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

par Page, Andrew J., Keane, Jacqueline A.
Publié dans PeerJ (2018)

Circlator: automated circularization of genome assemblies using long sequencing reads

par Hunt, Martin, Silva, Nishadi De, Otto, Thomas D., Parkhill, Julian, Keane, Jacqueline A., Harris, Simon R.
Publié dans Genome Biol (2015)

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

par Page, Andrew J., Alikhan, Nabil-Fareed, Carleton, Heather A., Seemann, Torsten, Keane, Jacqueline A., Katz, Lee S.
Publié dans Microb Genom (2017)

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

par Page, Andrew J., Taylor, Ben, Delaney, Aidan J., Soares, Jorge, Seemann, Torsten, Keane, Jacqueline A., Harris, Simon R.
Publié dans Microb Genom (2016)

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

par Epping, Lennard, van Tonder, Andries J., Gladstone, Rebecca A., Bentley, Stephen D., Page, Andrew J., Keane, Jacqueline A.
Publié dans Microb Genom (2018)

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

par Hunt, Martin, Mather, Alison E, Sánchez-Busó, Leonor, Page, Andrew J, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R
Publié dans Microb Genom (2017)

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

par Page, Andrew J., Wailan, Alexander, Shao, Yan, Judge, Kim, Dougan, Gordon, Klemm, Elizabeth J., Thomson, Nicholas R., Keane, Jacqueline A.
Publié dans Microb Genom (2018)

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

par Page, Andrew J., De Silva, Nishadi, Hunt, Martin, Quail, Michael A., Parkhill, Julian, Harris, Simon R., Otto, Thomas D., Keane, Jacqueline A.
Publié dans Microb Genom (2016)

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

par Croucher, Nicholas J., Page, Andrew J., Connor, Thomas R., Delaney, Aidan J., Keane, Jacqueline A., Bentley, Stephen D., Parkhill, Julian, Harris, Simon R.
Publié dans Nucleic Acids Res (2015)

IVA: accurate de novo assembly of RNA virus genomes

par Hunt, Martin, Gall, Astrid, Ong, Swee Hoe, Brener, Jacqui, Ferns, Bridget, Goulder, Philip, Nastouli, Eleni, Keane, Jacqueline A., Kellam, Paul, Otto, Thomas D.
Publié dans Bioinformatics (2015)

Roary: rapid large-scale prokaryote pan genome analysis

par 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
Publié dans Bioinformatics (2015)

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

par 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
Publié dans Bioinformatics (2016)

Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan

par 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
Publié dans Emerg Infect Dis (2017)

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

par 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.
Publié 2014

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

par 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.
Publié dans Nat Commun (2021)

The genomes of four tapeworm species reveal adaptations to parasitism

par 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
Publié 2013

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

par 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.
Publié dans Microb Genom (2018)

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

par 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
Publié dans Nat Commun (2018)

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

par Wong, Vanessa K, Baker, Stephen, Pickard, Derek J, Parkhill, Julian, Page, Andrew J, Feasey, Nicholas A, Kingsley, Robert A, Thomson, Nicholas R, Keane, Jacqueline A, Weill, François-Xavier, Edwards, David J, Hawkey, Jane, Harris, Simon R, Mather, Alison E, Cain, Amy K, Hadfield, James, Hart, Peter J, Thieu, Nga Tran Vu, Klemm, Elizabeth J, Glinos, Dafni A, Breiman, Robert F, Watson, Conall H, Kariuki, Samuel, Gordon, Melita A, Heyderman, Robert S, Okoro, Chinyere, Jacobs, Jan, Lunguya, Octavie, Edmunds, W John, Msefula, Chisomo, Chabalgoity, Jose A, Kama, Mike, Jenkins, Kylie, Dutta, Shanta, Marks, Florian, Campos, Josefina, Thompson, Corinne, Obaro, Stephen, MacLennan, Calman A, Dolecek, Christiane, Keddy, Karen H, Smith, Anthony M, Parry, Christopher M, Karkey, Abhilasha, Mulholland, E Kim, Campbell, James I, Dongol, Sabina, Basnyat, Buddha, Dufour, Muriel, Bandaranayake, Don, Naseri, Take Toleafoa, Singh, Shalini Pravin, Hatta, Mochammad, Newton, Paul, Onsare, Robert S, Isaia, Lupeoletalalei, Dance, David, Davong, Viengmon, Thwaites, Guy, Wijedoru, Lalith, Crump, John A, De Pinna, Elizabeth, Nair, Satheesh, Nilles, Eric J, Thanh, Duy Pham, Turner, Paul, Soeng, Sona, Valcanis, Mary, Powling, Joan, Dimovski, Karolina, Hogg, Geoff, Farrar, Jeremy, Holt, Kathryn E, Dougan, Gordon
Publié dans Nat Genet (2015)