Items where Author or Contributor is "Phelan, Jody E"

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Number of items: 94.

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; +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
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Phelan, Jody; Van den Heede, Klaas; Masyn, Serge; Verbeeck, Rudi; Lamprecht, Dirk A; Koul, Anil; Wall, Richard J; (2024) An open-access dashboard to interrogate the genetic diversity of Mycobacterium tuberculosis clinical isolates. Scientific reports, 14. p. 24792. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-024-75818-y
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Sung, Po-Yu; Phelan, Jody E; Luo, Dongsheng; Kulasegaran-Shylini, Raghavendran; Bohn, Patrick; Smyth, Redmond P; Roy, Polly; (2024) Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network. Nucleic acids research, 52 (14). pp. 8500-8514. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkae404
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2023

Hackman, Jada; Sheppard, Carmen; Phelan, Jody; Jones-Warner, William; Sobkowiak, Ben; Shah, Sonal; Litt, David; Fry, Norman K; Toizumi, Michiko; Yoshida, Lay-Myint; +4 more... Hibberd, Martin; Miller, Elizabeth; Flasche, Stefan; Hué, Stéphane; (2023) Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study. Wellcome open research, 8. 427-. DOI: https://doi.org/10.12688/wellcomeopenres.19219.1
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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
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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
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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
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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
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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
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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
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2022

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
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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
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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
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Darboe, Saffiatou; Bradbury, Richard S; Phelan, Jody; Kanteh, Abdoulie; Muhammad, Abdul-Khalie; Worwui, Archibald; Yang, Shangxin; Nwakanma, Davis; Perez-Sepulveda, Blanca; Kariuki, Samuel; +2 more... Kwambana-Adams, Brenda; Antonio, Martin; (2022) Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia. MICROBIAL GENOMICS, 8 (3). DOI: https://doi.org/10.1099/mgen.0.000785
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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
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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
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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
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Mujuni, Dennis; Kasemire, Dianah Linda; Ibanda, Ivan; Kabugo, Joel; Nsawotebba, Andrew; Phelan, Jody E; Majwala, Robert Kaos; Tugumisirize, Didas; Nyombi, Abdunoor; Orena, Beatrice; +6 more... Turyahabwe, Irene; Byabajungu, Henry; Nadunga, Diana; Musisi, Kenneth; Joloba, Moses Lutakoome; Ssengooba, Willy; (2022) Molecular characterisation of second-line drug resistance among drug resistant tuberculosis patients tested in Uganda: a two and a half-year's review. BMC INFECTIOUS DISEASES, 22 (1). 363-. ISSN 1471-2334 DOI: https://doi.org/10.1186/s12879-022-07339-w
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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
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Nyokabi, Ndungu S; Luning, Pieternel A; Phelan, Jody Emile; Creemers, Jos; Lukuyu, Ben; Bebe, Bockline Omedo; Oosting, Simon J; (2022) Intra-annual variation in feed and milk composition in smallholder dairy farms in Kenya. NJAS: Impact in Agricultural and Life Sciences, 94 (1). pp. 137-155. ISSN 2768-5241 DOI: https://doi.org/10.1080/27685241.2022.2135391
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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
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Verboven, Lennert; Phelan, Jody; Heupink, Tim H; Van Rie, Annelies; (2022) TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis. PloS One, 17 (12). e0279644-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0279644
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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; +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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Deelder, Wouter; Benavente, Ernest Diez; Phelan, Jody; Manko, Emilia; Campino, Susana; Palla, Luigi; Clark, Taane G; (2021) Using deep learning to identify recent positive selection in malaria parasite sequence data. Malaria journal, 20 (1). 270-. ISSN 1475-2875 DOI: https://doi.org/10.1186/s12936-021-03788-x
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Gröschel, Matthias I; Owens, Martin; Freschi, Luca; Vargas, Roger; Marin, Maximilian G; Phelan, Jody; Iqbal, Zamin; Dixit, Avika; Farhat, Maha R; (2021) GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. Genome medicine, 13 (1). 138-. ISSN 1756-994X DOI: https://doi.org/10.1186/s13073-021-00953-4
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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; +2 more... Phelan, Jody E; Clark, Taane G; (2021) Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid. Scientific reports, 11 (1). 19431-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-98862-4
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Khan, Anwar Sheed; Phelan, Jody E; Khan, Muhammad Tahir; Ali, Sajid; Qasim, Muhammad; Napier, Gary; Campino, Susana; Ahmad, Sajjad; Cabral-Marques, Otavio; Zhang, Shulin; +4 more... Rahman, Hazir; Wei, Dong-Qing; Clark, Taane G; Khan, Taj Ali; (2021) Author Correction: Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan. Scientific reports, 11 (1). 15100-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-94687-3
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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
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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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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; +18 more... 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; (2021) An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. Scientific Reports, 11 (1). 10590-. DOI: https://doi.org/10.1038/s41598-021-89881-2
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Spadar, Anton; Perdigão, João; Phelan, Jody; Charleston, James; Modesto, Ana; Elias, Rita; de Sessions, Paola Florez; Hibberd, Martin L; Campino, Susana; Duarte, Aida; +1 more... Clark, Taane G; (2021) Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals. Scientific reports, 11 (1). 6491-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-021-85724-2
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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; +4 more... Nosten, Francois; Sutherland, Colin J; Campino, Susana; Clark, Taane G; (2020) A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria. PLoS genetics, 16 (2). e1008576-. ISSN 1553-7390 DOI: https://doi.org/10.1371/journal.pgen.1008576
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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
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Grignard, Lynn; Nolder, Debbie; Sepúlveda, Nuno; Berhane, Araia; Mihreteab, Selam; Kaaya, Robert; Phelan, Jody; Moser, Kara; van Schalkwyk, Donelly A; Campino, Susana; +7 more... Parr, Jonathan B; Juliano, Jonathan J; Chiodini, Peter; Cunningham, Jane; Sutherland, Colin J; Drakeley, Chris; Beshir, Khalid B; (2020) A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections. EBioMedicine, 55. 102757-. ISSN 2352-3964 DOI: https://doi.org/10.1016/j.ebiom.2020.102757 Item availability may be restricted.
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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
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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
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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
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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
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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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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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Tunstall, Tanushree; Portelli, Stephanie; Phelan, Jody; Clark, Taane G; Ascher, David B; Furnham, Nicholas; (2020) Combining structure and genomics to understand antimicrobial resistance. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18. pp. 3377-3394. ISSN 2001-0370 DOI: https://doi.org/10.1016/j.csbj.2020.10.017
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2019

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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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
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Jabbar, Abdul; Phelan, Jody E; de Sessions, Paola Florez; Khan, Taj Ali; Rahman, Hazir; Khan, Sadiq Noor; Cantillon, Daire M; Wildner, Leticia Muraro; Ali, Sajid; Campino, Susana; +2 more... Waddell, Simon J; Clark, Taane G; (2019) Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan. Scientific reports, 9 (1). 14996-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-019-51562-6
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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
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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
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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
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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; +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
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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; (2018) Identification and validation of a novel panel of Plasmodium knowlesi biomarkers of serological exposure. PLoS neglected tropical diseases, 12 (6). e0006457-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0006457
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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
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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
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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
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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
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2017

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.

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
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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.

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
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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; +5 more... Phelan, Jody; Robello, Carlos; de Vasconcelos, Ana Tereza R; Alves, João Marcelo P; Ferreira, Marcelo U; (2017) Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax. PLoS neglected tropical diseases, 11 (7). e0005824-. ISSN 1935-2727 DOI: https://doi.org/10.1371/journal.pntd.0005824
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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; +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
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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
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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
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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
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2015

Phelan, Jody; Maitra, Arundhati; McNerney, Ruth; Nair, Mridul; Gupta, Antima; Coll, Francesc; Pain, Arnab; Bhakta, Sanjib; Clark, Taane G; (2015) The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae. International journal of mycobacteriology, 4 (3). pp. 207-216. ISSN 2212-5531 DOI: https://doi.org/10.1016/j.ijmyco.2015.05.001
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This list was generated on Mon Oct 28 06:51:00 2024 GMT.