Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus

por Page, Andrew J., Keane, Jacqueline A.
Publicado 2018

Circlator: automated circularization of genome assemblies using long sequencing reads

por Hunt, Martin, Silva, Nishadi De, Otto, Thomas D., Parkhill, Julian, Keane, Jacqueline A., Harris, Simon R.
Publicado 2015

Comparison of classical multi-locus sequence typing software for next-generation sequencing data

por Page, Andrew J., Alikhan, Nabil-Fareed, Carleton, Heather A., Seemann, Torsten, Keane, Jacqueline A., Katz, Lee S.
Publicado 2017

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

por Page, Andrew J., Taylor, Ben, Delaney, Aidan J., Soares, Jorge, Seemann, Torsten, Keane, Jacqueline A., Harris, Simon R.
Publicado 2016

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

por Epping, Lennard, van Tonder, Andries J., Gladstone, Rebecca A., Bentley, Stephen D., Page, Andrew J., Keane, Jacqueline A.
Publicado 2018

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

por Hunt, Martin, Mather, Alison E, Sánchez-Busó, Leonor, Page, Andrew J, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R
Publicado 2017

PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data

por Page, Andrew J., Wailan, Alexander, Shao, Yan, Judge, Kim, Dougan, Gordon, Klemm, Elizabeth J., Thomson, Nicholas R., Keane, Jacqueline A.
Publicado 2018

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

por Page, Andrew J., De Silva, Nishadi, Hunt, Martin, Quail, Michael A., Parkhill, Julian, Harris, Simon R., Otto, Thomas D., Keane, Jacqueline A.
Publicado 2016

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

por Croucher, Nicholas J., Page, Andrew J., Connor, Thomas R., Delaney, Aidan J., Keane, Jacqueline A., Bentley, Stephen D., Parkhill, Julian, Harris, Simon R.
Publicado 2015

IVA: accurate de novo assembly of RNA virus genomes

por Hunt, Martin, Gall, Astrid, Ong, Swee Hoe, Brener, Jacqui, Ferns, Bridget, Goulder, Philip, Nastouli, Eleni, Keane, Jacqueline A., Kellam, Paul, Otto, Thomas D.
Publicado 2015

Roary: rapid large-scale prokaryote pan genome analysis

por Page, Andrew J., Cummins, Carla A., Hunt, Martin, Wong, Vanessa K., Reuter, Sandra, Holden, Matthew T.G., Fookes, Maria, Falush, Daniel, Keane, Jacqueline A., Parkhill, Julian
Publicado 2015

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

por Barquist, Lars, Mayho, Matthew, Cummins, Carla, Cain, Amy K., Boinett, Christine J., Page, Andrew J., Langridge, Gemma C., Quail, Michael A., Keane, Jacqueline A., Parkhill, Julian
Publicado 2016

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan

por Ejaz, Hasan, Wang, Nancy, Wilksch, Jonathan J., Page, Andrew J., Cao, Hanwei, Gujaran, Shruti, Keane, Jacqueline A., Lithgow, Trevor, ul-Haq, Ikram, Dougan, Gordon, Strugnell, Richard A., Heinz, Eva
Publicado 2017

Epithelial IL-22RA1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen

por Pham, Tu Anh N., Clare, Simon, Goulding, David, Arasteh, Julia M., Stares, Mark D., Browne, Hilary P., Keane, Jacqueline A., Page, Andrew J., Kumasaka, Natsuhiko, Kane, Leanne, Mottram, Lynda, Harcourt, Katherine, Hale, Christine, Arends, Mark J., Gaffney, Daniel J., Dougan, Gordon, Lawley, Trevor D.
Publicado 2014

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch

por Argimón, Silvia, Yeats, Corin A., Goater, Richard J., Abudahab, Khalil, Taylor, Benjamin, Underwood, Anthony, Sánchez-Busó, Leonor, Wong, Vanessa K., Dyson, Zoe A., Nair, Satheesh, Park, Se Eun, Marks, Florian, Page, Andrew J., Keane, Jacqueline A., Baker, Stephen, Holt, Kathryn E., Dougan, Gordon, Aanensen, David M.
Publicado 2021

The genomes of four tapeworm species reveal adaptations to parasitism

por Tsai, Isheng J., Zarowiecki, Magdalena, Holroyd, Nancy, Garciarrubio, Alejandro, Sánchez-Flores, Alejandro, Brooks, Karen L., Tracey, Alan, Bobes, Raúl J., Fragoso, Gladis, Sciutto, Edda, Aslett, Martin, Beasley, Helen, Bennett, Hayley M., Cai, Xuepeng, Camicia, Federico, Clark, Richard, Cucher, Marcela, De Silva, Nishadi, Day, Tim A, Deplazes, Peter, Estrada, Karel, Fernández, Cecilia, Holland, Peter W. H., Hou, Junling, Hu, Songnian, Huckvale, Thomas, Hung, Stacy S., Kamenetzky, Laura, Keane, Jacqueline A., Kiss, Ferenc, Koziol, Uriel, Lambert, Olivia, Liu, Kan, Luo, Xuenong, Luo, Yingfeng, Macchiaroli, Natalia, Nichol, Sarah, Paps, Jordi, Parkinson, John, Pouchkina-Stantcheva, Natasha, Riddiford, Nick, Rosenzvit, Mara, Salinas, Gustavo, Wasmuth, James D., Zamanian, Mostafa, Zheng, Yadong, Cai, Jianping, Soberón, Xavier, Olson, Peter D., Laclette, Juan P., Brehm, Klaus, Berriman, Matthew
Publicado 2013

Corrigendum: SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

por Epping, Lennard, van Tonder, Andries J., Gladstone, Rebecca A., Bentley, Stephen D., Page, Andrew J., Keane, Jacqueline A., Aanensen, David, Brandileone, Maria-Cristina C., Antonio, Martin, Almeida, Samanta C.G., Campos, Francisco, Carter, P.E., Clarke, Stuart C., Cornick, Jennifer, Croucher, Nicholas, Dagan, Ron, Doiphode, Sanjay H., Donkor, Eric S., Ekaterina, Egorova, Eser, Ozgen Koseoglu, Dean, Everett, Ford, Rebecca, Gladstone, Rebecca A., Gottberg, Anne Von, Hasanuzzaman, Md., Hawkins, Paulina, Ho, PL, Hryniewicz, Waleria, Pollard, Andrew J., Kastrin, Tamara, Klugman, Keith P., Kwambana-Adams, Brenda, Law, Pierra, Lehmann, Deborah, Lietman, Thomas M., Mdaghri, Naima El, Moiane, Benild, Mucavele, Helio, Obaro, Stephen K., Ochoa, Theresa J., Paragi, Metka, Haoua, Tall, du Plessis, Mignon, Kandasamy, Rama, Porat, Nurit, Ravikumar, K. L., Regueira, Mabel, Sadowy, Ewa, Saha, Samir K., Shakoor, Sadia, Sigauque, Betuel, Skoczyoska, Anna, Ko, Kwan Soo, Tientcheu, Peggy-Estelle, Titov, Leonid P., Turner, Paul, Veeraraghavan, Balaji, Wolter, Nicole, Bentley, Stephen D., McGee, Lesley, Breiman, Robert F.
Publicado 2018

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

por Park, Se Eun, Pham, Duy Thanh, Boinett, Christine, Wong, Vanessa K., Pak, Gi Deok, Panzner, Ursula, Espinoza, Ligia Maria Cruz, von Kalckreuth, Vera, Im, Justin, Schütt-Gerowitt, Heidi, Crump, John A., Breiman, Robert F., Adu-Sarkodie, Yaw, Owusu-Dabo, Ellis, Rakotozandrindrainy, Raphaël, Soura, Abdramane Bassiahi, Aseffa, Abraham, Gasmelseed, Nagla, Keddy, Karen H., May, Jürgen, Sow, Amy Gassama, Aaby, Peter, Biggs, Holly M., Hertz, Julian T., Montgomery, Joel M., Cosmas, Leonard, Olack, Beatrice, Fields, Barry, Sarpong, Nimako, Razafindrabe, Tsiriniaina Jean Luco, Raminosoa, Tiana Mirana, Kabore, Leon Parfait, Sampo, Emmanuel, Teferi, Mekonnen, Yeshitela, Biruk, El Tayeb, Muna Ahmed, Sooka, Arvinda, Meyer, Christian G., Krumkamp, Ralf, Dekker, Denise Myriam, Jaeger, Anna, Poppert, Sven, Tall, Adama, Niang, Aissatou, Bjerregaard-Andersen, Morten, Løfberg, Sandra Valborg, Seo, Hye Jin, Jeon, Hyon Jin, Deerin, Jessica Fung, Park, Jinkyung, Konings, Frank, Ali, Mohammad, Clemens, John D., Hughes, Peter, Sendagala, Juliet Nsimire, Vudriko, Tobias, Downing, Robert, Ikumapayi, Usman N., Mackenzie, Grant A., Obaro, Stephen, Argimon, Silvia, Aanensen, David M., Page, Andrew, Keane, Jacqueline A., Duchene, Sebastian, Dyson, Zoe, Holt, Kathryn E., Dougan, Gordon, Marks, Florian, Baker, Stephen
Publicado 2018

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

por Carey, Megan E, Dyson, Zoe A, Ingle, Danielle J, Amir, Afreenish, Aworh, Mabel K, Chattaway, Marie Anne, Chew, Ka Lip, Crump, John A, Feasey, Nicholas A, Howden, Benjamin P, Keddy, Karen H, Maes, Mailis, Parry, Christopher M, Van Puyvelde, Sandra, Webb, Hattie E, Afolayan, Ayorinde Oluwatobiloba, Alexander, Anna P, Anandan, Shalini, Andrews, Jason R, Ashton, Philip M, Basnyat, Buddha, Bavdekar, Ashish, Bogoch, Isaac I, Clemens, John D, da Silva, Kesia Esther, De, Anuradha, de Ligt, Joep, Diaz Guevara, Paula Lucia, Dolecek, Christiane, Dutta, Shanta, Ehlers, Marthie M, Francois Watkins, Louise, Garrett, Denise O, Godbole, Gauri, Gordon, Melita A, Greenhill, Andrew R, Griffin, Chelsey, Gupta, Madhu, Hendriksen, Rene S, Heyderman, Robert S, Hooda, Yogesh, Hormazabal, Juan Carlos, Ikhimiukor, Odion O, Iqbal, Junaid, Jacob, Jobin John, Jenkins, Claire, Jinka, Dasaratha Ramaiah, John, Jacob, Kang, Gagandeep, Kanteh, Abdoulie, Kapil, Arti, Karkey, Abhilasha, Kariuki, Samuel, Kingsley, Robert A, Koshy, Roshine Mary, Lauer, AC, Levine, Myron M, Lingegowda, Ravikumar Kadahalli, Luby, Stephen P, Mackenzie, Grant Austin, Mashe, Tapfumanei, Msefula, Chisomo, Mutreja, Ankur, Nagaraj, Geetha, Nagaraj, Savitha, Nair, Satheesh, Naseri, Take K, Nimarota-Brown, Susana, Njamkepo, Elisabeth, Okeke, Iruka N, Perumal, Sulochana Putli Bai, Pollard, Andrew J, Pragasam, Agila Kumari, Qadri, Firdausi, Qamar, Farah N, Rahman, Sadia Isfat Ara, Rambocus, Savitra Devi, Rasko, David A, Ray, Pallab, Robins-Browne, Roy, Rongsen-Chandola, Temsunaro, Rutanga, Jean Pierre, Saha, Samir K, Saha, Senjuti, Saigal, Karnika, Sajib, Mohammad Saiful Islam, Seidman, Jessica C, Shakya, Jivan, Shamanna, Varun, Shastri, Jayanthi, Shrestha, Rajeev, Sia, Sonia, Sikorski, Michael J, Singh, Ashita, Smith, Anthony M, Tagg, Kaitlin A, Tamrakar, Dipesh, Tanmoy, Arif Mohammed, Thomas, Maria, Thomas, Mathew S, Thomsen, Robert, Thomson, Nicholas R, Tupua, Siaosi, Vaidya, Krista, Valcanis, Mary, Veeraraghavan, Balaji, Weill, François-Xavier, Wright, Jackie, Dougan, Gordon, Argimón, Silvia, Keane, Jacqueline A, Aanensen, David M, Baker, Stephen, Holt, Kathryn E
Publicado 2023