane G; Kelly, John M

Immune phenotype predicts risk for posttransplantation squamous cell carcinoma. (2010) Carroll, Robert P; Segundo, David San; Hollowood, Kevin; Marafioti, Teresa; Clark, Taane G; Harden, Paul N; Wood, Kathryn J

Survival analysis part I: basic concepts and first analyses. (2003) Clark, TG; Bradburn, MJ; Love, SB; Altman, DG

Survival analysis part IV: further concepts and methods in survival analysis. (2003) Clark, TG; Bradburn, MJ; Love, SB; Altman, DG

Long term risks of stroke, myocardial infarction, and vascular death in "low risk" patients with a non-recent transient ischaemic attack. (2003) Clark, TG; Murphy, MFG; Rothwell, PM

A prognostic model for ovarian cancer. (2001) Clark, TG; Stewart, ME; Altman, DG; Gabra, H; Smyth, JF

Developing a prognostic model in the presence of missing data: an ovarian cancer case study. (2003) Clark, Taane G; Altman, Douglas G

Quantification of the completeness of follow-up. (2002) Clark, Taane G; Altman, Douglas G; De Stavola, Bianca L

Functional constraint and small insertions and deletions in the ENCODE regions of the human genome. (2007) Clark, Taane G; Andrew, Toby; Cooper, Gregory M; Margulies, Elliott H; Mullikin, James C; Balding, David J

A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals. (2010) Clark, Taane G; Campino, Susana G; Anastasi, Elisa; Auburn, Sarah; Teo, Yik Y; Small, Kerrin; Rockett, Kirk A; Kwiatkowski, Dominic P; Holmes, Christopher C

Bayesian logistic regression using a perfect phylogeny. (2007) Clark, Taane G; De Iorio, Maria; Griffiths, Robert C

Finding associations in dense genetic maps: a genetic algorithm approach. (2005) Clark, Taane G; De Iorio, Maria; Griffiths, Robert C; Farrall, Martin

An Evolutionary Algorithm to Find Associations in Dense Genetic Maps. (2008) Clark, Taane G; De Iorio, Maria; Griffths, Robert C

Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populations. (2009) Clark, Taane G; Diakite, Mahamadou; Auburn, Sarah; Campino, Susana; Fry, Andrew E; Green, Angela; Richardson, Anna; Small, Kerrin; Teo, Yik Y; Wilson, Jonathan; 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

Allelic heterogeneity of G6PD deficiency in West Africa and severe malaria susceptibility. (2009) Clark, Taane G; Fry, Andrew E; Auburn, Sarah; Campino, Susana; Diakite, Mahamadou; Green, Angela; Richardson, Anna; Teo, Yik Y; Small, Kerrin; Wilson, Jonathan; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Sabeti, Pardis; Kwiatkowski, Dominic P; Rockett, Kirk A

Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. (2013) Clark, Taane G; Mallard, Kim; Coll, Francesc; Preston, Mark; Assefa, Samuel; Harris, David; Ogwang, Sam; Mumbowa, Francis; Kirenga, Bruce; O'Sullivan, Denise M; Okwera, Alphonse; Eisenach, Kathleen D; Joloba, Moses; Bentley, Stephen D; Ellner, Jerrold J; Parkhill, Julian; Jones-López, Edward C; McNerney, Ruth

Does smoking influence survival in cancer patients through effects on respiratory and vascular disease? (2006) Clark, Taane G; Murphy, Michael FG; Hey, Kate; Drury, Mark; Cheng, KK; Aveyard, Paul

Validation of a new prognostic index for advanced epithelial ovarian cancer: results from its application to a UK-based cohort. (2007) Clark, Taane G; Stewart, Moira; Rye, Tzyvia; Smyth, John F; Gourley, Charlie

Characterisation of the opposing effects of G6PD deficiency on cerebral malaria and severe malarial anaemia. (2016) Clarke, Geraldine M; Rockett, Kirk; Kivinen, Katja; Hubbart, Christina; Jeffreys, Anna E; Rowlands, Kate; Jallow, Muminatou; Conway, David J; Bojang, Kalifa A; Pinder, Margaret; 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

Distinct phases of blood gene expression pattern through tuberculosis treatment reflect modulation of the humoral immune response. (2012) 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; Walzl, Gerhard; Dockrell, Hazel M

Genetic signatures of Mycobacterium tuberculosis Nonthaburi genotype revealed by whole genome analysis of isolates from tuberculous meningitis patients in Thailand. (2016) 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

PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies. (2022) Coll, Francesc; Gouliouris, Theodore; Bruchmann, Sebastian; Phelan, Jody; Raven, Kathy E; Clark, Taane G; Parkhill, Julian; Peacock, Sharon J

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. (2012) Coll, Francesc; Mallard, Kim; Preston, Mark D; Bentley, Stephen; Parkhill, Julian; McNerney, Ruth; Martin, Nigel; Clark, Taane G

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. (2014) Coll, Francesc; McNerney, Ruth; Guerra-Assunção, José Afonso; Glynn, Judith R; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Pain, Arnab; Martin, Nigel; Clark, Taane G

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. (2015) Coll, Francesc; McNerney, Ruth; Preston, Mark D; Guerra-Assunção, José Afonso; Warry, Andrew; Hill-Cawthorne, Grant; Mallard, Kim; Nair, Mridul; Miranda, Anabela; Alves, Adriana; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Hasan, Zahra; Hasan, Rumina; Glynn, Judith R; Martin, Nigel; Pain, Arnab; Clark, Taane G

Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. (2018) 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; 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

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. (2017) 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; 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

PolyTB: a genomic variation map for Mycobacterium tuberculosis. (2014) Coll, Francesc; Preston, Mark; Guerra-Assunção, José Afonso; Hill-Cawthorn, Grant; Harris, David; Perdigão, João; Viveiros, Miguel; Portugal, Isabel; Drobniewski, Francis; Gagneux, Sebastien; Glynn, Judith R; Pain, Arnab; Parkhill, Julian; McNerney, Ruth; Martin, Nigel; Clark, Taane G

A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in mosquitoes from Cabo Verde. (2022) Collins, Emma L; Phelan, Jody E; Hubner, Magdalena; Spadar, Anton; Campos, Monica; Ward, Daniel; Acford-Palmer, Holly; Gomes, Ana Rita; Silva, Keily; Ferrero Gomez, Lara; Clark, Taane G; Campino, Susana

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. (2018) Cook, Sarah; Malyutina, Sofia; Kudryavtsev, Alexander V; Averina, Maria; Bobrova, Natalia; Boytsov, Sergey; Brage, Soren; Clark, Taane G; Diez Benavente, Ernest; Eggen, Anne Elise; 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

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. (2018) Cook, Sarah; Malyutina, Sofia; Kudryavtsev, Alexander V; Averina, Maria; Bobrova, Natalia; Boytsov, Sergey; Brage, Soren; Clark, Taane G; Diez Benavente, Ernest; Eggen, Anne Elise; 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

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. (2018) Cook, Sarah; Malyutina, Sofia; Kudryavtsev, Alexander; Averina, Maria; Bobrova, Natalia; Boytsov, Sergey; Brage, Soren; Clark, Taane; Diez Benavente, Ernest; Eggen, Anne Elise; 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

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. (2018) Cook, Sarah; Malyutina, Sofia; Kudryavtsev, Alexander; Averina, Maria; Bobrova, Natalia; Boytsov, Sergey; Brage, Soren; Clark, Taane; Diez Benavente, Ernest; Eggen, Anne Elise; 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

Genetic Diversity of norA, Coding for a Main Efflux Pump of Staphylococcus aureus. (2019) Costa, Sofia Santos; Sobkowiak, Benjamin; Parreira, Ricardo; Edgeworth, Jonathan D; Viveiros, Miguel; Clark, Taane G; Couto, Isabel

Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: the 2017 malaria outbreak. (2021) Da Veiga Leal, Silvania; Ward, Daniel; Campino, Susana; Benavente, Ernest Diez; Ibrahim, Amy; Claret, Tânia; Isaías, Varela; Monteiro, Davidson; Clark, Taane G; Gonçalves, Luzia; Valdez, Tomas; da Luz Lima Mendonça, Maria; Silveira, Henrique; Nogueira, Fatima

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. (2010) 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; Deloukas, Panos; Dermitzakis, Emmanouil T; Tavaré, Simon; Moore, Gudrun E; Dunham, Ian

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. (2015) 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; Pain, Arnab; Clark, Taane G; Rastogi, Nalin; Unis, Gisela; Rossetti, Maria Lucia R; Suffys, Philip Noel

Using deep learning to identify recent positive selection in malaria parasite sequence data. (2021) Deelder, Wouter; Benavente, Ernest Diez; Phelan, Jody; Manko, Emilia; Campino, Susana; Palla, Luigi; Clark, Taane G

Machine Learning Predicts Accurately Mycobacterium tuberculosis Drug Resistance From Whole Genome Sequencing Data. (2019) Deelder, Wouter; Christakoudi, Sofia; Phelan, Jody; Benavente, Ernest Diez; Campino, Susana; McNerney, Ruth; Palla, Luigi; Clark, Taane G

Geographical classification of malaria parasites through applying machine learning to whole genome sequence data. (2022) Deelder, Wouter; Manko, Emilia; Phelan, Jody E; Campino, Susana; Palla, Luigi; Clark, Taane G

A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis. (2022) Deelder, Wouter; Napier, Gary; Campino, Susana; Palla, Luigi; Phelan, Jody; Clark, Taane G

The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. (2016) Dheda, Keertan; Gumbo, Tawanda; Maartens, Gary; Dooley, Kelly E; McNerney, Ruth; Murray, Megan; Furin, Jennifer; Nardell, Edward A; London, Leslie; Lessem, Erica; 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

Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study. (2016) Dheda, Keertan; Limberis, Jason D; Pietersen, Elize; Phelan, Jody; Esmail, Aliasgar; Lesosky, Maia; Fennelly, Kevin P; Te Riele, Julian; Mastrapa, Barbara; Streicher, Elizabeth M; 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

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. (2009) Diakite, Mahamadou; Clark, Taane G; Auburn, Sarah; Campino, Susana; Fry, Andrew E; Green, Angela; Morris, Andrew P; Richardson, Anna; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Kwiatkowski, Dominic P; Rockett, Kirk A

A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali. (2019) Diakité, Seidina AS; Traoré, Karim; Sanogo, Ibrahim; Clark, Taane G; Campino, Susana; Sangaré, Modibo; Dabitao, Djeneba; Dara, Antoine; Konaté, Drissa S; Doucouré, Fousseyni; Cissé, Amadou; Keita, Bourama; Doumbouya, Mory; Guindo, Merepen A; Toure, Mahamoudou B; Sogoba, Nafomon; Doumbia, Seydou; Awandare, Gordon A; Diakité, Mahamadou

A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria. (2020) Diez Benavente, Ernest; Campos, Monica; Phelan, Jody; Nolder, Debbie; Dombrowski, Jamille G; Marinho, Claudio RF; Sriprawat, Kanlaya; Taylor, Aimee R; Watson, James; Roper, Cally; Nosten, Francois; Sutherland, Colin J; Campino, Susana; Clark, Taane G

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations. (2017) 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; Campino, Susana; Clark, Taane G

Studying accelerated cardiovascular ageing in Russian adults through a novel deep-learning ECG biomarker. (2021) Diez Benavente, Ernest; Jimenez-Lopez, Francisco; Attia, Zachi I; Malyutina, Sofia; Kudryavtsev, Alexander; Ryabikov, Andrew; Friedman, Paul A; Kapa, Suraj; Voevoda, Michael; Perel, Pablo; Schirmer, Henrik; Hughes, Alun D; Clark, Taane G; Leon, David A

Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure. (2017) Diez Benavente, Ernest; Ward, Zoe; Chan, Wilson; Mohareb, Fady R; Sutherland, Colin J; Roper, Cally; Campino, Susana; Clark, Taane G

G6PD deficiency alleles in a malaria-endemic region in the Western Brazilian Amazon. (2017) 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; Huggett, Jim; Clark, Taane G; Campino, Susana; Marinho, Claudio RF

Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: a prospective cohort study. (2023) Dombrowski, Jamille Gregório; Acford-Palmer, Holly; Campos, Monica; Separovic, Erika Paula Machado; Epiphanio, Sabrina; Clark, Taane Gregory; Campino, Susana; Marinho, Claudio Romero Farias

Adverse pregnancy outcomes are associated with Plasmodium vivax malaria in a prospective cohort of women from the Brazilian Amazon. (2021) 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; Epiphanio, Sabrina; Gonçalves, Lígia Antunes; Marinho, Claudio Romero Farias

Association of Malaria Infection During Pregnancy With Head Circumference of Newborns in the Brazilian Amazon. (2019) 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; 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

Development and Validation of a Nomogram for Assessing Survival in Patients With COVID-19 Pneumonia. (2020) Dong, Yi-Min; Sun, Jia; Li, Yi-Xin; Chen, Qian; Liu, Qing-Quan; Sun, Zhou; Pang, Ran; Chen, Fei; Xu, Bing-Yang; Manyande, Anne; Clark, Taane G; Li, Jin-Ping; Orhan, Ilkay Erdogan; Tian, Yu-Ke; Wang, Tao; Wu, Wei; Ye, Da-Wei

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. (2011) 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; Quail, Mike A; Rijal, Suman; Sanders, Mandy; Schönian, Gabriele; Stark, Olivia; Sundar, Shyam; Vanaerschot, Manu; Hertz-Fowler, Christiane; Dujardin, Jean-Claude; Berriman, Matthew

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. (2020) 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; 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 picture_as_pdf

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study. (2019) 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; 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

Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese. (2012) Dunstan, SJ; Rockett, KA; Quyen, NTN; Teo, YY; Thai, CQ; Hang, NT; Jeffreys, A; Clark, TG; Small, KS; Simmons, CP; Day, N; O'Riordan, SE; Kwiatkowski, DP; Farrar, J; Phu, NH; Hien, TT; MalariaGEN Consortium

Framing the Drivers of Antimicrobial Resistance in Tanzania. (2021) Durrance-Bagale, Anna; Jung, Anne-Sophie; Frumence, Gasto; Mboera, Leonard; Mshana, Stephen E; Sindato, Calvin; Clark, Taane G; Matee, Mecky; Legido-Quigley, Helena

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. 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A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. (2023) Eccleston, Ruth Charlotte; Manko, Emilia; Campino, Susana; Clark, Taane G; Furnham, Nicholas

Klebsiella pneumoniae and Colistin Susceptibility Testing: Performance Evaluation for Broth Microdilution, Agar Dilution and Minimum Inhibitory Concentration Test Strips and Impact of the "Skipped Well" Phenomenon. (2021) Elias, Rita; Melo-Cristino, José; Lito, Luís; Pinto, Margarida; Gonçalves, Luísa; Campino, Susana; Clark, Taane G; Duarte, Aida; Perdigão, João picture_as_pdf

Policy actors and human and animal health practitioners' perceptions of antimicrobial use and resistance in Tanzania: A qualitative study. (2021) Frumence, Gasto; Mboera, Leonard EG; Katale, Bugwesa Z; Sindato, Calvin; Kimera, Sharadhuli; Durrance-Bagale, Anna; Mshana, Stephen E; Clark, Taane G; Rweyemamu, Mark M; Legido-Quigley, Helena; Matee, Mecky

Practices and Challenges of Veterinary Paraprofessionals in Regards to Antimicrobial Use and Resistance in Animals in Dar Es Salaam, Tanzania. (2021) Frumence, Gasto; Mboera, Leonard EG; Sindato, Calvin; Durrance-Bagale, Anna; Jung, Anne-Sophie; Mshana, Stephen E; Clark, Taane G; Legido-Quigley, Helena; Matee, Mecky I

The Governance and Implementation of the National Action Plan on Antimicrobial Resistance in Tanzania: A Qualitative Study. (2021) Frumence, Gasto; Mboera, Leonard EG; Sindato, Calvin; Katale, Bugwesa Z; Kimera, Sharadhuli; Metta, Emmy; Durrance-Bagale, Anna; Jung, Anne-Sophie; Mshana, Stephen E; Clark, Taane G; Rweyemamu, Mark; Legido-Quigley, Helena; Matee, Mecky IN

Positive selection of a CD36 nonsense variant in sub-Saharan Africa, but no association with severe malaria phenotypes. (2009) Fry, Andrew E; Ghansa, Anita; Small, Kerrin S; Palma, Alejandro; Auburn, Sarah; Diakite, Mahamadou; Green, Angela; Campino, Susana; Teo, Yik Y; Clark, Taane G; Jeffreys, Anna E; Wilson, Jonathan; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Griffiths, Michael J; Peshu, Norbert; Williams, Thomas N; Newton, Charles R; Marsh, Kevin; Molyneux, Malcolm E; Taylor, Terrie E; Koram, Kwadwo A; Oduro, Abraham R; Rogers, William O; Rockett, Kirk A; Sabeti, Pardis C; Kwiatkowski, Dominic P

Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia. (2015) Getachew, Sisay; To, Sheren; Trimarsanto, Hidayat; Thriemer, Kamala; Clark, Taane G; Petros, Beyene; Aseffa, Abraham; Price, Ric N; Auburn, Sarah

Haplotype analyses of haemoglobin C and haemoglobin S and the dynamics of the evolutionary response to malaria in Kassena-Nankana District of Ghana. (2012) Ghansah, Anita; Rockett, Kirk A; Clark, Taane G; Wilson, Michael D; Koram, Kwadwo A; Oduro, Abraham R; Amenga-Etego, Lucas; Anyorigiya, Thomas; Hodgson, Abraham; Milligan, Paul; Rogers, William O; Kwiatkowski, Dominic P

Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq. (2021) Gibson, Amanda J; Passmore, Ian J; Faulkner, Valwynne; Xia, Dong; Nobeli, Irene; Stiens, Jennifer; Willcocks, Sam; Clark, Taane G; Sobkowiak, Ben; Werling, Dirk; Villarreal-Ramos, Bernardo; Wren, Brendan W; Kendall, Sharon L

Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi. (2015) Glynn, Judith R; Guerra-Assunção, José Afonso; Houben, Rein MGJ; Sichali, Lifted; Mzembe, Themba; Mwaungulu, Lorrain K; Mwaungulu, J Nimrod; McNerney, Ruth; Khan, Palwasha; Parkhill, Julian; Crampin, Amelia C; Clark, Taane G

Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes. (2017) Gomes, Ana Rita; Ravenhall, Matt; Benavente, Ernest Diez; Talman, Arthur; Sutherland, Colin; Roper, Cally; Clark, Taane G; Campino, Susana

Corrigendum to "Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes" [Int. J. Parasitol. Drugs and Drug Resist. 7 (2017) 174-180]. (2017) Gomes, Ana Rita; Ravenhall, Matt; Benavente, Ernest Diez; Talman, Arthur; Sutherland, Colin; Roper, Cally; Clark, Taane G; Campino, Susana

Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes. (2021) Gomes, Laura C; Campino, Susana; Marinho, Cláudio RF; Clark, Taane G; Phelan, Jody E

An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome. (2019) 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

Bead-based assays to simultaneously detect multiple human inherited blood disorders associated with malaria. (2019) Grignard, Lynn; Mair, Catherine; Curry, Jonathan; Mahey, Laleta; Bastiaens, Guide JH; Tiono, Alfred B; Okebe, Joseph; Coulibaly, Sam A; Gonçalves, Bronner P; Affara, Muna; Ouédraogo, Alphonse; Bougouma, Edith C; Sanou, Guillaume S; Nébié, Issa; Lanke, Kjerstin HW; Sirima, Sodiomon B; d'Alessandro, Umberto; Clark, Taane G; Campino, Susana; Bousema, Teun; Drakeley, Chris

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. (2015) Guerra-Assunção, JA; Crampin, AC; Houben, RMGJ; Mzembe, T; Mallard, K; Coll, F; Khan, P; Banda, L; Chiwaya, A; Pereira, RPA; McNerney, R; Fine, PEM; Parkhill, J; Clark, TG; Glynn, JR

Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. (2014) Guerra-Assunção, José Afonso; Houben, Rein MGJ; Crampin, Amelia C; Mzembe, Themba; Mallard, Kim; Coll, Francesc; Khan, Palwasha; Banda, Louis; Chiwaya, Arthur; Pereira, Rui PA; McNerney, Ruth; Harris, David; Parkhill, Julian; Clark, Taane G; Glynn, Judith R

Newly Identified Mycobacterium africanum Lineage 10, Central Africa. (2024) Guyeux, Christophe; Senelle, Gaetan; Le Meur, Adrien; Supply, Philip; Gaudin, Cyril; Phelan, Jody E; Clark, Taane G; Rigouts, Leen; de Jong, Bouke; Sola, Christophe; Refrégier, Guislaine

Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications. (2022) Gómez-González, Paula J; Campino, Susana; Phelan, Jody E; Clark, Taane G

Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid. (2021) Gómez-González, Paula J; Perdigao, Joao; Gomes, Pedro; Puyen, Zully M; Santos-Lazaro, David; Napier, Gary; Hibberd, Martin L; Viveiros, Miguel; Portugal, Isabel; Campino, Susana; Phelan, Jody E; Clark, Taane G

Functional genetic variation in pe/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host. (2023) Gómez-González, Paula Josefina; Grabowska, Anna D; Tientcheu, Leopold D; Tsolaki, Anthony G; Hibberd, Martin L; Campino, Susana; Phelan, Jody E; Clark, Taane G

Epidemiology of SARS-CoV-2 infection among staff and students in a cohort of English primary and secondary schools during 2020-2021. (2022) Hargreaves, James R; Langan, Sinéad M; Oswald, William E; Halliday, Katherine E; Sturgess, Joanna; Phelan, Jody; Nguipdop-Djomo, Patrick; Ford, Benjamin; Allen, Elizabeth; Sundaram, Neisha; Ireland, Georgina; Poh, John; Ijaz, Samreen; Diamond, Ian; Rourke, Emma; Dawe, Fiona; Judd, Alison; Warren-Gash, Charlotte; Clark, Taane G; Glynn, Judith R; Edmunds, W John; Bonell, Chris; Mangtani, Punam; Ladhani, Shamez N; COVID-19 Schools Infection Survey Study Group

Artemisinin resistance-associated markers in Plasmodium falciparum parasites from the China-Myanmar border: predicted structural stability of K13 propeller variants detected in a low-prevalence area. (2019) He, Yan; Campino, Susana; Diez Benavente, Ernest; Warhurst, David C; Beshir, Khalid B; Lubis, Inke; Gomes, Ana Rita; Feng, Jun; Jiazhi, Wang; Sun, Xiaodong; Huang, Fang; Tang, Lin-Hua; Sutherland, Colin J; Clark, Taane G

Directional selection at the pfmdr1, pfcrt, pfubp1, and pfap2mu loci of Plasmodium falciparum in Kenyan children treated with ACT. (2014) Henriques, Gisela; Hallett, Rachel L; Beshir, Khalid B; Gadalla, Nahla B; Johnson, Rachel E; Burrow, Rebekah; van Schalkwyk, Donelly A; Sawa, Patrick; Omar, Sabah A; Clark, Taane G; Bousema, Teun; Sutherland, Colin J

A Pan Plasmodium lateral flow recombinase polymerase amplification assay for monitoring malaria parasites in vectors and human populations. (2024) Higgins, Matthew; Kristan, Mojca; Collins, Emma L; Messenger, Louisa A; Dombrowski, Jamille G; Vanheer, Leen N; Nolder, Debbie; Drakeley, Christopher J; Stone, William; Mahamar, Almahamoudou; Bousema, Teun; Delves, Michael; Bandibabone, Janvier; N'Do, Sévérin; Bantuzeko, Chimanuka; Zawadi, Bertin; Walker, Thomas; Sutherland, Colin J; Marinho, Claudio RF; Cameron, Mary M; Clark, Taane G; Campino, Susana picture_as_pdf

PrimedRPA: primer design for recombinase polymerase amplification assays. (2018) Higgins, Matthew; Ravenhall, Matt; Ward, Daniel; Phelan, Jody; Ibrahim, Amy; Forrest, Matthew S; Clark, Taane G; Campino, Susana

Characterizing the Impact of Primer-Template Mismatches on Recombinase Polymerase Amplification. (2022) Higgins, Matthew; Stringer, Oliver W; Ward, Daniel; Andrews, Jennifer M; Forrest, Matthew S; Campino, Susana; Clark, Taane G picture_as_pdf

Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus. (2014) 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

Whole-genome sequencing analysis of Burkholderia pseudomallei comparing drug-resistant and pan-susceptible isolates reveals novel biomarkers for drug resistance. (2025) Hinwan, Yothin; Nithimongkolchai, Nut; Trisakul, Kanwara; Kaewseekhao, Benjawan; Wonglakorn, Lumyai; Chetchotisakd, Ploenchan; Chareonsudjai, Sorujsiri; Sirichoat, Auttawit; Nithichanon, Arnone; Phelan, Jody; Clark, Taane G; Faksri, Kiatichai picture_as_pdf

Sequence-level population simulations over large genomic regions. (2007) Hoggart, Clive J; Chadeau-Hyam, Marc; Clark, Taane G; Lampariello, Riccardo; Whittaker, John C; De Iorio, Maria; Balding, David J

Genome-wide significance for dense SNP and resequencing data. (2008) Hoggart, Clive J; Clark, Taane G; De Iorio, Maria; Whittaker, John C; Balding, David J

Selective whole genome amplification of Plasmodium malariae DNA from clinical samples reveals insights into population structure. (2020) Ibrahim, Amy; Diez Benavente, Ernest; Nolder, Debbie; Proux, Stephane; Higgins, Matthew; Muwanguzi, Julian; Gomez Gonzalez, Paula Josefina; Fuehrer, Hans-Peter; Roper, Cally; Nosten, Francois; Sutherland, Colin; Clark, Taane G; Campino, Susana picture_as_pdf

Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America. (2023) Ibrahim, Amy; Manko, Emilia; Dombrowski, Jamille G; Campos, Mónica; Benavente, Ernest Diez; Nolder, Debbie; Sutherland, Colin J; Nosten, Francois; Fernandez, Diana; Vélez-Tobón, Gabriel; Castaño, Alberto Tobón; Aguiar, Anna Caroline C; Pereira, Dhelio Batista; da Silva Santos, Simone; Suarez-Mutis, Martha; Di Santi, Silvia Maria; Regina de Souza Baptista, Andrea; Dantas Machado, Ricardo Luiz; Marinho, Claudio RF; Clark, Taane G; Campino, Susana

Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan. (2019) 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; Waddell, Simon J; Clark, Taane G

Differences in the frequency of genetic variants associated with iron imbalance among global populations. (2020) Jallow, Momodou W; Cerami, Carla; Clark, Taane G; Prentice, Andrew M; Campino, Susana picture_as_pdf

Genome-wide and fine-resolution association analysis of malaria in West Africa. (2009) Jallow, Muminatou; Teo, Yik Ying; Small, Kerrin S; Rockett, Kirk A; Deloukas, Panos; Clark, Taane G; Kivinen, Katja; Bojang, Kalifa A; Conway, David J; Pinder, Margaret; Sirugo, Giorgio; Sisay-Joof, Fatou; Usen, Stanley; Auburn, Sarah; Bumpstead, Suzannah J; Campino, Susana; Coffey, Alison; Dunham, Andrew; Fry, Andrew E; Green, Angela; Gwilliam, Rhian; Hunt, Sarah E; Inouye, Michael; Jeffreys, Anna E; Mendy, Alieu; Palotie, Aarno; Potter, Simon; Ragoussis, Jiannis; Rogers, Jane; Rowlands, Kate; Somaskantharajah, Elilan; Whittaker, Pamela; Widden, Claire; Donnelly, Peter; Howie, Bryan; Marchini, Jonathan; Morris, Andrew; SanJoaquin, Miguel; Achidi, Eric Akum; Agbenyega, Tsiri; Allen, Angela; Amodu, Olukemi; Corran, Patrick; Djimde, Abdoulaye; Dolo, Amagana; Doumbo, Ogobara K; Drakeley, Chris; Dunstan, Sarah; Evans, Jennifer; Farrar, Jeremy; Fernando, Deepika; Hien, Tran Tinh; Horstmann, Rolf D; Ibrahim, Muntaser; Karunaweera, Nadira; Kokwaro, Gilbert; Koram, Kwadwo A; Lemnge, Martha; Makani, Julie; Marsh, Kevin; Michon, Pascal; Modiano, David; Molyneux, Malcolm E; Mueller, Ivo; Parker, Michael; Peshu, Norbert; Plowe, Christopher V; Puijalon, Odile; Reeder, John; Reyburn, Hugh; Riley, Eleanor M; Sakuntabhai, Anavaj; Singhasivanon, Pratap; Sirima, Sodiomon; Tall, Adama; Taylor, Terrie E; Thera, Mahamadou; Troye-Blomberg, Marita; Williams, Thomas N; Wilson, Michael; Kwiatkowski, Dominic P; Wellcome Trust Case Control Consortium; Malaria Genomic Epidemiology Network

The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China. (2023) Jiang, Qi; Liu, Hai-Can; Liu, Qing-Yun; Phelan, Jody E; Tao, Feng-Xi; Zhao, Xiu-Qin; Wang, Jian; Glynn, Judith R; Takiff, Howard E; Clark, Taane G; Wan, Kang-Lin; Gao, Qian

Polymorphisms in dopamine metabolic enzymes and tobacco consumption in smokers: seeking confirmation of the association in a follow-up study. (2002) Johnstone, Elaine C; Clark, Taane G; Griffiths, Siân-Elin; Murphy, Michael F; Walton, Robert T

A transcriptional switch underlies commitment tosexual development in malaria parasites. (2014) Kafsack, BF; Rovira-Graells, N; Clark, TG; Bancells, C; Crowley, VM; Campino, SG; Williams, AE; Drought, LG; Kwiatkowski, DP; Baker, DA; Cortés, A; Llinás, M

A transcriptional switch underlies commitment to sexual development in malaria parasites. (2014) Kafsack, Björn FC; Rovira-Graells, Núria; Clark, Taane G; Bancells, Cristina; Crowley, Valerie M; Campino, Susana G; Williams, April E; Drought, Laura G; Kwiatkowski, Dominic P; Baker, David A; Cortés, Alfred; Llinás, Manuel

Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan. (2017) Kanji, A; Hasan, R; Ali, A; Zaver, A; Zhang, Y; Imtiaz, K; Shi, W; Clark, TG; McNerney, R; Phelan, J; Rao, S; Shafiq, S; Hasan, Z

Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan. (2017) Kanji, Akbar; Hasan, Rumina; Ali, Asho; Zaver, Ambreen; Zhang, Ying; Imtiaz, Kehkashan; Shi, Wanliang; Clark, Taane G; McNerney, Ruth; Phelan, Jody; Rao, Shoaib; Shafiq, Samreen; Hasan, Zahra

Alternate efflux pump mechanism may contribute to drug resistance in extensively drug-resistant isolates of Mycobacterium tuberculosis. (2016) Kanji, Akbar; Hasan, Rumina; Zaver, Ambreen; Ali, Asho; Imtiaz, Kehkashan; Ashraf, Mussarat; Clark, Taane G; McNerney, Ruth; Shafiq, Samreen; Hasan, Zahra

Characterization of genomic variations in SNPs of PE_PGRS genes reveals deletions and insertions in extensively drug resistant (XDR) M. tuberculosis strains from Pakistan. (2015) Kanji, Akbar; Hasan, Zahra; Ali, Asho; McNerney, Ruth; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant; Nair, Mridul; Clark, Taane G; Zaver, Ambreen; Jafri, Sana; Hasan, Rumina

The genetic risk of acute seizures in African children with falciparum malaria. (2013) Kariuki, Symon M; Rockett, Kirk; Clark, Taane G; Reyburn, Hugh; Agbenyega, Tsiri; Taylor, Terrie E; Birbeck, Gretchen L; Williams, Thomas N; Newton, Charles RJC

Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania. (2020) Katale, Bugwesa Z; Mbelele, Peter M; Lema, Nsiande A; Campino, Susana; Mshana, Stephen E; Rweyemamu, Mark M; Phelan, Jody E; Keyyu, Julius D; Majigo, Mtebe; Mbugi, Erasto V; Dockrell, Hazel M; Clark, Taane G; Matee, Mecky I; Mpagama, Stellah

Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review. (2020) Katale, Bugwesa Z; Misinzo, Gerald; Mshana, Stephen E; Chiyangi, Harriet; Campino, Susana; Clark, Taane G; Good, Liam; Rweyemamu, Mark M; Matee, Mecky I

Estimating the number of coding mutations in genotypic and phenotypic driven N-ethyl-N-nitrosourea (ENU) screens: revisited. (2007) Keays, David A; Clark, Taane G; Campbell, Thomas G; Broxholme, John; Valdar, William

Estimating the number of coding mutations in genotypic- and phenotypic-driven N-ethyl-N-nitrosourea (ENU) screens. (2006) Keays, David A; Clark, Taane G; Flint, Jonathan

Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan. (2021) Khan, Anwar Sheed; Phelan, Jody E; Khan, Muhammad Tahir; Ali, Sajid; Qasim, Muhammad; Napier, Gary; Campino, Susana; Ahmad, Sajjad; Cabral-Marques, Otavio; Zhang, Shulin; Rahman, Hazir; Wei, Dong-Qing; Clark, Taane G; Khan, Taj Ali

Author Correction: Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan. (2021) Khan, Anwar Sheed; Phelan, Jody E; Khan, Muhammad Tahir; Ali, Sajid; Qasim, Muhammad; Napier, Gary; Campino, Susana; Ahmad, Sajjad; Cabral-Marques, Otavio; Zhang, Shulin; Rahman, Hazir; Wei, Dong-Qing; Clark, Taane G; Khan, Taj Ali

Further Evidence of Increasing Diversity of Plasmodium vivax in the Republic of Korea in Recent Years. (2016) Kim, Jung-Yeon; Goo, Youn-Kyoung; Zo, Young-Gun; Ji, So-Young; Trimarsanto, Hidayat; To, Sheren; Clark, Taane G; Price, Ric N; Auburn, Sarah

Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya. (2018) Kiyuka, Patience K; Agoti, Charles N; Munywoki, Patrick K; Njeru, Regina; Bett, Anne; Otieno, James R; Otieno, Grieven P; Kamau, Everlyn; Clark, Taane G; van der Hoek, Lia; Kellam, Paul; Nokes, D James; Cotten, Matthew

Towards environmental detection, quantification, and molecular characterization of Anopheles stephensi and Aedes aegypti from experimental larval breeding sites. (2023) Kristan, Mojca; Acford-Palmer, Holly; Campos, Monica Oliveira; Collins, Emma L; Phelan, Jody; Portwood, Natalie M; Pelloquin, Bethanie; Clarke, Sian; Lines, Jo; Clark, Taane G; Walker, Thomas; Campino, Susana; Messenger, Louisa A

Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya. (2022) Kuja, Josiah O; Kanoi, Bernard N; Balboa, Renzo F; Shiluli, Clement; Maina, Michael; Waweru, Harrison; Gathii, Kimita; Mungai, Mary; Masika, Moses; Anzala, Omu; Mwau, Matilu; Clark, Taane G; Waitumbi, John; Gitaka, Jesse

The UK ME/CFS Biobank for biomedical research on Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Multiple Sclerosis. (2017) Lacerda, Eliana M; Bowman, Erinna W; Cliff, Jacqueline M; Kingdon, Caroline C; King, Elizabeth C; Lee, Ji-Sook; Clark, Taane G; Dockrell, Hazel M; Riley, Eleanor M; Curran, Hayley; Nacul, Luis

Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity. (2018) Last, AR; Pickering, H; Roberts, CH; Coll, F; Phelan, J; Burr, SE; Cassama, E; Nabicassa, M; Seth-Smith, HMB; Hadfield, J; Cutcliffe, LT; Clarke, IN; Mabey, DCW; Bailey, RL; Clark, TG; Thomson, NR; Holland, MJ

Population-based analysis of ocular<i>Chlamydia trachomatis</i>in trachoma-endemic West African communities identifies genomic markers of disease severity. (2017) Last, AR; Pickering, H; Roberts, Ch; Coll, F; Phelan, J; Burr, SE; Cassama, E; Nabicassa, M; Seth-Smith, HMB; Hadfield, J; Cutcliffe, LT; Clarke, IN; Mabey, DCW; Bailey, RL; Clark, TG; Thomson, NR; Holland, MJ

Use of purified Clostridium difficile spores to facilitate evaluation of health care disinfection regimens. (2010) Lawley, Trevor D; Clare, Simon; Deakin, Laura J; Goulding, David; Yen, Jennifer L; Raisen, Claire; Brandt, Cordelia; Lovell, Jon; Cooke, Fiona; Clark, Taane G; Dougan, Gordon

Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. (2012) Lawley, Trevor D; Clare, Simon; Walker, Alan W; Stares, Mark D; Connor, Thomas R; Raisen, Claire; Goulding, David; Rad, Roland; Schreiber, Fernanda; Brandt, Cordelia; Deakin, Laura J; Pickard, Derek J; Duncan, Sylvia H; Flint, Harry J; Clark, Taane G; Parkhill, Julian; Dougan, Gordon

Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom. (2018) Leon, Lydia J; Doyle, Ronan; Diez-Benavente, Ernest; Clark, Taane G; Klein, Nigel; Stanier, Philip; Moore, Gudrun E

Deep learning-derived cardiovascular age shares a genetic basis with other cardiac phenotypes. (2022) Libiseller-Egger, Julian; Phelan, Jody E; Attia, Zachi I; Benavente, Ernest Diez; Campino, Susana; Friedman, Paul A; Lopez-Jimenez, Francisco; Leon, David A; Clark, Taane G

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers. (2020) Libiseller-Egger, Julian; Phelan, Jody; Campino, Susana; Mohareb, Fady; Clark, Taane G picture_as_pdf

TB-ML-a framework for comparing machine learning approaches to predict drug resistance of Mycobacterium tuberculosis. (2023) Libiseller-Egger, Julian; Wang, Linfeng; Deelder, Wouter; Campino, Susana; Clark, Taane G; Phelan, Jody E

Detecting and characterizing genomic signatures of positive selection in global populations. (2013) Liu, Xuanyao; Ong, Rick Twee-Hee; Pillai, Esakimuthu Nisha; Elzein, Abier M; Small, Kerrin S; Clark, Taane G; Kwiatkowski, Dominic P; Teo, Yik-Ying

Genetic diversity and population structure of Plasmodium vivax in Central China. (2014) Liu, Yaobao; Auburn, Sarah; Cao, Jun; Trimarsanto, Hidayat; Zhou, Huayun; Gray, Karen-Ann; Clark, Taane G; Price, Ric N; Cheng, Qin; Huang, Rui; Gao, Qi

Fc gamma receptor IIa-H131R polymorphism and malaria susceptibility in sympatric ethnic groups, Fulani and Dogon of Mali. (2013) Maiga, B; Dolo, A; Touré, O; Dara, V; Tapily, A; Campino, S; Sepulveda, N; Corran, P; Rockett, K; Clark, TG; Blomberg, M Troye; Doumbo, OK

Glucose-6-phosphate dehydrogenase polymorphisms and susceptibility to mild malaria in Dogon and Fulani, Mali. (2014) Maiga, Bakary; Dolo, Amagana; Campino, Susana; Sepulveda, Nuno; Corran, Patrick; Rockett, Kirk A; Troye-Blomberg, Marita; Doumbo, Ogobara K; Clark, Taane G

Human candidate polymorphisms in sympatric ethnic groups differing in malaria susceptibility in Mali. (2013) Maiga, Bakary; Dolo, Amagana; Touré, Ousmane; Dara, Victor; Tapily, Amadou; Campino, Susana; Sepulveda, Nuno; Risley, Paul; Silva, Nilupa; Corran, Patrick; Rockett, Kirk A; Kwiatkowski, Dominic; MalariaGEN Consortium; Clark, Taane G; Troye-Blomberg, Marita; Doumbo, Ogobara K

Interferon regulatory factor-1 polymorphisms are associated with the control of Plasmodium falciparum infection. (2008) Mangano, VD; Luoni, G; Rockett, KA; Sirima, BS; Konaté, A; Forton, J; Clark, TG; Bancone, G; Sadighi Akha, E; Kwiatkowski, DP; Modiano, D

Lack of association of interferon regulatory factor 1 with severe malaria in affected child-parental trio studies across three African populations. (2009) Mangano, Valentina D; Clark, Taane G; Auburn, Sarah; Campino, Susana; Diakite, Mahamadou; Fry, Andrew E; Green, Angela; Richardson, Anna; Jallow, Muminatou; Sisay-Joof, Fatou; Pinder, Margaret; Griffiths, Michael J; Newton, Charles; Peshu, Norbert; Williams, Thomas N; Marsh, Kevin; Molyneux, Malcolm E; Taylor, Terrie E; Modiano, David; Kwiatkowski, Dominic P; Rockett, Kirk A

Candidate human genetic polymorphisms and severe malaria in a Tanzanian population. (2012) Manjurano, Alphaxard; Clark, Taane G; Nadjm, Behzad; Mtove, George; Wangai, Hannah; Sepulveda, Nuno; Campino, Susana G; Maxwell, Caroline; Olomi, Raimos; Rockett, Kirk R; Jeffreys, Anna; MalariaGen Consortium; Riley, Eleanor M; Reyburn, Hugh; Drakeley, Christopher

Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania. (2011) Manjurano, Alphaxard; Okell, Lucy; Lukindo, Tedson; Reyburn, Hugh; Olomi, Raimos; Roper, Cally; Clark, Taane G; Joseph, Sarah; Riley, Eleanor M; Drakeley, Chris

African glucose-6-phosphate dehydrogenase alleles associated with protection from severe malaria in heterozygous females in Tanzania. (2015) Manjurano, Alphaxard; Sepulveda, Nuno; Nadjm, Behzad; Mtove, George; Wangai, Hannah; Maxwell, Caroline; Olomi, Raimos; Reyburn, Hugh; Riley, Eleanor M; Drakeley, Christopher J; Clark, Taane G; MalariaGEN Consortium

USP38, FREM3, SDC1, DDC, and LOC727982 Gene Polymorphisms and Differential Susceptibility to Severe Malaria in Tanzania. (2015) Manjurano, Alphaxard; Sepúlveda, Nuno; Nadjm, Behzad; Mtove, George; Wangai, Hannah; Maxwell, Caroline; Olomi, Raimos; Reyburn, Hugh; Drakeley, Christopher J; Riley, Eleanor M; Clark, Taane G; in Collaboration With MalariaGEN

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. (2012) Manske, Magnus; Miotto, Olivo; Campino, Susana; Auburn, Sarah; Almagro-Garcia, Jacob; Maslen, Gareth; O'Brien, Jack; Djimde, Abdoulaye; Doumbo, Ogobara; Zongo, Issaka; Ouedraogo, Jean-Bosco; Michon, Pascal; Mueller, Ivo; Siba, Peter; Nzila, Alexis; Borrmann, Steffen; Kiara, Steven M; Marsh, Kevin; Jiang, Hongying; Su, Xin-Zhuan; Amaratunga, Chanaki; Fairhurst, Rick; Socheat, Duong; Nosten, Francois; Imwong, Mallika; White, Nicholas J; Sanders, Mandy; Anastasi, Elisa; Alcock, Dan; Drury, Eleanor; Oyola, Samuel; Quail, Michael A; Turner, Daniel J; Ruano-Rubio, Valentin; Jyothi, Dushyanth; Amenga-Etego, Lucas; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Sutherland, Colin; Roper, Cally; Mangano, Valentina; Modiano, David; Tan, John C; Ferdig, Michael T; Amambua-Ngwa, Alfred; Conway, David J; Takala-Harrison, Shannon; Plowe, Christopher V; Rayner, Julian C; Rockett, Kirk A; Clark, Taane G; Newbold, Chris I; Berriman, Matthew; MacInnis, Bronwyn; Kwiatkowski, Dominic P

Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones. (2022) Mazumder, Razib; Hussain, Arif; Phelan, Jody E; Campino, Susana; Haider, SM Arefeen; Mahmud, Araf; Ahmed, Dilruba; Asadulghani, Md; Clark, Taane G; Mondal, Dinesh

Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action. (2016) McNerney, Ruth; Clark, Taane G; Campino, Susana; Rodrigues, Camilla; Dolinger, David; Smith, Liezel; Cabibbe, Andrea M; Dheda, Keertan; Schito, Marco

Use of whole genome sequencing in surveillance of drug resistant tuberculosis. (2018) McNerney, Ruth; Zignol, Matteo; Clark, Taane G

The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957. (2021) Miguel-Blanco, Celia; Murithi, James M; Benavente, Ernest Diez; Angrisano, Fiona; Sala, Katarzyna A; van Schalkwyk, Donelly A; Vanaerschot, Manu; Schwach, Frank; Fuchter, Matthew J; Billker, Oliver; Sutherland, Colin J; Campino, Susana G; Clark, Taane G; Blagborough, Andrew M; Fidock, David A; Herreros, Esperanza; Gamo, Francisco Javier; Baum, Jake; Delves, Michael J

Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity. (2014) Mobegi, Victor A; Duffy, Craig W; Amambua-Ngwa, Alfred; Loua, Kovana M; Laman, Eugene; Nwakanma, Davis C; MacInnis, Bronwyn; Aspeling-Jones, Harvey; Murray, Lee; Clark, Taane G; Kwiatkowski, Dominic P; Conway, David J

Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016. (2022) Montoya, Jaime C; Malabad, John Carlo M; Ang, Concepcion F; Reyes, Lorenzo T; Basilio, Ramon P; Lim, Dodge R; Amarillo, Maria Lourdes E; Ama, Ma Cecilia G; Phelan, Jody E; Hibberd, Martin L; Clark, Taane G

Phenotypic evidence of deltamethrin resistance and identification of selective sweeps in Anopheles mosquitoes on the Bijagós Archipelago, Guinea-Bissau. (2024) Moss, Sophie; Jones, Robert T; Pretorius, Elizabeth; da Silva, Eunice Teixeira; Higgins, Matthew; Kristan, Mojca; Acford-Palmer, Holly; Collins, Emma L; Rodrigues, Amabelia; Krishna, Sanjeev; Clark, Taane G; Last, Anna; Campino, Susana

How has mass drug administration with dihydroartemisinin-piperaquine impacted molecular markers of drug resistance? A systematic review. (2022) Moss, Sophie; Mańko, Emilia; Krishna, Sanjeev; Campino, Susana; Clark, Taane G; Last, Anna

Population dynamics and drug resistance mutations in Plasmodium falciparum on the Bijagós Archipelago, Guinea-Bissau. (2023) Moss, Sophie; Mańko, Emilia; Vasileva, Hristina; Da Silva, Eunice Teixeira; Goncalves, Adriana; Osborne, Ashley; Phelan, Jody; Rodrigues, Amabelia; Djata, Paulo; D'Alessandro, Umberto; Mabey, David; Krishna, Sanjeev; Last, Anna; Clark, Taane G; Campino, Susana

Whole genome sequence analysis of population structure and insecticide resistance markers in Anopheles melas from the Bijagós Archipelago, Guinea-Bissau. (2024) Moss, Sophie; Pretorius, Elizabeth; Ceesay, Sainey; da Silva, Eunice Teixeira; Hutchins, Harry; Ndiath, Mamadou Ousmane; Acford-Palmer, Holly; Collins, Emma L; Higgins, Matthew; Phelan, Jody; Jones, Robert T; Vasileva, Hristina; Rodrigues, Amabelia; Krishna, Sanjeev; Clark, Taane G; Last, Anna; Campino, Susana

Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development. (2014) Moule, Madeleine G; Hemsley, Claudia M; Seet, Qihui; Guerra-Assunção, José Afonso; Lim, Jiali; Sarkar-Tyson, Mitali; Clark, Taane G; Tan, Patrick BO; Titball, Richard W; Cuccui, Jon; Wren, Brendan W

Characterization of New Virulence Factors Involved in the Intracellular Growth and Survival of Burkholderia pseudomallei. (2015) Moule, Madeleine G; Spink, Natasha; Willcocks, Sam; Lim, Jiali; Guerra-Assunção, José Afonso; Cia, Felipe; Champion, Olivia L; Senior, Nicola J; Atkins, Helen S; Clark, Taane; Bancroft, Gregory J; Cuccui, Jon; Wren, Brendan W

Lack of association of the COMT (Val158/108 Met) gene and schizophrenia: a meta-analysis of case-control studies. (2005) Munafò, MR; Bowes, L; Clark, TG; Flint, J

Does measurement instrument moderate the association between the serotonin transporter gene and anxiety-related personality traits? A meta-analysis. (2005) Munafò, MR; Clark, T; Flint, J

Are there sex differences in the association between the 5HTT gene and neuroticism? A meta-analysis. (2004) Munafò, MR; Clark, TG; Flint, J

Genetic polymorphisms and personality in healthy adults: a systematic review and meta-analysis. (2003) Munafò, MR; Clark, TG; Moore, LR; Payne, E; Walton, R; Flint, J

Association of the NRG1 gene and schizophrenia: a meta-analysis. (2006) Munafò, MR; Thiselton, DL; Clark, TG; Flint, J

Assessing publication bias in genetic association studies: evidence from a recent meta-analysis. (2004) Munafò, Marcus R; Clark, Taane G; Flint, Jonathan

Neuroticism mediates the association of the serotonin transporter gene with lifetime major depression. (2006) Munafò, Marcus R; Clark, Taane G; Roberts, Kate H; Johnstone, Elaine C

Personality and smoking status: a meta-analysis. (2007) Munafò, Marcus R; Zetteler, Jessica I; Clark, Taane G

The genetic basis for smoking behavior: a systematic review and meta-analysis. (2004) Munafò, Marcus; Clark, Taane; Johnstone, Elaine; Murphy, Michael; Walton, Robert

Hand Grip Strength as a Clinical Biomarker for ME/CFS and Disease Severity. (2018) Nacul, Luis Carlos; Mudie, Kathleen; Kingdon, Caroline C; Clark, Taane G; Lacerda, Eliana Mattos

How Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) Progresses: The Natural History of ME/CFS. (2020) Nacul, Luis; O'Boyle, Shennae; Palla, Luigi; Nacul, Flavio E; Mudie, Kathleen; Kingdon, Caroline C; Cliff, Jacqueline M; Clark, Taane G; Dockrell, Hazel M; Lacerda, Eliana M

Evidence of Clinical Pathology Abnormalities in People with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) from an Analytic Cross-Sectional Study. (2019) Nacul, Luis; de Barros, Barbara; Kingdon, Caroline C; Cliff, Jacqueline M; Clark, Taane G; Mudie, Kathleen; Dockrell, Hazel M; Lacerda, Eliana M picture_as_pdf

SVAMP: sequence variation analysis, maps and phylogeny. (2014) Naeem, Raeece; Hidayah, Lailatul; Preston, Mark D; Clark, Taane G; Pain, Arnab

Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance. (2017) Nakatani, Yoshio; Opel-Reading, Helen K; Merker, Matthias; Machado, Diana; Andres, Sönke; Kumar, S Siva; Moradigaravand, Danesh; Coll, Francesc; Perdigão, João; Portugal, Isabel; Schön, Thomas; Nair, Dina; Devi, KR Uma; Kohl, Thomas A; Beckert, Patrick; Clark, Taane G; Maphalala, Gugu; Khumalo, Derrick; Diel, Roland; Klaos, Kadri; Aung, Htin Lin; Cook, Gregory M; Parkhill, Julian; Peacock, Sharon J; Swaminathan, Soumya; Viveiros, Miguel; Niemann, Stefan; Krause, Kurt L; Köser, Claudio U

Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. (2020) Napier, Gary; Campino, Susana; Merid, Yared; Abebe, Markos; Woldeamanuel, Yimtubezinash; Aseffa, Abraham; Hibberd, Martin L; Phelan, Jody; Clark, Taane G

Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan. (2022) Napier, Gary; Khan, Anwar Sheed; Jabbar, Abdul; Khan, Muhammad Tahir; Ali, Sajid; Qasim, Muhammad; Mohammad, Noor; Hasan, Rumina; Hasan, Zahra; Campino, Susana; Ahmad, Sajjad; Khattak, Baharullah; Waddell, Simon J; Khan, Taj Ali; Phelan, Jody E; Clark, Taane G picture_as_pdf

Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study. (2018) Ndila, Carolyne M; Uyoga, Sophie; Macharia, Alexander W; Nyutu, Gideon; Peshu, Norbert; Ojal, John; Shebe, Mohammed; Awuondo, Kennedy O; Mturi, Neema; Tsofa, Benjamin; Sepúlveda, Nuno; Clark, Taane G; Band, Gavin; Clarke, Geraldine; Rowlands, Kate; Hubbart, Christina; Jeffreys, Anna; Kariuki, Silvia; Marsh, Kevin; Mackinnon, Margaret; Maitland, Kathryn; Kwiatkowski, Dominic P; Rockett, Kirk A; Williams, Thomas N; MalariaGEN Consortium

Risk factors for SARS-CoV-2 infection in primary and secondary school students and staff in England in the 2020/2021 school year: a longitudinal study. (2023) Nguipdop-Djomo, Patrick; Oswald, William E; Halliday, Katherine E; Cook, Sarah; Sturgess, Joanna; Sundaram, Neisha; Warren-Gash, Charlotte; Fine, Paul Em; Glynn, Judith; Allen, Elizabeth; Clark, Taane G; Ford, Benjamin; Judd, Alison; Ireland, Georgina; Poh, John; Bonell, Chris; Dawe, Fiona; Rourke, Emma; Diamond, Ian; Ladhani, Shamez N; Langan, Sinéad M; Hargreaves, James; Mangtani, Punam; COVID-19 Schools Infection Survey Study Group

Clusters of Drug-Resistant Mycobacterium tuberculosis Detected by Whole-Genome Sequence Analysis of Nationwide Sample, Thailand, 2014-2017. (2021) Nonghanphithak, Ditthawat; Chaiprasert, Angkana; Smithtikarn, Saijai; Kamolwat, Phalin; Pungrassami, Petchawan; Chongsuvivatwong, Virasakdi; Mahasirimongkol, Surakameth; Reechaipichitkul, Wipa; Leepiyasakulchai, Chaniya; Phelan, Jody E; Blair, David; Clark, Taane G; Faksri, Kiatichai

Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination. (2015) Noviyanti, Rintis; Coutrier, Farah; Utami, Retno AS; Trimarsanto, Hidayat; Tirta, Yusrifar K; Trianty, Leily; Kusuma, Andreas; Sutanto, Inge; Kosasih, Ayleen; Kusriastuti, Rita; Hawley, William A; Laihad, Ferdinand; Lobo, Neil; Marfurt, Jutta; Clark, Taane G; Price, Ric N; Auburn, Sarah

Changes in malaria parasite drug resistance in an endemic population over a 25-year period with resulting genomic evidence of selection. (2013) Nwakanma, Davis C; Duffy, Craig W; Amambua-Ngwa, Alfred; Oriero, Eniyou C; Bojang, Kalifa A; Pinder, Margaret; Drakeley, Chris J; Sutherland, Colin J; Milligan, Paul J; Macinnis, Bronwyn; Kwiatkowski, Dominic P; Clark, Taane G; Greenwood, Brian M; Conway, David J

A Natural History of Disease Framework for Improving the Prevention, Management, and Research on Post-viral Fatigue Syndrome and Other Forms of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. (2021) O'Boyle, Shennae; Nacul, Luis; Nacul, Flavio E; Mudie, Kathleen; Kingdon, Caroline C; Cliff, Jacqueline M; Clark, Taane G; Dockrell, Hazel M; Lacerda, Eliana M

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. (2021) O'Sullivan, Denise M; Doyle, Ronan M; Temisak, Sasithon; Redshaw, Nicholas; Whale, Alexandra S; Logan, Grace; Huang, Jiabin; Fischer, Nicole; Amos, Gregory CA; Preston, Mark D; Marchesi, Julian R; Wagner, Josef; Parkhill, Julian; Motro, Yair; Denise, Hubert; Finn, Robert D; Harris, Kathryn A; Kay, Gemma L; O'Grady, Justin; Ransom-Jones, Emma; Wu, Huihai; Laing, Emma; Studholme, David J; Benavente, Ernest Diez; Phelan, Jody; Clark, Taane G; Moran-Gilad, Jacob; Huggett, Jim F

Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates. (2014) Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa; Jensen, Anja TR; Campino, Susana; MacInnis, Bronwyn; Alcock, Daniel; Terlouw, Anja; Zongo, Issaka; Oudraogo, Jean-Bosco; Djimde, Abdoulaye A; Assefa, Samuel; Doumbo, Ogobara K; Borrmann, Steffen; Nzila, Alexis; Marsh, Kevin; Fairhurst, Rick M; Nosten, Francois; Anderson, Tim JC; Kwiatkowski, Dominic P; Craig, Alister; Clark, Taane G; Montgomery, Jacqui

Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance. (2019) Oppong, Yaa EA; Phelan, Jody; Perdigão, João; Machado, Diana; Miranda, Anabela; Portugal, Isabel; Viveiros, Miguel; Clark, Taane G; Hibberd, Martin L picture_as_pdf

De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members. (2022) Oresegun, Damilola R; Thorpe, Peter; Benavente, Ernest Diez; Campino, Susana; Muh, Fauzi; Moon, Robert William; Clark, Taane Gregory; Cox-Singh, Janet

Electrochemical Detection of Single-Nucleotide Polymorphism Associated with Rifampicin Resistance in Mycobacterium tuberculosis Using Solid-Phase Primer Elongation with Ferrocene-Linked Redox-Labeled Nucleotides. (2021) Ortiz, Mayreli; Jauset-Rubio, Miriam; Skouridou, Vasso; Machado, Diana; Viveiros, Miguel; Clark, Taane G; Simonova, Anna; Kodr, David; Hocek, Michal; O'Sullivan, Ciara K

Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya. (2021) Osborne, Ashley; Manko, Emilia; Takeda, Mika; Kaneko, Akira; Kagaya, Wataru; Chan, Chim; Ngara, Mtakai; Kongere, James; Kita, Kiyoshi; Campino, Susana; Kaneko, Osamu; Gitaka, Jesse; Clark, Taane G

The genome of the simian and human malaria parasite Plasmodium knowlesi. (2008) Pain, A; Böhme, U; Berry, AE; Mungall, K; Finn, RD; Jackson, AP; Mourier, T; Mistry, J; Pasini, EM; Aslett, MA; Balasubrammaniam, S; Borgwardt, K; Brooks, K; Carret, C; Carver, TJ; Cherevach, I; Chillingworth, T; Clark, TG; Galinski, MR; Hall, N; Harper, D; Harris, D; Hauser, H; Ivens, A; Janssen, CS; Keane, T; Larke, N; Lapp, S; Marti, M; Moule, S; Meyer, IM; Ormond, D; Peters, N; Sanders, M; Sanders, S; Sargeant, TJ; Simmonds, M; Smith, F; Squares, R; Thurston, S; Tivey, AR; Walker, D; White, B; Zuiderwijk, E; Churcher, C; Quail, MA; Cowman, AF; Turner, CMR; Rajandream, MA; Kocken, CHM; Thomas, AW; Newbold, CI; Barrell, BG; Berriman, M

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. (2018) Palittapongarnpim, Prasit; Ajawatanawong, Pravech; Viratyosin, Wasna; Smittipat, Nat; Disratthakit, Areeya; Mahasirimongkol, Surakameth; Yanai, Hideki; Yamada, Norio; Nedsuwan, Supalert; Imasanguan, Worarat; Kantipong, Pacharee; Chaiyasirinroje, Boonchai; Wongyai, Jiraporn; Toyo-Oka, Licht; Phelan, Jody; Parkhill, Julian; Clark, Taane G; Hibberd, Martin L; Ruengchai, Wuthiwat; Palittapongarnpim, Panawun; Juthayothin, Tada; Tongsima, Sissades; Tokunaga, Katsushi

Expression profile of wild-type ETV6 in childhood acute leukaemia. (2003) Patel, Naina; Goff, Lindsey K; Clark, Taane; Ford, Anthony M; Foot, Nicola; Lillington, Debra; Hing, Sandra; Pritchard-Jones, Kathy; Jones, Louise K; Saha, Vaskar

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. (2020) Perdigão, João; Caneiras, Cátia; Elias, Rita; Modesto, Ana; Spadar, Anton; Phelan, Jody; Campino, Susana; Clark, Taane G; Costa, Eliana; Saavedra, Maria José; Duarte, Aida

Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal. (2020) Perdigão, João; Gomes, Pedro; Miranda, Anabela; Maltez, Fernando; Machado, Diana; Silva, Carla; Phelan, Jody E; Brum, Laura; Campino, Susana; Couto, Isabel; Viveiros, Miguel; Clark, Taane G; Portugal, Isabel

Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital. (2020) Perdigão, João; Modesto, Ana; Pereira, AL; Neto, O; Matos, V; Godinho, A; Phelan, Jody; Charleston, James; Spadar, Anton; de Sessions, Paola Florez; Hibberd, Martin; Campino, Susana; Costa, A; Fernandes, F; Ferreira, F; Correia, AB; Gonçalves, Luisa; Clark, Taane G; Duarte, Aida

Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries. (2018) Perdigão, João; Silva, Carla; Diniz, Jaciara; Pereira, Catarina; Machado, Diana; Ramos, Jorge; Silva, Hugo; Abilleira, Fernanda; Brum, Clarice; Reis, Ana J; 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

Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing. (2020) Perdigão, João; Silva, Carla; Maltez, Fernando; Machado, Diana; Miranda, Anabela; Couto, Isabel; Rabna, Paulo; Florez de Sessions, Paola; Phelan, Jody; Pain, Arnab; McNerney, Ruth; Hibberd, Martin L; Mokrousov, Igor; Clark, Taane G; Viveiros, Miguel; Portugal, Isabel

Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting. (2014) Perdigão, João; Silva, Hugo; Machado, Diana; Macedo, Rita; Maltez, Fernando; Silva, Carla; Jordao, Luisa; Couto, Isabel; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant A; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Viveiros, Miguel; Portugal, Isabel

Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages. (2016) 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; 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

Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines. (2019) 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; 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

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. (2019) 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; Huggett, Jim F; Clark, Taane G

Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control. (2023) Phelan, Jody E; Turkiewicz, Anna; Manko, Emilia; Thorpe, Joseph; Vanheer, Leen N; van de Vegte-Bolmer, Marga; Ngoc, Nguyen Thi Hong; Binh, Nguyen Thi Huong; Thieu, Nguyen Quang; Gitaka, Jesse; Nolder, Debbie; Beshir, Khalid B; Dombrowski, Jamille G; Di Santi, Silvia Maria; Bousema, Teun; Sutherland, Colin J; Campino, Susana; Clark, Taane G

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. (2016) 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; Ramsay, Andrew; Campino, Susana; Hibberd, Martin L; Pain, Arnab; Rigouts, Leen; Clark, Taane G

COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data. (2022) Phelan, Jody; Deelder, Wouter; Ward, Daniel; Campino, Susana; Hibberd, Martin L; Clark, Taane G

Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease. (2023) Phelan, Jody; Gomez-Gonzalez, Paula Josefina; Andreu, Nuria; Omae, Yosuke; Toyo-Oka, Licht; Yanai, Hideki; Miyahara, Reiko; Nedsuwan, Supalert; de Sessions, Paola Florez; Campino, Susana; Sallah, Neneh; Parkhill, Julian; Smittipat, Nat; Palittapongarnpim, Prasit; Mushiroda, Taisei; Kubo, Michiaki; Tokunaga, Katsushi; Mahasirimongkol, Surakameth; Hibberd, Martin L; Clark, Taane G

The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae. (2015) Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane G

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs. (2016) Phelan, Jody; O'Sullivan, Denise M; Machado, Diana; Ramos, Jorge; Whale, Alexandra S; O'Grady, Justin; Dheda, Keertan; Campino, Susana; McNerney, Ruth; Viveiros, Miguel; Huggett, Jim F; Clark, Taane G

An open-access dashboard to interrogate the genetic diversity of Mycobacterium tuberculosis clinical isolates. (2024) Phelan, Jody; Van den Heede, Klaas; Masyn, Serge; Verbeeck, Rudi; Clark, Taane G; Lamprecht, Dirk A; Koul, Anil; Wall, Richard J

Methylation in Mycobacterium tuberculosis is lineage specific with associated mutations present globally. (2017) Phelan, Jody; de Sessions, Paola Florez; Tientcheu, Leopold; Perdigao, Joao; Machado, Diana; Hasan, Rumina; Hasan, Zahra; Bergval, Indra L; Anthony, Richard; McNerney, Ruth; Antonio, Martin; Portugal, Isabel; Viveiros, Miguel; Campino, Susana; Hibberd, Martin L; Clark, Taane G

Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. (2018) Portelli, Stephanie; Phelan, Jody E; Ascher, David B; Clark, Taane G; Furnham, Nicholas

PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation. (2013) 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; Zongo, Issaka; Ouédraogo, Jean-Bosco; Djimde, Abdoulaye A; Doumbo, Ogobara K; Nosten, Francois; Fairhurst, Rick M; Conway, David J; Roper, Cally; Clark, Taane G

A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains. (2014) 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; 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

VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data. (2012) Preston, Mark D; Manske, Magnus; Horner, Neil; Assefa, Samuel; Campino, Susana; Auburn, Sarah; Zongo, Issaka; Ouedraogo, Jean-Bosco; Nosten, Francois; Anderson, Tim; Clark, Taane G

Gametocyte production and transmission fitness of African and Asian Plasmodium falciparum isolates with differential susceptibility to artemisinins. (2025) Proellochs, Nicholas I; Andolina, Chiara; Ramjith, Jordache; Stoter, Rianne; van Gemert, Geert-Jan; Graumans, Wouter; Campino, Susana; Vanheer, Leen N; Okitwi, Martin; Tumwebaze, Patrick K; Conrad, Melissa D; Clark, Taane G; Fidock, David A; Ménard, Didier; Mok, Sachel; Bousema, Teun

Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi. (2016) 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; Terlouw, Anja; Craig, Alister; Campino, Susana; Ocholla, Harold; Clark, Taane G

An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene. (2019) Ravenhall, Matt; Benavente, Ernest Diez; Sutherland, Colin J; Baker, David A; Campino, Susana; Clark, Taane G

SV-Pop: population-based structural variant analysis and visualization. (2019) Ravenhall, Matt; Campino, Susana; Clark, Taane G

Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania. (2017) Ravenhall, Matt; Campino, Susana; Sepúlveda, Nuno; Manjurano, Alphaxard; Nadjm, Behzad; Mtove, George; Wangai, Hannah; Maxwell, Caroline; Olomi, Raimos; Reyburn, Hugh; Drakeley, Christopher J; Riley, Eleanor M; Clark, Taane G; MalariaGEN

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. (2016) Refrégier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cömert, Füsun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; Phelan, Jody; Coll, Francesc; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Sola, Christophe

Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study. (2015) Roberts, Chrissy H; Franklin, Christopher S; Makalo, Pateh; Joof, Hassan; Sarr, Isatou; Mahdi, Olaimatu S; Sillah, Ansumana; Bah, Momodou; Payne, Felicity; Jeffreys, Anna E; 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

Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients. (2011) 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; Quail, Michael A; Chiodini, Peter L; Kwiatkowski, Dominic P; Clark, Taane G; Sutherland, Colin J

Complete and draft genome sequences of clinical <i>Mycobacterium tuberculosis</i> isolates from the Philippines. (2025) Rojas, Saul M; Tujan, Ma Angelica A; Valencia, Angela Kae C; Capin, Jessel Babe G; Dizon, Timothy John R; Ama, Ma Cecilia G; Basilio, Ramon P; Lim, Dodge R; Reyes, Lorenzo T; Phelan, Jody; Campino, Susana; Clark, Taane G; De Los Reyes, Mari Rose A picture_as_pdf

Fibrinogen concentration and risk of ischemic stroke and acute coronary events in 5113 patients with transient ischemic attack and minor ischemic stroke. (2004) 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

Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites. (2015) Samad, Hanif; Coll, Francesc; Preston, Mark D; Ocholla, Harold; Fairhurst, Rick M; Clark, Taane G

Transforming growth factor beta 2 and heme oxygenase 1 genes are risk factors for the cerebral malaria syndrome in Angolan children. (2010) Sambo, Maria Rosário; Trovoada, Maria Jesus; Benchimol, Carla; Quinhentos, Vatúsia; Gonçalves, Lígia; Velosa, Rute; Marques, Maria Isabel; Sepúlveda, Nuno; Clark, Taane G; Mustafa, Stefan; Wagner, Oswald; Coutinho, António; Penha-Gonçalves, Carlos

Ribosome profiling in<i>Mycobacterium tuberculosis</i>reveals robust leaderless translation. (2020) Sawyer, Elizabeth B; Phelan, Jody E; Clark, Taane G; Cortes, Teresa picture_as_pdf

A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling. (2021) Sawyer, Elizabeth B; Phelan, Jody E; Clark, Taane G; Cortes, Teresa

Bayesian compositional regression with microbiome features via variational inference. (2023) Scott, Darren AV; Benavente, Ernest; Libiseller-Egger, Julian; Fedorov, Dmitry; Phelan, Jody; Ilina, Elena; Tikhonova, Polina; Kudryavstev, Alexander; Galeeva, Julia; Clark, Taane; Lewin, Alex

Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia. (2017) 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

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data. (2013) Sepúlveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G

G6PD Polymorphisms and Hemolysis After Antimalarial Treatment With Low Single-Dose Primaquine: A Pooled Analysis of Six African Clinical Trials. (2021) Sepúlveda, Nuno; Grignard, Lynn; Curry, Jonathan; Mahey, Laleta; Bastiaens, Guido JH; Tiono, Alfred B; Okebe, Joseph; Coulibaly, Sam A; Gonçalves, Bronner P; Affara, Muna; 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

Malaria Host Candidate Genes Validated by Association With Current, Recent, and Historical Measures of Transmission Intensity. (2017) Sepúlveda, Nuno; Manjurano, Alphaxard; Campino, Susana G; Lemnge, Martha; Lusingu, John; Olomi, Raimos; Rockett, Kirk A; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Clark, Taane G; Riley, Eleanor M; Drakeley, Chris J; MalariaGEN Consortium

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. (2014) Sepúlveda, Nuno; Manjurano, Alphaxard; Drakeley, Chris; Clark, Taane G

Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. (2018) Sepúlveda, Nuno; Phelan, Jody; Diez-Benavente, Ernest; Campino, Susana; Clark, Taane G; Hopkins, Heidi; Sutherland, Colin; Drakeley, Chris J; Beshir, Khalid B

A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. (2017) Sheen, Patricia; Requena, David; Gushiken, Eduardo; Gilman, Robert H; Antiparra, Ricardo; Lucero, Bryan; Lizárraga, Pilar; Cieza, Basilio; Roncal, Elisa; Grandjean, Louis; Pain, Arnab; McNerney, Ruth; Clark, Taane G; Moore, David; Zimic, Mirko

Genetic determinants of anti-malarial acquired immunity in a large multi-centre study. (2015) Shelton, Jennifer MG; Corran, Patrick; Risley, Paul; Silva, Nilupa; Hubbart, Christina; Jeffreys, Anna; Rowlands, Kate; Craik, Rachel; Cornelius, Victoria; Hensmann, Meike; 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

Knowledge, attitudes and practices regarding antimicrobial use and resistance among communities of Ilala, Kilosa and Kibaha districts of Tanzania. (2020) 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

An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS. (2012) Smith, Miriam; Campino, Susana; Gu, Yong; Clark, Taane G; Otto, Thomas D; Maslen, Gareth; Manske, Magnus; Imwong, Mallika; Dondorp, Arjen M; Kwiatkowski, Dominic P; Quail, Michael A; Swerdlow, Harold

Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants. (2020) Sobkowiak, Benjamin; Banda, Louis; Mzembe, Themba; Crampin, Amelia C; Glynn, Judith R; Clark, Taane G

A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission. (2025) Sobkowiak, Benjamin; Cudahy, Patrick; Chitwood, Melanie H; Clark, Taane G; Colijn, Caroline; Grandjean, Louis; Walter, Katharine S; Crudu, Valeriu; Cohen, Ted

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. (2018) 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; Parkhill, Julian; Crampin, Amelia C; Clark, Taane G

Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry. (2010) 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; Monaco, Anthony P; International Molecular Genetic Study of Autism Consortium (IMGS

MET and autism susceptibility: family and case-control studies. (2009) Sousa, Inês; Clark, Taane G; Toma, Claudio; Kobayashi, Kazuhiro; Choma, Maja; Holt, Richard; Sykes, Nuala H; Lamb, Janine A; Bailey, Anthony J; Battaglia, Agatino; Maestrini, Elena; Monaco, Anthony P; International Molecular Genetic Study of Autism Consortium (IMGS

Uncovering the genetic diversity in Aedes aegypti insecticide resistance genes through global comparative genomics. (2024) Spadar, Anton; Collins, Emma; Messenger, Louisa A; Clark, Taane G; Campino, Susana

Genomic analysis of hypervirulent Klebsiella pneumoniae reveals potential genetic markers for differentiation from classical strains. (2022) Spadar, Anton; Perdigão, João; Campino, Susana; Clark, Taane G

Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains. (2023) Spadar, Anton; Perdigão, João; Campino, Susana; Clark, Taane G

Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals. (2021) Spadar, Anton; Perdigão, João; Phelan, Jody; Charleston, James; Modesto, Ana; Elias, Rita; de Sessions, Paola Florez; Hibberd, Martin L; Campino, Susana; Duarte, Aida; Clark, Taane G

Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus. (2021) Spadar, Anton; Phelan, Jody E; Benavente, Ernest Diez; Campos, Monica; Gomez, Lara Ferrero; Mohareb, Fady; Clark, Taane G; Campino, Susana

Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data. (2023) Spadar, Anton; Phelan, Jody E; Clark, Taane G; Campino, Susana

Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance. (2022) Spadar, Anton; Phelan, Jody; Elias, Rita; Modesto, Ana; Caneiras, Cátia; Marques, Cátia; Lito, Luís; Pinto, Margarida; Cavaco-Silva, Patrícia; Ferreira, Helena; Pomba, Constança; Da Silva, Gabriela J; Saavedra, Maria José; Melo-Cristino, José; Duarte, Aida; Campino, Susana; Perdigão, João; Clark, Taane G

Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype. (2020) Srilohasin, Prapaporn; Prammananan, Therdsak; Faksri, Kiatichai; Phelan, Jody E; Suriyaphol, Prapat; Kamolwat, Phalin; Smithtikarn, Saijai; Disratthakit, Areeya; Regmi, Sanjib Mani; Leechawengwongs, Manoon; Twee-Hee Ong, Rick; Teo, Yik Ying; Tongsima, Sissades; Clark, Taane G; Chaiprasert, Angkana

The <i>ahpC</i> c−54t compensatory mutation is not always a valid surrogate for isoniazid resistance in <i>Mycobacterium tuberculosis</i>. (2025) Szél, Viktória; Phelan, Jody E; Georghiou, Sophia B; Dolinger, David L; Clark, Taane G; Niemann, Stefan; Lőrinczi, Lilla K; Köser, Claudio U picture_as_pdf

Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. (2012) 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; 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

Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia. (2014) 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; 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

Perturbation analysis: a simple method for filtering SNPs with erroneous genotyping in genome-wide association studies. (2008) Teo, YY; Small, KS; Clark, TG; Kwiatkowski, DP

Genome-wide comparisons of variation in linkage disequilibrium. (2009) Teo, Yik Y; Fry, Andrew E; Bhattacharya, Kanishka; Small, Kerrin S; Kwiatkowski, Dominic P; Clark, Taane G

On the usage of HWE for identifying genotyping errors. (2007) Teo, Yik Y; Fry, Andrew E; Clark, Taane G; Tai, ES; Seielstad, Mark

Assessing genuine parents-offspring trios for genetic association studies. (2009) Teo, Yik Y; Fry, Andrew E; Sanjoaquin, Miguel A; Pederson, Bonnie; Small, Kerrin S; Rockett, Kirk A; Kwiatkowski, Dominic P; Clark, Taane G

A genotype calling algorithm for the Illumina BeadArray platform. (2007) Teo, Yik Y; Inouye, Michael; Small, Kerrin S; Gwilliam, Rhian; Deloukas, Panagiotis; Kwiatkowski, Dominic P; Clark, Taane G

Power consequences of linkage disequilibrium variation between populations. (2009) Teo, Yik Y; Small, Kerrin S; Fry, Andrew E; Wu, Yumeng; Kwiatkowski, Dominic P; Clark, Taane G

Frequent Undetected Ward-Based Methicillin-Resistant Staphylococcus aureus Transmission Linked to Patient Sharing Between Hospitals. (2017) Tosas Auguet, Olga; Stabler, Richard A; Betley, Jason; Preston, Mark D; Dhaliwal, Mandeep; Gaunt, Michael; Ioannou, Avgousta; Desai, Nergish; Karadag, Tacim; Batra, Rahul; Otter, Jonathan A; Marbach, Helene; Clark, Taane G; Edgeworth, Jonathan D

Candidate polymorphisms and severe malaria in a Malian population. (2012) Toure, Ousmane; Konate, Salimata; Sissoko, Sibiri; Niangaly, Amadou; Barry, Abdoulaye; Sall, Abdourahmane H; Diarra, Elisabeth; Poudiougou, Belco; Sepulveda, Nuno; Campino, Susana; Rockett, Kirk A; Clark, Taane G; Thera, Mahamadou A; Doumbo, Ogobara; Collaboration with The MalariaGEN Consortium

VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations. (2017) 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; Liu, Yaobao; Gao, Qi; Dowd, Simone; Cheng, Qin; Clark, Taane G; Price, Ric N; Auburn, Sarah

High clustering rate and genotypic drug-susceptibility screening for the newly recommended anti-tuberculosis drugs among global extensively drug-resistant Mycobacterium tuberculosis isolates. (2022) Trisakul, Kanwara; Nonghanphithak, Ditthawat; Chaiyachat, Pratchakan; Kaewprasert, Orawee; Sakmongkoljit, Kankanon; Reechaipichitkul, Wipa; Chaiprasert, Angkana; Blair, David; Clark, Taane G; Faksri, Kiatichai

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae. (2024) Tsang, Kara K; Lam, Margaret MC; Wick, Ryan R; Wyres, Kelly L; Bachman, Michael; Baker, Stephen; Barry, Katherine; Brisse, Sylvain; Campino, Susana; Chiaverini, Alexandra; Cirillo, Daniela Maria; Clark, Taane; Corander, Jukka; Corbella, Marta; Cornacchia, Alessandra; Cuénod, Aline; D'Alterio, Nicola; Di Marco, Federico; Donado-Godoy, Pilar; Egli, Adrian; Farzana, Refath; Feil, Edward J; Fostervold, Aasmund; Gorrie, Claire L; Hassan, Brekhna; Hetland, Marit Andrea Klokkhammer; Hoa, Le Nguyen Minh; Hoi, Le Thi; Howden, Benjamin; Ikhimiukor, Odion O; Jenney, Adam WJ; Kaspersen, Håkon; Khokhar, Fahad; Leangapichart, Thongpan; Ligowska-Marzęta, Małgorzata; Löhr, Iren Høyland; Long, Scott W; Mathers, Amy J; McArthur, Andrew G; Nagaraj, Geetha; Oaikhena, Anderson O; Okeke, Iruka N; Perdigão, João; Parikh, Hardik; Pham, My H; Pomilio, Francesco; Raffelsberger, Niclas; Rakotondrasoa, Andriniaina; Kumar, KL Ravi; Roberts, Leah W; Rodrigues, Carla; Samuelsen, Ørjan; Sands, Kirsty; Sassera, Davide; Seth-Smith, Helena; Shamanna, Varun; Sherry, Norelle L; Sia, Sonia; Spadar, Anton; Stoesser, Nicole; Sunde, Marianne; Sundsfjord, Arnfinn; Thach, Pham Ngoc; Thomson, Nicholas R; Thorpe, Harry A; Torok, M Estée; Trang, Van Dinh; Trung, Nguyen Vu; Vornhagen, Jay; Walsh, Timothy; Warne, Ben; Wilson, Hayley; Wright, Gerard D; Holt, Kathryn E; KlebNET-Gsp Amr Genotype-Phenotype Group

Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages. (2021) Tunstall, Tanushree; Phelan, Jody; Eccleston, Charlotte; Clark, Taane G; Furnham, Nicholas

Combining structure and genomics to understand antimicrobial resistance. (2020) Tunstall, Tanushree; Portelli, Stephanie; Phelan, Jody; Clark, Taane G; Ascher, David B; Furnham, Nicholas

Population genetic analysis of Plasmodium knowlesi reveals differential selection and exchange events between Borneo and Peninsular sub-populations. (2023) Turkiewicz, Anna; Manko, Emilia; Oresegun, Damiola R; Nolder, Debbie; Spadar, Anton; Sutherland, Colin J; Cox-Singh, Janet; Moon, Robert W; Lau, Yee-Ling; Campino, Susana; Clark, Taane G

Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance. (2020) Turkiewicz, Anna; Manko, Emilia; Sutherland, Colin J; Diez Benavente, Ernest; Campino, Susana; Clark, Taane G

Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial. (2017) 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; 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

Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines. (2024) Wang, Linfeng; Lim, Dodge R; Phelan, Jody E; Reyes, Lorenzo T; Palparan, Alma G; Sanchez, Maria Guileane C; Asuncion, Louella Abigail A; Tujan, Ma Angelica A; Medado, Inez Andrea P; Daga, Chona Mae A; Llames, Jo-Hannah S; Mitarai, Satoshi; Murase, Yoshiro; Morishige, Yuta; Ang, Concepcion F; Malabad, John Carlo M; Montoya, Jaime C; Hafalla, Julius C; Campino, Susana; Hibberd, Martin L; Ama, Cecilia G; Basilio, Ramon P; La Paz, Eva Maria Cutiongoco-De; Clark, Taane G

Sero-epidemiological study of arbovirus infection following the 2015-2016 Zika virus outbreak in Cabo Verde. (2022) Ward, Daniel; Gomes, Ana Rita; Tetteh, Kevin KA; Sepúlveda, Nuno; Gomez, Lara Ferrero; Campino, Susana; Clark, Taane G

An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. (2021) Ward, Daniel; Higgins, Matthew; Phelan, Jody E; Hibberd, Martin L; Campino, Susana; Clark, Taane G

An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. (2021) Ward, Daniel; Higgins, Matthew; Phelan, Jody E; Hibberd, Martin L; Campino, Susana; Clark, Taane G

Serological insights from SARS-CoV-2 heterologous prime and boost responses in Thailand. (2025) Ward, Daniel; Pattarapreeyakul, Lapasrada; Pitaksalee, Rujiraporn; Thawong, Naphatcha; Sawaengdee, Waritta; Tuntigumthon, Suthida; Patterson, Catriona; Tetteh, Kevin; Campino, Susana; Dhepakson, Panadda; Mahasirimongkol, Surakameth; Clark, Taane G

Random errors in the measurement of 10 cardiovascular risk factors. (2001) Whitlock, G; Clark, T; Vander Hoorn, S; Rodgers, A; Jackson, R; Norton, R; MacMahon, S

Motor vehicle driver injury and marital status: a cohort study with prospective and retrospective driver injuries. (2004) Whitlock, G; Norton, R; Clark, T; Jackson, R; MacMahon, S

Motor vehicle driver injury and socioeconomic status: a cohort study with prospective and retrospective driver injuries. (2003) Whitlock, G; Norton, R; Clark, T; Pledger, M; Jackson, R; MacMahon, S

The effect of missing values for covariates. (2002) Whitlock, Gary; Clark, Taane

Is body mass index a risk factor for motor vehicle driver injury? A cohort study with prospective and retrospective outcomes. (2003) Whitlock, Gary; Norton, Robyn; Clark, Taane; Jackson, Rodney; MacMahon, Stephen

Association of the dopamine-β-hydroxylase gene with nicotine dependence: No evidence for mediation by personality. (2005) Zetteler, Jessica I; Clark, Taane G; Johnstone, Elaine C; Munafò, Marcus R

Investigation of host candidate malaria-associated risk/protective SNPs in a Brazilian Amazonian population. (2012) da Silva Santos, Simone; Clark, Taane G; Campino, Susana; Suarez-Mutis, Martha Cecília; Rockett, Kirk A; Kwiatkowski, Dominic P; Fernandes, Octavio

Conference or Workshop Item

HUMAN GENETIC POLYMORPHISMS AND THE RISK OF MALARIA-ASSOCIATED SEIZURES IN AFRICAN POPULATIONS. (2011) Kariuki, SM; Rockett, K; Clark, TG; Reyburn, H; Agbenyega, T; Taylor, TE; Williams, TN; Newton, CR

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. (2013) Last, A; Cassama, E; Nabicassa, M; Clark, T; Coll, F; Gundogdu, O; Burr, S; Cutcliffe, L; Clarke, I; Thompson, N; Mabey, D; Bailey, R; Holland, M

Thesis

A genomic investigation into three malaria vectors: An. darlingi, An. funestus, and An. stephensi. (2024) Acford-Palmer, H

Bioinformatic analysis of Mycobacterium tuberculosis whole genome data. (2015) Coll I Cerezo, F

Utilising genomic approaches to explore genetic diversity and insecticide resistance in Aedes aegypti populations. (2025) Collins, EL picture_as_pdf

Machine learning methods for infectious diseases: Applications for Tuberculosis and Malaria. (2022) Deelder, WA

Using whole genome sequence data to study genomic diversity and develop molecular barcodes to profile Plasmodium malaria parasites. (2018) Díez Benavente, E

Analysis of Mycobacterium tuberculosis ‘omics data to inform on loci linked to drug resistance, pathogenicity and virulence. (2023) Gómez González, PJ

Developing an RPA-based Molecular Barcoding Tool for Plasmodium Malaria. (2023) Higgins, MCW

From genome to function: A genomic investigation into understudied populations of the malaria parasites Plasmodium malariae and P.vivax. (2023) Ibrahim, A

Genomic epidemiology of Plasmodium falciparum and its Anopheline vectors in the context of malaria control on the Bijagós Archipelago of Guinea-Bissau. (2024) Moss, SJ

Using whole genome sequencing data to identify strain-types, transmission enhancers and novel drug resistance mutations of Mycobacterium tuberculosis. (2023) Napier, G

Investigating the genomic basis of antimicrobial resistance in Mycobacterium tuberculosis (Mtb) using genome-wide methodologies. (2020) Oppong, YEA

A multifaceted investigation of the genomics of malaria, from parasite to host, using next-generation sequencing technologies. (2023) Osborne, AA

A bioinformatic analysis of Mycobacterium tuberculosis and host genomic data. (2018) Phelan, J

A bioinformatic analysis of malaria host and pathogen genomics. (2019) Ravenhall, M

Understanding the genetic diversity, antimicrobial resistance, and virulence of Klebsiella pneumoniae bacteria. (2023) Spadar, A

Using Machine Learning to Anticipate Antimicrobial Resistance in Mycobacterium Tuberculosis. (2023) Tunstall, T

Zika virus surveillance in human and mosquito populations in Cabo Verde – exploring molecular and serological tools for the surveillance of emerging infectious diseases. (2023) Ward, D