Acford-Palmer, H; (2024) A genomic investigation into three malaria vectors: An. darlingi, An. funestus, and An. stephensi. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04672667

Guyeux, Christophe; Senelle, Gaetan; Le Meur, Adrien; Supply, Philip; Gaudin, Cyril; Phelan, Jody E; Clark, Taane G; Rigouts, Leen; de Jong, Bouke; Sola, Christophe; +1 more... Refrégier, Guislaine; (2024) Newly Identified Mycobacterium africanum Lineage 10, Central Africa. Emerging infectious diseases, 30 (3). pp. 560-563. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid3003.231466

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; +12 more... 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; (2024) A Pan Plasmodium lateral flow recombinase polymerase amplification assay for monitoring malaria parasites in vectors and human populations. Scientific reports, 14 (1). 20165-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-024-71129-4

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; +3 more... Clark, Taane G; Last, Anna; Campino, Susana; (2024) Phenotypic evidence of deltamethrin resistance and identification of selective sweeps in Anopheles mosquitoes on the Bijagós Archipelago, Guinea-Bissau. Scientific reports, 14 (1). 22840-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-024-73996-3

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; +7 more... Jones, Robert T; Vasileva, Hristina; Rodrigues, Amabelia; Krishna, Sanjeev; Clark, Taane G; Last, Anna; Campino, Susana; (2024) Whole genome sequence analysis of population structure and insecticide resistance markers in Anopheles melas from the Bijagós Archipelago, Guinea-Bissau. Parasites & vectors, 17 (1). 396-. ISSN 1756-3305 DOI: https://doi.org/10.1186/s13071-024-06476-2

Spadar, Anton; Collins, Emma; Messenger, Louisa A; Clark, Taane G; Campino, Susana; (2024) Uncovering the genetic diversity in Aedes aegypti insecticide resistance genes through global comparative genomics. Scientific Reports, 14 (1). 13447-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-024-64007-6

Tsang, Kara K; Lam, Margaret MC; Wick, Ryan R; Wyres, Kelly L; Bachman, Michael; Baker, Stephen; Barry, Katherine; Brisse, Sylvain; Campino, Susana; Chiaverini, Alexandra; +65 more... 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; (2024) Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae. Microbial genomics, 10 (10). ISSN 2057-5858 DOI: https://doi.org/10.1099/mgen.0.001294

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; +14 more... 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; (2024) Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines. Scientific reports, 14 (1). 19602-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-024-70471-x

Billows, Nina; Phelan, Jody E; Xia, Dong; Peng, Yonghong; Clark, Taane G; Chang, Yu-Mei; (2023) Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences. Bioinformatics, 39 (7). btad428-. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btad428

Dombrowski, Jamille Gregório; Acford-Palmer, Holly; Campos, Monica; Separovic, Erika Paula Machado; Epiphanio, Sabrina; Clark, Taane Gregory; Campino, Susana; Marinho, Claudio Romero Farias; (2023) Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: a prospective cohort study. Lancet regional health - Americas, 18. 100407-. ISSN 2667-193X DOI: https://doi.org/10.1016/j.lana.2022.100407

Eccleston, Ruth Charlotte; Manko, Emilia; Campino, Susana; Clark, Taane G; Furnham, Nicholas; (2023) A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. eLife, 12. e84756-. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.84756

Gómez González, PJ; (2023) Analysis of Mycobacterium tuberculosis ‘omics data to inform on loci linked to drug resistance, pathogenicity and virulence. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670763

Gómez-González, Paula Josefina; Grabowska, Anna D; Tientcheu, Leopold D; Tsolaki, Anthony G; Hibberd, Martin L; Campino, Susana; Phelan, Jody E; Clark, Taane G; (2023) Functional genetic variation in pe/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host. Frontiers in microbiology, 14. 1244319-. ISSN 1664-302X DOI: https://doi.org/10.3389/fmicb.2023.1244319

Higgins, MCW; (2023) Developing an RPA-based Molecular Barcoding Tool for Plasmodium Malaria. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670986

Ibrahim, A; (2023) From genome to function: A genomic investigation into understudied populations of the malaria parasites Plasmodium malariae and P.vivax. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670765

Ibrahim, Amy; Manko, Emilia; Dombrowski, Jamille G; Campos, Mónica; Benavente, Ernest Diez; Nolder, Debbie; Sutherland, Colin J; Nosten, Francois; Fernandez, Diana; Vélez-Tobón, Gabriel; +11 more... 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; (2023) Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America. Lancet regional health. Americas, 18. 100420-. ISSN 2667-193X DOI: https://doi.org/10.1016/j.lana.2022.100420

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; +2 more... Wan, Kang-Lin; Gao, Qian; (2023) The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China. Microbiology spectrum, 11 (2). e0399122-. ISSN 2165-0497 DOI: https://doi.org/10.1128/spectrum.03991-22

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; +3 more... Walker, Thomas; Campino, Susana; Messenger, Louisa A; (2023) Towards environmental detection, quantification, and molecular characterization of Anopheles stephensi and Aedes aegypti from experimental larval breeding sites. Scientific Reports, 13 (1). 2729-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-023-29657-y

Libiseller-Egger, Julian; Wang, Linfeng; Deelder, Wouter; Campino, Susana; Clark, Taane G; Phelan, Jody E; (2023) TB-ML-a framework for comparing machine learning approaches to predict drug resistance of Mycobacterium tuberculosis. Bioinformatics advances, 3 (1). vbad040-. ISSN 2635-0041 DOI: https://doi.org/10.1093/bioadv/vbad040

Moss, Sophie; Mańko, Emilia; Vasileva, Hristina; Da Silva, Eunice Teixeira; Goncalves, Adriana; Osborne, Ashley; Phelan, Jody; Rodrigues, Amabelia; Djata, Paulo; D'Alessandro, Umberto; +5 more... Mabey, David; Krishna, Sanjeev; Last, Anna; Clark, Taane G; Campino, Susana; (2023) Population dynamics and drug resistance mutations in Plasmodium falciparum on the Bijagós Archipelago, Guinea-Bissau. Scientific reports, 13 (1). 6311-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-023-33176-1

Napier, G; (2023) Using whole genome sequencing data to identify strain-types, transmission enhancers and novel drug resistance mutations of Mycobacterium tuberculosis. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670881

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; +14 more... 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; (2023) 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. International Journal of Infectious Diseases, 128. pp. 230-243. ISSN 1201-9712 DOI: https://doi.org/10.1016/j.ijid.2022.12.030

Osborne, AA; (2023) A multifaceted investigation of the genomics of malaria, from parasite to host, using next-generation sequencing technologies. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04671412

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; +8 more... Nolder, Debbie; Beshir, Khalid B; Dombrowski, Jamille G; Di Santi, Silvia Maria; Bousema, Teun; Sutherland, Colin J; Campino, Susana; Clark, Taane G; (2023) Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control. Genome medicine, 15 (1). 96-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-023-01247-7

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; +10 more... Sallah, Neneh; Parkhill, Julian; Smittipat, Nat; Palittapongarnpim, Prasit; Mushiroda, Taisei; Kubo, Michiaki; Tokunaga, Katsushi; Mahasirimongkol, Surakameth; Hibberd, Martin L; Clark, Taane G; (2023) Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease. Nature communications, 14 (1). 549-. ISSN 2041-1723 DOI: https://doi.org/10.1038/s41467-023-36282-w

Scott, Darren AV; Benavente, Ernest; Libiseller-Egger, Julian; Fedorov, Dmitry; Phelan, Jody; Ilina, Elena; Tikhonova, Polina; Kudryavstev, Alexander; Galeeva, Julia; Clark, Taane; +1 more... Lewin, Alex; (2023) Bayesian compositional regression with microbiome features via variational inference. BMC bioinformatics, 24 (1). 210-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-023-05219-x

Spadar, A; (2023) Understanding the genetic diversity, antimicrobial resistance, and virulence of Klebsiella pneumoniae bacteria. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670853

Spadar, Anton; Perdigão, João; Campino, Susana; Clark, Taane G; (2023) Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains. Genome medicine, 15 (1). 3-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-023-01153-y

Spadar, Anton; Phelan, Jody E; Clark, Taane G; Campino, Susana; (2023) Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data. Parasites & vectors, 16 (1). 265-. ISSN 1756-3305 DOI: https://doi.org/10.1186/s13071-023-05898-8

Tunstall, T; (2023) Using Machine Learning to Anticipate Antimicrobial Resistance in Mycobacterium Tuberculosis. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670981

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; +1 more... Clark, Taane G; (2023) Population genetic analysis of Plasmodium knowlesi reveals differential selection and exchange events between Borneo and Peninsular sub-populations. Scientific reports, 13 (1). 2142-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-023-29368-4

Ward, D; (2023) Zika virus surveillance in human and mosquito populations in Cabo Verde – exploring molecular and serological tools for the surveillance of emerging infectious diseases. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670855

Campos, Monica; Phelan, Jody; Spadar, Anton; Collins, Emma; Gonçalves, Adéritow; Pelloquin, Bethanie; Vaselli, Natasha Marcella; Meiwald, Anne; Clark, Emma; Stica, Caleb; +12 more... 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; (2022) High-throughput barcoding method for the genetic surveillance of insecticide resistance and species identification in Anopheles gambiae complex malaria vectors. Scientific Reports, 12 (1). 13893-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-022-17822-8

Coll, Francesc; Gouliouris, Theodore; Bruchmann, Sebastian; Phelan, Jody; Raven, Kathy E; Clark, Taane G; Parkhill, Julian; Peacock, Sharon J; (2022) PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies. Communications Biology, 5 (1). 266-. ISSN 2399-3642 DOI: https://doi.org/10.1038/s42003-022-03194-2

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; +2 more... Clark, Taane G; Campino, Susana; (2022) 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. PLoS neglected tropical diseases, 16 (12). e0010935-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0010935

Deelder, WA; (2022) Machine learning methods for infectious diseases: Applications for Tuberculosis and Malaria. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670671

Deelder, Wouter; Manko, Emilia; Phelan, Jody E; Campino, Susana; Palla, Luigi; Clark, Taane G; (2022) Geographical classification of malaria parasites through applying machine learning to whole genome sequence data. Scientific reports, 12 (1). 21150-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-022-25568-6

Deelder, Wouter; Napier, Gary; Campino, Susana; Palla, Luigi; Phelan, Jody; Clark, Taane G; (2022) A modified decision tree approach to improve the prediction and mutation discovery for drug resistance in Mycobacterium tuberculosis. BMC genomics, 23 (1). 46-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-022-08291-4

Gómez-González, Paula J; Campino, Susana; Phelan, Jody E; Clark, Taane G; (2022) Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications. Briefings in Bioinformatics, 23 (5). bbac256. ISSN 1467-5463 DOI: https://doi.org/10.1093/bib/bbac256

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; +15 more... 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; (2022) Epidemiology of SARS-CoV-2 infection among staff and students in a cohort of English primary and secondary schools during 2020-2021. The Lancet Regional Health Europe, 21. 100471-. ISSN 2666-7762 DOI: https://doi.org/10.1016/j.lanepe.2022.100471

Higgins, Matthew; Stringer, Oliver W; Ward, Daniel; Andrews, Jennifer M; Forrest, Matthew S; Campino, Susana; Clark, Taane G; (2022) Characterizing the Impact of Primer-Template Mismatches on Recombinase Polymerase Amplification. The Journal of molecular diagnostics, 24 (11). pp. 1207-1216. ISSN 1525-1578 DOI: https://doi.org/10.1016/j.jmoldx.2022.08.005

Kuja, Josiah O; Kanoi, Bernard N; Balboa, Renzo F; Shiluli, Clement; Maina, Michael; Waweru, Harrison; Gathii, Kimita; Mungai, Mary; Masika, Moses; Anzala, Omu; +4 more... Mwau, Matilu; Clark, Taane G; Waitumbi, John; Gitaka, Jesse; (2022) Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya. BMC Genomics, 23 (1). 627-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-022-08853-6

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; (2022) Deep learning-derived cardiovascular age shares a genetic basis with other cardiac phenotypes. Scientific reports, 12 (1). 22625-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-022-27254-z

Mazumder, Razib; Hussain, Arif; Phelan, Jody E; Campino, Susana; Haider, SM Arefeen; Mahmud, Araf; Ahmed, Dilruba; Asadulghani, Md; Clark, Taane G; Mondal, Dinesh; (2022) Non-lactose fermenting Escherichia coli: Following in the footsteps of lactose fermenting E. coli high-risk clones. Frontiers in Microbiology, 13. 1027494-. ISSN 1664-302X DOI: https://doi.org/10.3389/fmicb.2022.1027494

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; +1 more... Clark, Taane G; (2022) Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016. Tuberculosis, 135. 102211-. ISSN 1472-9792 DOI: https://doi.org/10.1016/j.tube.2022.102211

Moss, Sophie; Mańko, Emilia; Krishna, Sanjeev; Campino, Susana; Clark, Taane G; Last, Anna; (2022) How has mass drug administration with dihydroartemisinin-piperaquine impacted molecular markers of drug resistance? A systematic review. Malaria journal, 21 (1). 186-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-022-04181-y

Napier, Gary; Khan, Anwar Sheed; Jabbar, Abdul; Khan, Muhammad Tahir; Ali, Sajid; Qasim, Muhammad; Mohammad, Noor; Hasan, Rumina; Hasan, Zahra; Campino, Susana; +6 more... Ahmad, Sajjad; Khattak, Baharullah; Waddell, Simon J; Khan, Taj Ali; Phelan, Jody E; Clark, Taane G; (2022) Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan. Scientific reports, 12 (1). 7703-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-022-11795-4

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; (2022) 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. Frontiers in medicine, 8. 688159-. ISSN 2296-858X DOI: https://doi.org/10.3389/fmed.2021.688159

Oresegun, Damilola R; Thorpe, Peter; Benavente, Ernest Diez; Campino, Susana; Muh, Fauzi; Moon, Robert William; Clark, Taane Gregory; Cox-Singh, Janet; (2022) De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members. Frontiers in genetics, 13. 855052-. ISSN 1664-8021 DOI: https://doi.org/10.3389/fgene.2022.855052

Phelan, Jody; Deelder, Wouter; Ward, Daniel; Campino, Susana; Hibberd, Martin L; Clark, Taane G; (2022) COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data. BMC Bioinformatics, 23 (1). 137-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-022-04632-y

Spadar, Anton; Perdigão, João; Campino, Susana; Clark, Taane G; (2022) Genomic analysis of hypervirulent Klebsiella pneumoniae reveals potential genetic markers for differentiation from classical strains. Scientific Reports, 12 (1). 13671-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-022-17995-2

Spadar, Anton; Phelan, Jody; Elias, Rita; Modesto, Ana; Caneiras, Cátia; Marques, Cátia; Lito, Luís; Pinto, Margarida; Cavaco-Silva, Patrícia; Ferreira, Helena; +8 more... Pomba, Constança; Da Silva, Gabriela J; Saavedra, Maria José; Melo-Cristino, José; Duarte, Aida; Campino, Susana; Perdigão, João; Clark, Taane G; (2022) Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance. Scientific Reports, 12 (1). 13791-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-022-17996-1

Trisakul, Kanwara; Nonghanphithak, Ditthawat; Chaiyachat, Pratchakan; Kaewprasert, Orawee; Sakmongkoljit, Kankanon; Reechaipichitkul, Wipa; Chaiprasert, Angkana; Blair, David; Clark, Taane G; Faksri, Kiatichai; (2022) High clustering rate and genotypic drug-susceptibility screening for the newly recommended anti-tuberculosis drugs among global extensively drug-resistant Mycobacterium tuberculosis isolates. Emerging Microbes & Infections, 11 (1). pp. 1857-1866. ISSN 2222-1751 DOI: https://doi.org/10.1080/22221751.2022.2099304

Ward, Daniel; Gomes, Ana Rita; Tetteh, Kevin KA; Sepúlveda, Nuno; Gomez, Lara Ferrero; Campino, Susana; Clark, Taane G; (2022) Sero-epidemiological study of arbovirus infection following the 2015-2016 Zika virus outbreak in Cabo Verde. Scientific Reports, 12 (1). 11719-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-022-16115-4

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

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

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Khan, Anwar Sheed; Phelan, Jody E; Khan, Muhammad Tahir; Ali, Sajid; Qasim, Muhammad; Napier, Gary; Campino, Susana; Ahmad, Sajjad; Cabral-Marques, Otavio; Zhang, Shulin; +4 more... Rahman, Hazir; Wei, Dong-Qing; Clark, Taane G; Khan, Taj Ali; (2021) Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan. Scientific reports, 11 (1). 14194-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-93501-4

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; +9 more... 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; (2021) The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957. Scientific reports, 11 (1). 1888-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-81343-z

Nonghanphithak, Ditthawat; Chaiprasert, Angkana; Smithtikarn, Saijai; Kamolwat, Phalin; Pungrassami, Petchawan; Chongsuvivatwong, Virasakdi; Mahasirimongkol, Surakameth; Reechaipichitkul, Wipa; Leepiyasakulchai, Chaniya; Phelan, Jody E; +3 more... Blair, David; Clark, Taane G; Faksri, Kiatichai; (2021) Clusters of Drug-Resistant Mycobacterium tuberculosis Detected by Whole-Genome Sequence Analysis of Nationwide Sample, Thailand, 2014-2017. Emerging infectious diseases, 27 (3). pp. 813-822. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2703.204364

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Ortiz, Mayreli; Jauset-Rubio, Miriam; Skouridou, Vasso; Machado, Diana; Viveiros, Miguel; Clark, Taane G; Simonova, Anna; Kodr, David; Hocek, Michal; O'Sullivan, Ciara K; (2021) Electrochemical Detection of Single-Nucleotide Polymorphism Associated with Rifampicin Resistance in Mycobacterium tuberculosis Using Solid-Phase Primer Elongation with Ferrocene-Linked Redox-Labeled Nucleotides. ACS sensors, 6 (12). pp. 4398-4407. ISSN 2379-3694 DOI: https://doi.org/10.1021/acssensors.1c01710

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

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

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

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

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

Ibrahim, Amy; Diez Benavente, Ernest; Nolder, Debbie; Proux, Stephane; Higgins, Matthew; Muwanguzi, Julian; Gomez Gonzalez, Paula Josefina; Fuehrer, Hans-Peter; Roper, Cally; Nosten, Francois; +3 more... Sutherland, Colin; Clark, Taane G; Campino, Susana; (2020) Selective whole genome amplification of Plasmodium malariae DNA from clinical samples reveals insights into population structure. SCIENTIFIC REPORTS, 10 (1). 10832-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-020-67568-4

Jallow, Momodou W; Cerami, Carla; Clark, Taane G; Prentice, Andrew M; Campino, Susana; (2020) Differences in the frequency of genetic variants associated with iron imbalance among global populations. PLOS ONE, 15 (7). e0235141-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0235141 Item availability may be restricted.

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; +4 more... Dockrell, Hazel M; Clark, Taane G; Matee, Mecky I; Mpagama, Stellah; (2020) Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania. BMC GENOMICS, 21 (1). 174-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-020-6577-1

Katale, Bugwesa Z; Misinzo, Gerald; Mshana, Stephen E; Chiyangi, Harriet; Campino, Susana; Clark, Taane G; Good, Liam; Rweyemamu, Mark M; Matee, Mecky I; (2020) Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review. ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL, 9 (1). 127-. ISSN 2047-2994 DOI: https://doi.org/10.1186/s13756-020-00786-7

Libiseller-Egger, Julian; Phelan, Jody; Campino, Susana; Mohareb, Fady; Clark, Taane G; (2020) Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers. PLOS COMPUTATIONAL BIOLOGY, 16 (12). e1008518-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1008518 Item availability may be restricted.

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; (2020) How Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) Progresses: The Natural History of ME/CFS. Frontiers in neurology, 11. 826-. ISSN 1664-2295 DOI: https://doi.org/10.3389/fneur.2020.00826

Napier, Gary; Campino, Susana; Merid, Yared; Abebe, Markos; Woldeamanuel, Yimtubezinash; Aseffa, Abraham; Hibberd, Martin L; Phelan, Jody; Clark, Taane G; (2020) Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. GENOME MEDICINE, 12 (1). 114-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-020-00817-3

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Gomez-Gonzalez, Paula J; Andreu, Nuria; Phelan, Jody E; de Sessions, Paola Florez; Glynn, Judith R; Crampin, Amelia C; Campino, Susana; Butcher, Philip D; Hibberd, Martin L; Clark, Taane G; (2019) An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome. SCIENTIFIC REPORTS, 9 (1). 5204-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-41692-2

Grignard, Lynn; Mair, Catherine; Curry, Jonathan; Mahey, Laleta; Bastiaens, Guide JH; Tiono, Alfred B; Okebe, Joseph; Coulibaly, Sam A; Gonçalves, Bronner P; Affara, Muna; +11 more... 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; (2019) Bead-based assays to simultaneously detect multiple human inherited blood disorders associated with malaria. Malaria journal, 18 (1). 14-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-019-2648-7

He, Yan; Campino, Susana; Diez Benavente, Ernest; Warhurst, David C; Beshir, Khalid B; Lubis, Inke; Gomes, Ana Rita; Feng, Jun; Jiazhi, Wang; Sun, Xiaodong; +4 more... Huang, Fang; Tang, Lin-Hua; Sutherland, Colin J; Clark, Taane G; (2019) 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. PLoS One, 14 (3). e0213686-. DOI: https://doi.org/10.1371/journal.pone.0213686

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

Mohring, Franziska; Hart, Melissa Natalie; Rawlinson, Thomas A; Henrici, Ryan; Charleston, James A; Diez Benavente, Ernest; Patel, Avnish; Hall, Joanna; Almond, Neil; Campino, Susana; +5 more... Clark, Taane G; Sutherland, Colin J; Baker, David A; Draper, Simon J; Moon, Robert William; (2019) Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research. eLife, 8. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.45829

Nacul, Luis; de Barros, Barbara; Kingdon, Caroline C; Cliff, Jacqueline M; Clark, Taane G; Mudie, Kathleen; Dockrell, Hazel M; Lacerda, Eliana M; (2019) Evidence of Clinical Pathology Abnormalities in People with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) from an Analytic Cross-Sectional Study. Diagnostics (Basel, Switzerland), 9 (2). p. 41. ISSN 2075-4418 DOI: https://doi.org/10.3390/diagnostics9020041

Oppong, Yaa EA; Phelan, Jody; Perdigão, João; Machado, Diana; Miranda, Anabela; Portugal, Isabel; Viveiros, Miguel; Clark, Taane G; Hibberd, Martin L; (2019) Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance. BMC genomics, 20 (1). 252-. ISSN 1471-2164 DOI: https://doi.org/10.1186/s12864-019-5615-3

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

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

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

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

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

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

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

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

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

Campos, Monica C; Dombrowski, Jamille G; Phelan, Jody; Marinho, Claudio RF; Hibberd, Martin; Clark, Taane G; Campino, Susana; (2018) Zika might not be acting alone: Using an ecological study approach to investigate potential co-acting risk factors for an unusual pattern of microcephaly in Brazil. PloS one, 13 (8). e0201452-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0201452

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

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

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

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

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

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

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

Higgins, Matthew; Ravenhall, Matt; Ward, Daniel; Phelan, Jody; Ibrahim, Amy; Forrest, Matthew S; Clark, Taane G; Campino, Susana; (2018) PrimedRPA: primer design for recombinase polymerase amplification assays. Bioinformatics (Oxford, England), 35 (4). pp. 682-684. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bty701

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; +3 more... Kellam, Paul; Nokes, D James; Cotten, Matthew; (2018) Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya. The Journal of infectious diseases, 217 (11). pp. 1728-1739. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiy098

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

Leon, Lydia J; Doyle, Ronan; Diez-Benavente, Ernest; Clark, Taane G; Klein, Nigel; Stanier, Philip; Moore, Gudrun E; (2018) 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. Applied and environmental microbiology, 84 (14). ISSN 0099-2240 DOI: https://doi.org/10.1128/AEM.00483-18

McNerney, Ruth; Zignol, Matteo; Clark, Taane G; (2018) Use of whole genome sequencing in surveillance of drug resistant tuberculosis. Expert review of anti-infective therapy, 16 (5). pp. 433-442. ISSN 1478-7210 DOI: https://doi.org/10.1080/14787210.2018.1472577 Full text not available from this repository.

Nacul, Luis Carlos; Mudie, Kathleen; Kingdon, Caroline C; Clark, Taane G; Lacerda, Eliana Mattos; (2018) Hand Grip Strength as a Clinical Biomarker for ME/CFS and Disease Severity. Frontiers in Neurology, 9 (NOV). 992-. DOI: https://doi.org/10.3389/fneur.2018.00992

Ndila, Carolyne M; Uyoga, Sophie; Macharia, Alexander W; Nyutu, Gideon; Peshu, Norbert; Ojal, John; Shebe, Mohammed; Awuondo, Kennedy O; Mturi, Neema; Tsofa, Benjamin; +15 more... 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; (2018) Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study. The Lancet Haematology, 5 (8). e333-e345. ISSN 2352-3026 DOI: https://doi.org/10.1016/S2352-3026(18)30107-8

Palittapongarnpim, Prasit; Ajawatanawong, Pravech; Viratyosin, Wasna; Smittipat, Nat; Disratthakit, Areeya; Mahasirimongkol, Surakameth; Yanai, Hideki; Yamada, Norio; Nedsuwan, Supalert; Imasanguan, Worarat; +13 more... 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; (2018) Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. Scientific reports, 8 (1). 11597-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-29986-3

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

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

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

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

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

Sepúlveda, Nuno; Phelan, Jody; Diez-Benavente, Ernest; Campino, Susana; Clark, Taane G; Hopkins, Heidi; Sutherland, Colin; Drakeley, Chris J; Beshir, Khalid B; (2018) Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. Infection, genetics and evolution, 62. pp. 211-219. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2018.04.039

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

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

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

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

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

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

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

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

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

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

Gomes, Ana Rita; Ravenhall, Matt; Benavente, Ernest Diez; Talman, Arthur; Sutherland, Colin; Roper, Cally; Clark, Taane G; Campino, Susana; (2017) 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]. International journal for parasitology Drugs and drug resistance, 7 (3). 433-. ISSN 2211-3207 DOI: https://doi.org/10.1016/j.ijpddr.2017.11.001

Gomes, Ana Rita; Ravenhall, Matt; Benavente, Ernest Diez; Talman, Arthur; Sutherland, Colin; Roper, Cally; Clark, Taane G; Campino, Susana; (2017) Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes. International journal for parasitology Drugs and drug resistance, 7 (2). pp. 174-180. ISSN 2211-3207 DOI: https://doi.org/10.1016/j.ijpddr.2017.03.001

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

Kanji, Akbar; Hasan, Rumina; Ali, Asho; Zaver, Ambreen; Zhang, Ying; Imtiaz, Kehkashan; Shi, Wanliang; Clark, Taane G; McNerney, Ruth; Phelan, Jody; +3 more... Rao, Shoaib; Shafiq, Samreen; Hasan, Zahra; (2017) Single nucleotide polymorphisms in efflux pumps genes in extensively drug resistant Mycobacterium tuberculosis isolates from Pakistan. Tuberculosis (Edinburgh, Scotland), 107 (Supple). pp. 20-30. ISSN 1472-9792 DOI: https://doi.org/10.1016/j.tube.2017.07.012 Full text not available from this repository.

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; +1 more... Nacul, Luis; (2017) The UK ME/CFS Biobank for biomedical research on Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Multiple Sclerosis. Open J Bioresour, 4. 4-. ISSN 2056-5542 DOI: https://doi.org/10.5334/ojb.28

Last, AR; Pickering, H; Roberts, Ch; Coll, F; Phelan, J; Burr, SE; Cassama, E; Nabicassa, M; Seth-Smith, HMB; Hadfield, J; +7 more... Cutcliffe, LT; Clarke, IN; Mabey, DCW; Bailey, RL; Clark, TG; Thomson, NR; Holland, MJ; (2017) Population-based analysis of ocular<i>Chlamydia trachomatis</i>in trachoma-endemic West African communities identifies genomic markers of disease severity. BioRxiv. DOI: https://doi.org/10.1101/205336

Nakatani, Yoshio; Opel-Reading, Helen K; Merker, Matthias; Machado, Diana; Andres, Sönke; Kumar, S Siva; Moradigaravand, Danesh; Coll, Francesc; Perdigão, João; Portugal, Isabel; +19 more... 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; (2017) Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance. Antimicrobial agents and chemotherapy, 61 (12). ISSN 0066-4804 DOI: https://doi.org/10.1128/AAC.01575-17

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

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

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

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

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

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

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

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

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

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

Kim, Jung-Yeon; Goo, Youn-Kyoung; Zo, Young-Gun; Ji, So-Young; Trimarsanto, Hidayat; To, Sheren; Clark, Taane G; Price, Ric N; Auburn, Sarah; (2016) Further Evidence of Increasing Diversity of Plasmodium vivax in the Republic of Korea in Recent Years. PloS one, 11 (3). e0151514-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0151514

McNerney, Ruth; Clark, Taane G; Campino, Susana; Rodrigues, Camilla; Dolinger, David; Smith, Liezel; Cabibbe, Andrea M; Dheda, Keertan; Schito, Marco; (2016) Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action. International journal of infectious diseases, 56. pp. 130-135. ISSN 1201-9712 DOI: https://doi.org/10.1016/j.ijid.2016.11.422

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

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

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

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

Refrégier, Guislaine; Abadia, Edgar; Matsumoto, Tomoshige; Ano, Hiromi; Takashima, Tetsuya; Tsuyuguchi, Izuo; Aktas, Elif; Cömert, Füsun; Gomgnimbou, Michel Kireopori; Panaiotov, Stefan; +6 more... Phelan, Jody; Coll, Francesc; McNerney, Ruth; Pain, Arnab; Clark, Taane G; Sola, Christophe; (2016) Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. Infection, genetics and evolution, 45. pp. 461-473. ISSN 1567-1348 DOI: https://doi.org/10.1016/j.meegid.2016.10.009

Abdallah, Abdallah M; Hill-Cawthorne, Grant A; Otto, Thomas D; Coll, Francesc; Guerra-Assunção, José Afonso; Gao, Ge; Naeem, Raeece; Ansari, Hifzur; Malas, Tareq B; Adroub, Sabir A; +10 more... Verboom, Theo; Ummels, Roy; Zhang, Huoming; Panigrahi, Aswini Kumar; McNerney, Ruth; Brosch, Roland; Clark, Taane G; Behr, Marcel A; Bitter, Wilbert; Pain, Arnab; (2015) Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific reports, 5 (1). 15443-. ISSN 2045-2322 DOI: https://doi.org/10.1038/srep15443

Ali, Asho; Hasan, Zahra; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant; Coll, Francesc; Nair, Mridul; Pain, Arnab; Clark, Taane G; Hasan, Rumina; (2015) Whole genome sequencing based characterization of extensively drug-resistant Mycobacterium tuberculosis isolates from Pakistan. PloS one, 10 (2). e0117771-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0117771

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

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

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

Coll I Cerezo, F; (2015) Bioinformatic analysis of Mycobacterium tuberculosis whole genome data. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.02124343

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

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

Getachew, Sisay; To, Sheren; Trimarsanto, Hidayat; Thriemer, Kamala; Clark, Taane G; Petros, Beyene; Aseffa, Abraham; Price, Ric N; Auburn, Sarah; (2015) Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia. PloS one, 10 (10). e0140780-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0140780

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; +2 more... Crampin, Amelia C; Clark, Taane G; (2015) Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi. PloS one, 10 (7). e0132840-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0132840

Guerra-Assunção, JA; Crampin, AC; Houben, RMGJ; Mzembe, T; Mallard, K; Coll, F; Khan, P; Banda, L; Chiwaya, A; Pereira, RPA; +5 more... McNerney, R; Fine, PEM; Parkhill, J; Clark, TG; Glynn, JR; (2015) Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife, 4 (4). ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.05166

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Samad, Hanif; Coll, Francesc; Preston, Mark D; Ocholla, Harold; Fairhurst, Rick M; Clark, Taane G; (2015) Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites. PLoS genetics, 11 (4). e1005131-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1005131

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

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Bergval, Indra; Coll, Francesc; Schuitema, Anja; de Ronde, Hans; Mallard, Kim; Pain, Arnab; McNerney, Ruth; Clark, Taane G; Anthony, Richard M; (2014) A proportion of mutations fixed in the genomes of in vitro selected isogenic drug-resistant Mycobacterium tuberculosis mutants can be detected as minority variants in the parent culture. FEMS microbiology letters, 362 (2). pp. 1-7. ISSN 0378-1097 DOI: https://doi.org/10.1093/femsle/fnu037

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

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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; +5 more... McNerney, Ruth; Harris, David; Parkhill, Julian; Clark, Taane G; Glynn, Judith R; (2014) 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. The Journal of infectious diseases, 211 (7). pp. 1154-1163. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiu574

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; +2 more... Bousema, Teun; Sutherland, Colin J; (2014) Directional selection at the pfmdr1, pfcrt, pfubp1, and pfap2mu loci of Plasmodium falciparum in Kenyan children treated with ACT. The Journal of infectious diseases, 210 (12). pp. 2001-2008. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiu358

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

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

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; +2 more... Cortés, Alfred; Llinás, Manuel; (2014) A transcriptional switch underlies commitment to sexual development in malaria parasites. Nature, 507 (7491). pp. 248-252. ISSN 0028-0836 DOI: https://doi.org/10.1038/nature12920 Full text not available from this repository.

Liu, Yaobao; Auburn, Sarah; Cao, Jun; Trimarsanto, Hidayat; Zhou, Huayun; Gray, Karen-Ann; Clark, Taane G; Price, Ric N; Cheng, Qin; Huang, Rui; +1 more... Gao, Qi; (2014) Genetic diversity and population structure of Plasmodium vivax in Central China. Malaria journal, 13 (1). 262-. ISSN 1475-2875 DOI: https://doi.org/10.1186/1475-2875-13-262

Maiga, Bakary; Dolo, Amagana; Campino, Susana; Sepulveda, Nuno; Corran, Patrick; Rockett, Kirk A; Troye-Blomberg, Marita; Doumbo, Ogobara K; Clark, Taane G; (2014) Glucose-6-phosphate dehydrogenase polymorphisms and susceptibility to mild malaria in Dogon and Fulani, Mali. MALARIA JOURNAL, 13 (1). 270-. ISSN 1475-2875 DOI: https://doi.org/10.1186/1475-2875-13-270

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; +2 more... Kwiatkowski, Dominic P; Conway, David J; (2014) Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity. Molecular biology and evolution, 31 (6). pp. 1490-1499. ISSN 0737-4038 DOI: https://doi.org/10.1093/molbev/msu106

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; +1 more... Wren, Brendan W; (2014) Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development. mBio, 5 (1). e00926-e00913. ISSN 2150-7511 DOI: https://doi.org/10.1128/mBio.00926-13

Naeem, Raeece; Hidayah, Lailatul; Preston, Mark D; Clark, Taane G; Pain, Arnab; (2014) SVAMP: sequence variation analysis, maps and phylogeny. Bioinformatics (Oxford, England), 30 (15). pp. 2227-2229. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/btu176

Ocholla, Harold; Preston, Mark D; Mipando, Mwapatsa; Jensen, Anja TR; Campino, Susana; MacInnis, Bronwyn; Alcock, Daniel; Terlouw, Anja; Zongo, Issaka; Oudraogo, Jean-Bosco; +13 more... 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; (2014) Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates. The Journal of infectious diseases, 210 (12). pp. 1991-2000. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jiu349

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

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

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

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

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

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

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

Clark, Taane G; Mallard, Kim; Coll, Francesc; Preston, Mark; Assefa, Samuel; Harris, David; Ogwang, Sam; Mumbowa, Francis; Kirenga, Bruce; O'Sullivan, Denise M; +8 more... Okwera, Alphonse; Eisenach, Kathleen D; Joloba, Moses; Bentley, Stephen D; Ellner, Jerrold J; Parkhill, Julian; Jones-López, Edward C; McNerney, Ruth; (2013) Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PloS one, 8 (12). e83012-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0083012

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

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

Liu, Xuanyao; Ong, Rick Twee-Hee; Pillai, Esakimuthu Nisha; Elzein, Abier M; Small, Kerrin S; Clark, Taane G; Kwiatkowski, Dominic P; Teo, Yik-Ying; (2013) Detecting and characterizing genomic signatures of positive selection in global populations. American journal of human genetics, 92 (6). pp. 866-881. ISSN 0002-9297 DOI: https://doi.org/10.1016/j.ajhg.2013.04.021 Full text not available from this repository.

Maiga, B; Dolo, A; Touré, O; Dara, V; Tapily, A; Campino, S; Sepulveda, N; Corran, P; Rockett, K; Clark, TG; +2 more... Blomberg, M Troye; Doumbo, OK; (2013) Fc gamma receptor IIa-H131R polymorphism and malaria susceptibility in sympatric ethnic groups, Fulani and Dogon of Mali. Scandinavian journal of immunology, 79 (1). pp. 43-50. ISSN 0300-9475 DOI: https://doi.org/10.1111/sji.12122

Maiga, Bakary; Dolo, Amagana; Touré, Ousmane; Dara, Victor; Tapily, Amadou; Campino, Susana; Sepulveda, Nuno; Risley, Paul; Silva, Nilupa; Corran, Patrick; +6 more... Rockett, Kirk A; Kwiatkowski, Dominic; MalariaGEN Consortium; Clark, Taane G; Troye-Blomberg, Marita; Doumbo, Ogobara K; (2013) Human candidate polymorphisms in sympatric ethnic groups differing in malaria susceptibility in Mali. PloS one, 8 (10). e75675-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0075675

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; +4 more... Kwiatkowski, Dominic P; Clark, Taane G; Greenwood, Brian M; Conway, David J; (2013) Changes in malaria parasite drug resistance in an endemic population over a 25-year period with resulting genomic evidence of selection. The Journal of infectious diseases, 209 (7). pp. 1126-1135. ISSN 0022-1899 DOI: https://doi.org/10.1093/infdis/jit618

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

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

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

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

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

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

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

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; +2 more... Rogers, William O; Kwiatkowski, Dominic P; (2012) Haplotype analyses of haemoglobin C and haemoglobin S and the dynamics of the evolutionary response to malaria in Kassena-Nankana District of Ghana. PloS one, 7 (4). e34565-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0034565

Lawley, Trevor D; Clare, Simon; Walker, Alan W; Stares, Mark D; Connor, Thomas R; Raisen, Claire; Goulding, David; Rad, Roland; Schreiber, Fernanda; Brandt, Cordelia; +7 more... Deakin, Laura J; Pickard, Derek J; Duncan, Sylvia H; Flint, Harry J; Clark, Taane G; Parkhill, Julian; Dougan, Gordon; (2012) Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS pathogens, 8 (10). e1002995-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1002995

Manjurano, Alphaxard; Clark, Taane G; Nadjm, Behzad; Mtove, George; Wangai, Hannah; Sepulveda, Nuno; Campino, Susana G; Maxwell, Caroline; Olomi, Raimos; Rockett, Kirk R; +5 more... Jeffreys, Anna; MalariaGen Consortium; Riley, Eleanor M; Reyburn, Hugh; Drakeley, Christopher; (2012) Candidate human genetic polymorphisms and severe malaria in a Tanzanian population. PloS one, 7 (10). e47463-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0047463

Manske, Magnus; Miotto, Olivo; Campino, Susana; Auburn, Sarah; Almagro-Garcia, Jacob; Maslen, Gareth; O'Brien, Jack; Djimde, Abdoulaye; Doumbo, Ogobara; Zongo, Issaka; +46 more... 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; (2012) Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature, 487 (7407). pp. 375-379. ISSN 0028-0836 DOI: https://doi.org/10.1038/nature11174

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

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

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

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

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

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

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

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

Manjurano, Alphaxard; Okell, Lucy; Lukindo, Tedson; Reyburn, Hugh; Olomi, Raimos; Roper, Cally; Clark, Taane G; Joseph, Sarah; Riley, Eleanor M; Drakeley, Chris; (2011) Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania. Malaria journal, 10 (1). 370-. ISSN 1475-2875 DOI: https://doi.org/10.1186/1475-2875-10-370

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

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

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

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

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

Lawley, Trevor D; Clare, Simon; Deakin, Laura J; Goulding, David; Yen, Jennifer L; Raisen, Claire; Brandt, Cordelia; Lovell, Jon; Cooke, Fiona; Clark, Taane G; +1 more... Dougan, Gordon; (2010) Use of purified Clostridium difficile spores to facilitate evaluation of health care disinfection regimens. Applied and environmental microbiology, 76 (20). pp. 6895-6900. ISSN 0099-2240 DOI: https://doi.org/10.1128/AEM.00718-10 Full text not available from this repository.

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

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

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

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

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

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

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

Fry, Andrew E; Ghansa, Anita; Small, Kerrin S; Palma, Alejandro; Auburn, Sarah; Diakite, Mahamadou; Green, Angela; Campino, Susana; Teo, Yik Y; Clark, Taane G; +18 more... 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; (2009) Positive selection of a CD36 nonsense variant in sub-Saharan Africa, but no association with severe malaria phenotypes. Human molecular genetics, 18 (14). pp. 2683-2692. ISSN 0964-6906 DOI: https://doi.org/10.1093/hmg/ddp192