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

Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study. (2016) Dheda, Keertan; Limberis, Jason D; Pietersen, Elize; Phelan, Jody; Esmail, Aliasgar; Lesosky, Maia; Fennelly, Kevin P; Te Riele, Julian; Mastrapa, Barbara; Streicher, Elizabeth M; Dolby, Tania; Abdallah, Abdallah M; Ben-Rached, Fathia; Simpson, John; Smith, Liezel; Gumbo, Tawanda; van Helden, Paul; Sirgel, Frederick A; McNerney, Ruth; Theron, Grant; Pain, Arnab; Clark, Taane G; Warren, Robin M

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

Public

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

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

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

A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages. (2019) Ajawatanawong, Pravech; Yanai, Hideki; Smittipat, Nat; Disratthakit, Areeya; Yamada, Norio; Miyahara, Reiko; Nedsuwan, Supalert; Imasanguan, Worarat; Kantipong, Pacharee; Chaiyasirinroje, Boonchai; Wongyai, Jiraporn; Plitphonganphim, Supada; Tantivitayakul, Pornpen; Phelan, Jody; Parkhill, Julian; Clark, Taane G; Hibberd, Martin L; Ruangchai, Wuthiwat; Palittapongarnpim, Panawun; Juthayothin, Tada; Thawornwattana, Yuttapong; Viratyosin, Wasna; Tongsima, Sissades; Mahasirimongkol, Surakameth; Tokunaga, Katsushi; Palittapongarnpim, Prasit

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

Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa. (2021) Benavente, Ernest Diez; Manko, Emilia; Phelan, Jody; Campos, Monica; Nolder, Debbie; Fernandez, Diana; Velez-Tobon, Gabriel; Castaño, Alberto Tobón; Dombrowski, Jamille G; Marinho, Claudio RF; Aguiar, Anna Caroline C; Pereira, Dhelio Batista; Sriprawat, Kanlaya; Nosten, Francois; Moon, Robert; Sutherland, Colin J; Campino, Susana; Clark, Taane G

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

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

Zika might not be acting alone: Using an ecological study approach to investigate potential co-acting risk factors for an unusual pattern of microcephaly in Brazil. (2018) Campos, Monica C; Dombrowski, Jamille G; Phelan, Jody; Marinho, Claudio RF; Hibberd, Martin; Clark, Taane G; Campino, Susana

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

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

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

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. (2017) Coll, Francesc; Phelan, Jody; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; Ali, Shahjahan; Abdallah, Abdallah M; Alghamdi, Saad; Alsomali, Mona; Ahmed, Abdallah O; Portelli, Stephanie; Oppong, Yaa; Alves, Adriana; Bessa, Theolis Barbosa; Campino, Susana; Caws, Maxine; Chatterjee, Anirvan; Crampin, Amelia C; Dheda, Keertan; Furnham, Nicholas; Glynn, Judith R; Grandjean, Louis; Minh Ha, Dang; Hasan, Rumina; Hasan, Zahra; Hibberd, Martin L; Joloba, Moses; Jones-López, Edward C; Matsumoto, Tomoshige; Miranda, Anabela; Moore, David J; Mocillo, Nora; Panaiotov, Stefan; Parkhill, Julian; Penha, Carlos; Perdigão, João; Portugal, Isabel; Rchiad, Zineb; Robledo, Jaime; Sheen, Patricia; Shesha, Nashwa Talaat; Sirgel, Frik A; Sola, Christophe; Oliveira Sousa, Erivelton; Streicher, Elizabeth M; Helden, Paul Van; Viveiros, Miguel; Warren, Robert M; McNerney, Ruth; Pain, Arnab; Clark, Taane G

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

Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia. (2022) Darboe, Saffiatou; Bradbury, Richard S; Phelan, Jody; Kanteh, Abdoulie; Muhammad, Abdul-Khalie; Worwui, Archibald; Yang, Shangxin; Nwakanma, Davis; Perez-Sepulveda, Blanca; Kariuki, Samuel; Kwambana-Adams, Brenda; Antonio, Martin

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

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

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

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

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

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

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

An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome. (2019) Gomez-Gonzalez, Paula J; Andreu, Nuria; Phelan, Jody E; de Sessions, Paola Florez; Glynn, Judith R; Crampin, Amelia C; Campino, Susana; Butcher, Philip D; Hibberd, Martin L; Clark, Taane G

Corrigendum to 'A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections'. (2021) Grignard, Lynn; Nolder, Debbie; Sepulveda, Nuno; Berhane, Araia; Mihreteab, Selam; Kaaya, Robert; Phelan, Jody; Moser, Kara; van Schalkwyk, Donelly A; Campino, Susana; Parr, Jonathan B; Juliano, Jonathan J; Chiodini, Peter; Cunningham, Jane; Sutherland, Colin J; Drakeley, Chris; Beshir, Khalid B

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. (2021) Gröschel, Matthias I; Owens, Martin; Freschi, Luca; Vargas, Roger; Marin, Maximilian G; Phelan, Jody; Iqbal, Zamin; Dixit, Avika; Farhat, Maha R

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

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

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

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

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

Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study. (2023) Hackman, Jada; Sheppard, Carmen; Phelan, Jody; Jones-Warner, William; Sobkowiak, Ben; Shah, Sonal; Litt, David; Fry, Norman K; Toizumi, Michiko; Yoshida, Lay-Myint; Hibberd, Martin; Miller, Elizabeth; Flasche, Stefan; Hué, Stéphane

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

Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure. (2018) Herman, Lou S; Fornace, Kimberly; Phelan, Jody; Grigg, Matthew J; Anstey, Nicholas M; William, Timothy; Moon, Robert W; Blackman, Michael J; Drakeley, Chris J; Tetteh, Kevin KA

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

Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan. (2019) Jabbar, Abdul; Phelan, Jody E; de Sessions, Paola Florez; Khan, Taj Ali; Rahman, Hazir; Khan, Sadiq Noor; Cantillon, Daire M; Wildner, Leticia Muraro; Ali, Sajid; Campino, Susana; Waddell, Simon J; Clark, Taane G

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

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

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

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

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

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

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

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

All parts of the WHO Mycobacterium tuberculosis mutation catalog need to be applied when evaluating its performance. (2025) Laurent, Sacha; Phelan, Jody E; Chindelevitch, Leonid; Walker, Timothy M; Cirillo, Daniela M; Suresh, Anita; Rodwell, Timothy C; Miotto, Paolo; Köser, Claudio U

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

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

Acute and long-term outcomes of SARS-CoV-2 infection in school-aged children in England: Study protocol for the joint analysis of the COVID-19 schools infection survey (SIS) and the COVID-19 mapping and mitigation in schools (CoMMinS) study. (2024) Looker, Katharine J; McClenaghan, Elliot; Judd, Alison; Pierotti, Livia; Downing, Harriet; Phelan, Jody; Warren-Gash, Charlotte; Ngozi, Kalu; Dawe, Fiona; Relton, Caroline; Christensen, Hannah; Hay, Alastair D; Mangtani, Punam; Nguipdop-Djomo, Patrick; Denholm, Rachel

Genetic risk of obesity as a modifier of associations between neighbourhood environment and body mass index: an observational study of 335 046 UK Biobank participants. (2020) Mason, Kate E; Palla, Luigi; Pearce, Neil; Phelan, Jody; Cummins, Steven

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

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

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

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

Molecular characterisation of second-line drug resistance among drug resistant tuberculosis patients tested in Uganda: a two and a half-year's review. (2022) Mujuni, Dennis; Kasemire, Dianah Linda; Ibanda, Ivan; Kabugo, Joel; Nsawotebba, Andrew; Phelan, Jody E; Majwala, Robert Kaos; Tugumisirize, Didas; Nyombi, Abdunoor; Orena, Beatrice; Turyahabwe, Irene; Byabajungu, Henry; Nadunga, Diana; Musisi, Kenneth; Joloba, Moses Lutakoome; Ssengooba, Willy

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

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

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

Intra-annual variation in feed and milk composition in smallholder dairy farms in Kenya. (2022) Nyokabi, Ndungu S; Luning, Pieternel A; Phelan, Jody Emile; Creemers, Jos; Lukuyu, Ben; Bebe, Bockline Omedo; Oosting, Simon J

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

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

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

Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain. (2020) Perdigão, João; Caneiras, Cátia; Elias, Rita; Modesto, Ana; Spadar, Anton; Phelan, Jody; Campino, Susana; Clark, Taane G; Costa, Eliana; Saavedra, Maria José; Duarte, Aida

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

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

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

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

Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines. (2019) Phelan, Jody E; Lim, Dodge R; Mitarai, Satoshi; de Sessions, Paola Florez; Tujan, Ma Angelica A; Reyes, Lorenzo T; Medado, Inez Andrea P; Palparan, Alma G; Naim, Ahmad Nazri Mohamed; Jie, Song; Segubre-Mercado, Edelwisa; Simoes, Beatriz; Campino, Susana; Hafalla, Julius C; Murase, Yoshiro; Morishige, Yuta; Hibberd, Martin L; Kato, Seiya; Ama, Ma Cecilia G; Clark, Taane G

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. (2019) Phelan, Jody E; O'Sullivan, Denise M; Machado, Diana; Ramos, Jorge; Oppong, Yaa EA; Campino, Susana; O'Grady, Justin; McNerney, Ruth; Hibberd, Martin L; Viveiros, Miguel; Huggett, Jim F; Clark, Taane G

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

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. (2016) Phelan, Jody; Coll, Francesc; McNerney, Ruth; Ascher, David B; Pires, Douglas EV; Furnham, Nick; Coeck, Nele; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; Ramsay, Andrew; Campino, Susana; Hibberd, Martin L; Pain, Arnab; Rigouts, Leen; Clark, Taane G

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

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

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

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

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

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

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

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

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

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

Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia. (2017) Sengstake, Sarah; Bergval, Indra L; Schuitema, Anja R; de Beer, Jessica L; Phelan, Jody; de Zwaan, Rina; Clark, Taane G; van Soolingen, Dick; Anthony, Richard M

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

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. (2018) Sobkowiak, Benjamin; Glynn, Judith R; Houben, Rein MGJ; Mallard, Kim; Phelan, Jody E; Guerra-Assunção, José Afonso; Banda, Louis; Mzembe, Themba; Viveiros, Miguel; McNerney, Ruth; Parkhill, Julian; Crampin, Amelia C; Clark, Taane G

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

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

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

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

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

Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network. (2024) Sung, Po-Yu; Phelan, Jody E; Luo, Dongsheng; Kulasegaran-Shylini, Raghavendran; Bohn, Patrick; Smyth, Redmond P; Roy, Polly

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

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

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

Preferential transmission of minority and drug-resistant clones in polyclonal infections in Mali. (2025) Vanheer, Leen N; Manko, Emilia; Mahamar, Almahamoudou; Phelan, Jody; Sanogo, Koualy; Sinaba, Youssouf; Niambele, Sidi M; Sacko, Adama; Keita, Sekouba; Youssouf, Ahamadou; Diallo, Makonon; Soumare, Harouna M; Lanke, Kjerstin; Issiaka, Djibrilla; Diawara, Halimatou; Traore, Sekou F; Grignard, Lynn; Dicko, Alassane; Drakeley, Chris; Campino, Susana; Stone, William

TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis. (2022) Verboven, Lennert; Phelan, Jody; Heupink, Tim H; Van Rie, Annelies

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

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

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

Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax. (2017) de Oliveira, Thais C; Rodrigues, Priscila T; Menezes, Maria José; Gonçalves-Lopes, Raquel M; Bastos, Melissa S; Lima, Nathália F; Barbosa, Susana; Gerber, Alexandra L; Loss de Morais, Guilherme; Berná, Luisa; Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R; Alves, João Marcelo P; Ferreira, Marcelo U

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A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections. (2020) Grignard, Lynn; Nolder, Debbie; Sepúlveda, Nuno; Berhane, Araia; Mihreteab, Selam; Kaaya, Robert; Phelan, Jody; Moser, Kara; van Schalkwyk, Donelly A; Campino, Susana; Parr, Jonathan B; Juliano, Jonathan J; Chiodini, Peter; Cunningham, Jane; Sutherland, Colin J; Drakeley, Chris; Beshir, Khalid B picture_as_pdf

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

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