Data Creators(s) Item Type No Grouping

PolyTB: A web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale. (2014) Coll, Francesc, Preston, Mark, Guerra-Assunção, José Afonso, Hill-Cawthorn, Grant, Harris, David, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Drobniewski, Francis, Gagneux, Sebastien, Glynn, Judith R., Pain, Arnab, Parkhill, Julian, McNerney, Ruth, Martin, Nigel, Clark, Taane

Integrated view of Vibrio cholerae in the Americas. (2017) Domman, Daryl, Quilici, Marie-Laure, Dorman, Matthew J., Njamkepo, Elisabeth, Mutreja, Ankur, Mather, Alison E., Delgado, Gabriella, Morales-Espinosa, Rosario, Grimont, Patrick A. D., Lizárraga-Partida, Marcial Leonardo, Bouchier, Christiane, Aanensen, David M., Kuri-Morales, Pablo, Tarr, Cheryl L., Dougan, Gordon, Parkhill, Julian, Campos, Josefina, Cravioto, Alejandro, Weill, François-Xavier, Thomson, Nicholas R.

Supporting data for 'High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139'. (2019) Dorman, Matthew J, Domman, Daryl, Uddin, Muhammad Ikhtear, Sharmin, Salma, Hassan Afrad, Mokibul, Begum, Yasmin Ara, Qadri, Firdausi, Thomson, Nicholas R

Accession numbers and data for S. Typhi sequences used in this study. (2022) Dyson, Zoe Anne, Malau, Elisheba, Horwood, Paul F, Ford, Rebecca, Siba, Valentine, Yoannes, Mition, Pomat, William, Passey, Megan, Judd, Louise M, Ingle, Danielle J, Williamson, Deborah A, Dougan, Gordon, Greenhill, Andrew R, Holt, Kathryn E

Excluded repeat and phage regions in PNG MDUST348 2.1.7.2 completed reference sequence. (2022) Dyson, Zoe Anne, Malau, Elisheba, Horwood, Paul F, Ford, Rebecca, Siba, Valentine, Yoannes, Mition, Pomat, William, Passey, Megan, Judd, Louise M, Ingle, Danielle J, Williamson, Deborah A, Dougan, Gordon, Greenhill, Andrew R, Holt, Kathryn E

Outgroups used for phylogenetic tree rooting. (2022) Dyson, Zoe Anne, Malau, Elisheba, Horwood, Paul F, Ford, Rebecca, Siba, Valentine, Yoannes, Mition, Pomat, William, Passey, Megan, Judd, Louise M, Ingle, Danielle J, Williamson, Deborah A, Dougan, Gordon, Greenhill, Andrew R, Holt, Kathryn E

Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. (2023) Foster-Nyarko, Ebenezer, Holt, Kathryn E., Cottingham, Hugh, Wick, Ryan, Judd, Louise M., Lam, Margaret, Wyres, Kelly L., Stanton, Thomas, Tsang, Kara K., David, Sophia, Bridel, Sébastien, Palma, Federica, Aanensen, David M, Brisse, Sylvain

Profile of the organisms selected for sequencing. (2021) Guevara, Paula Diaz, Maes, Mailis, Thanh, Duy Pham, Duarte, Carolina, Rodriguez, Edna Catering, Montaño, Lucy Angeline, Dan, Thanh Ho Ngoc, Nguyen, To Nguyen Thi, Carey, Megan E, Campos, Josefina, Chinen, Isabel, Perez, Enrique, Baker, Stephen

Additional file 2 of A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs. (2025) Hetland, Marit A. K., Winkler, Mia A., Kaspersen, Håkon P., Håkonsholm, Fredrik, Bakksjø, Ragna-Johanne, Bernhoff, Eva, Delgado-Blas, Jose F., Brisse, Sylvain, Correia, Annapaula, Fostervold, Aasmund, Lam, Margaret M. C., Lunestad, Bjørn-Tore, Marathe, Nachiket P., Raffelsberger, Niclas, Samuelsen, Ørjan, Sunde, Marianne, Sundsfjord, Arnfinn, Urdahl, Anne Margrete, Wick, Ryan R., Löhr, Iren H., Holt, Kathryn E.

Acinetobacter baumannii GC1 recombination analysis. (2016) Holt, Kathryn E.

Convergent evolution of artemisinin and chloroquine resistance in Ethiopian Plasmodium falciparum parasites. (2025) Letebo, Alemayehu, Vanheer, Leen N., Engdaw, Mengst, Alemayehu, Dawit Hailu, Deressa, Jimma Dinsa, Adnew, Bethlehem, Ayele, Abaysew, Keffale, Migbaru, Demisse, Mulugeta, Seyoum, Tamrayehu, Shiferaw, Meklit, Sime, Heven, Gebreegziabxier, Atsbeha, Shimelash, Amanuel, Tafa, Elias B., Chali, Wakweya, Alemayehu, Lina, Kassa, Fikregabrail Aberra, Zeleke, Ayalew Jejaw, Hamza, Tajudin Abdurhaman, Tamirat, Abel Beliyu, Misganaw, Tadesse, Bogale, Alayu, Abriham, Zufan Yiheyis, Nasir, Yasin, Jebessa, Gutema, Ejigu, Legesse Alamerie, Yohannes, Metmiku, Kebede, Betelhem Akililu, Ayele, Matiwos Kidane, Abdo, Melat, Habtamu, Getinet, Gizat, Addisu, Phelan, Jody, Matlock, Bryce, Fidock, David A., Campino, Susana, Assefa, Ashenafi, Koepfli, Cristian, Massebo, Fekadu, Tadesse, Fitsum G.

Plasmodium falciparum sequencing Bijagos Archipelago 2018. (2022) London School of Hygiene & Tropical Medicine

Contexts, Facilitators, and Barriers to Integrating Portable Genomic Sequencing in Outbreak Response: A Qualitative Study from Coastal Kenya. (2025) Makena, Evelyn, Wang, Ling, Okanda, Dorcas, Carter, Daniel, Leggio, Cristina, Odhiambo, Juliet, Munyoki, Catherine, Abdalla, Abbbas, Agoti, Charles N., Gatie, Victor, Adam, Ahmed, Wasike, Hildergard, Kassim, Salim, Onwonga, Vera, Robaa, Abdi, Ndia, Millicent, Kiiru, John, Kingwara, Leonard, Madada, Rukia, Lang'at, Paul, Hargreaves, James R., Hughes, Gwenda, Eunice Wangeci, Kagucia, Haque, Farhana, Githinji, George

Files for "Evolution and epidemiology of multidrug resistant Klebsiella pneumoniae in the UK and Ireland". (2016) Moradigaravand, Danesh, Martin, Veronique, Peacock, Sharon J., Parkhill, Julian

Whole genome sequences for M.tuberculosis isolates from the TDR strain bank. (2015) Phelan, Jody, Coll, Francesc, Mcnerney, Ruth, Ascher, David B., Pires, Douglas E. V., Furnham, Nick, Coeck, Nele, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ramsay, Andrew, Campino, Susana, Hibberd, Martin, Pain, Arnab, Rigouts, Leen, Clark, Taane description

jodyphelan/malaria-db. (2023) Phelan, Jody, Manko, Emilia

jodyphelan/malaria-profiler. (2023) Phelan, Jody, Thorpe, Joseph

Wolbachia endosymbionts in two Anopheles species indicates independent acquisitions and lack of prophage elements. (2022) Quek, Shannon, Cerdeira, Louise, Jeffries, Claire L., Tomlinson, Sean, Walker, Thomas, Hughes, Grant L., Heinz, Eva

Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. (2020) Rahman, Sadia Isfat Ara, Dyson, Zoe A., Klemm, Elizabeth J., Khanam, Farhana, Holt, Kathryn E., Chowdhury, Emran Kabir, Dougan, Gordon, Qadri, Firdausi

Dataset for "Genomic characterisation of Salmonella enterica serovar Wangata isolates obtained from different sources reveals low genomic diversity". (2020) Simpson, Kelly M J, Mor, Siobhan M, Ward, Michael P, Collins, Julie, Flint, James, Hill-Cawthorne, Grant A, El Ghany, Moataz Abd

TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis. S1 File. (2022) Verboven, Lennert, Phelan, Jody, Heupink, Tim H., Van Rie, Annelies

TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis. S2 File. (2022) Verboven, Lennert, Phelan, Jody, Heupink, Tim H., Van Rie, Annelies

linfeng-wang/GMM4TB. (2023) Wang, Linfeng

Genome details for the simulated-read tests. (2022) Wick, Ryan R., Holt, Kathryn E.

Polypolish: Short-read polishing of long-read bacterial genome assemblies. (2022) Wick, Ryan R., Holt, Kathryn E.

Assembly and polishing details for the real-read tests. (2022) Wick, Ryan R, Holt, Kathryn E

Confusion matrices for the simulated-read tests. (2022) Wick, Ryan R, Holt, Kathryn E

Predictors of assembly quality. (2022) Wick, Ryan R, Holt, Kathryn E

Raw results for the real-read tests. (2022) Wick, Ryan R, Holt, Kathryn E

Raw results for the simulated-read tests. (2022) Wick, Ryan R, Holt, Kathryn E

Transmission analysis of a large TB outbreak in London: a mathematical modelling study using genomic data. (2020) Xu, Yuanwei, Stockdale, Jessica E, Naidu, Vijay, Hatherell, Hollie, Stimson, James, Stagg, Helen R, Abubakar, Ibrahim, Colijn, Caroline