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Number of items: 55.

Bush, Stephen J., Connor, Thomas R., Peto, Tim E.A., Crook, Derrick W. and Walker, A. Sarah 2020. Evaluation of methods for detecting human reads in microbial sequencing datasets. Microbial Genomics 10.1099/mgen.0.000393

Millar, Jane R., Bengu, Nomonde, Fillis, Rowena, Sprenger, Ken, Ntlantsana, Vuyokazi, Vieira, Vinicius A., Khambati, Nisreen, Archary, Moherndran, Muenchhoff, Maximilian, Groll, Andreas, Grayson, Nicholas, Adamson, John, Govender, Katya, Dong, Krista, Kiepiela, Photini, Walker, Bruce D., Bonsall, David, Connor, Thomas, Bull, Matthew J., Nxele, Nelisiwe, Roider, Julia, Ismail, Nasreen, Adland, Emily, Puertas, Maria C., Martinez-Picado, Javier, Matthews, Philippa C., Ndung'u, Thumbi and Goulder, Philip 2020. High-frequency failure of combination antiretroviral therapy in paediatric HIV infection is associated with unmet maternal needs causing maternal non-adherence. EClinicalMedicine 22 , 100344. 10.1016/j.eclinm.2020.100344

Southgate, J.A., Bull, M.J., Brown, C.M., Watkins, J., Corden, S., Southgate, B., Moore, C. and Connor, T.R. 2020. Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications. Bioinformatics 36 (6) , pp. 1681-1688. 10.1093/bioinformatics/btz814

Cunningham-Oakes, Edward, Pointon, Tom, Murphy, Barry, Connor, Thomas R and Mahenthiralingam, Eshwar 2020. Genome sequence of pluralibacter gergoviae ECO77, a unique multireplicon isolate of industrial origin. Microbiology Resource Announcements 9 (9) , e01561-19. 10.1128/MRA.01561-19

Webster, Gordon, Mullins, Alex J, Bettridge, Aimee, Jones, Cerith, Cunningham-Oakes, Edward, Connor, Thomas R, Parkhill, Julian and Mahenthiralingam, Eshwar 2019. Genome sequences of three Paraburkholderia spp. strains isolated from Wood-decay fungi reveals them as novel taxa with antimicrobial biosynthetic potential. Microbiology Resource Announcements 8 (34) , e00778-19. 10.1128/MRA.00778-19

Mullins, Alex J., Murray, James A. H., Bull, Matthew J., Jenner, Matthew, Jones, Cerith, Webster, Gordon, Green, Angharad E., Neill, Daniel R., Connor, Thomas R., Parkhill, Julian, Challis, Gregory L. and Mahenthiralingam, Eshwar 2019. Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria. Nature Microbiology 4 , pp. 996-1005. 10.1038/s41564-019-0383-z

Weiser, Rebecca, Green, Angharad E., Bull, Matthew J., Cunningham-Oakes, Edward, Jolley, Keith A., Maiden, Martin C.J., Hall, Amanda J., Winstanley, Craig, Weightman, Andrew J., Donoghue, Denise, Amezquita, Alejandro, Connor, Thomas R. and Mahenthiralingam, Eshwar 2019. Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes. Microbial Genomics , 000276. 10.1099/mgen.0.000276

Green, Angharad, Amezquita, Alejandro, Le-Marc, Yvan, Bull, Matthew, Connor, Thomas and Mahenthiralingam, Eshwar 2018. The consistent differential expression of genetic pathways following exposure of an industrial Pseudomonas aeruginosa strain to preservatives and a laundry detergent formulation. FEMS Microbiology Letters 365 (9) , fny062. 10.1093/femsle/fny062

Rius, Cristina, Attaf, Meriem, Tungatt, Katie, Bianchi, Valentina, Legut, Mateusz, Bovay, Amandine, Donia, Marco, Straten, Per thor, Peakman, Mark, Svane, Inge Marie, Ott, Sascha, Connor, Tom, Szomolay, Barbara, Dolton, Garry and Sewell, Andrew K. 2018. Peptide-MHC class 1 tetramers can fail to detect relevant functional T-cell clonotypes and underestimate antigen-reactive T-cell populations. Journal of Immunology 200 (7) , pp. 2263-2279. 10.4049/jimmunol.1700242

Knetsch, C. W., Kumar, N., Forster, S. C., Connor, Thomas, Browne, H. P., Harmanus, C., Sanders, I. M., Harris, S. R., Turner, L., Morris, T., Perry, M., Miyajima, F., Roberts, P., Pirmohamed, M., Songer, J. G., Weese, J. S., Indra, A., Corver, J., Rupnik, M., Wren, B. W., Riley, T. V., Kuijper, E. J. and Lawley, T. D. 2018. Zoonotic transfer of clostridium difficile harboring antimicrobial resistance between farm animals and humans. Journal of Clinical Microbiology 56 (3) , e01384-17. 10.1128/JCM.01384-17

Baker, K.S., Campos, J., Pichel, M., Della Gaspera, A., Duarte-Martínez, F., Campos-Chacón, E., Bolaños-Acuña, H.M., Guzmán-Verri, C., Mather, A.E., Diaz Velasco, S., Zamudio Rojas, M.L., Forbester, J.L., Connor, Thomas, Keddy, K.H., Smith, A.M., López de Delgado, E.A., Angiolillo, G., Cuaical, N., Fernández, J., Aguayo, C., Morales Aguilar, M., Valenzuela, C., Morales Medrano, A.J., Sirok, A., Weiler Gustafson, N., Diaz Guevara, P.L., Montaño, L.A., Perez, E. and Thomson, N.R. 2017. Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses. Clinical Microbiology and Infection 23 (11) , pp. 845-853. 10.1016/j.cmi.2017.03.021

Pollard, Dominic J., Young, Joanna C., Covarelli, Valentina, Herrera-León, Silvia, Connor, Thomas Richard, Fookes, Maria, Walker, Danielle, Echeita, Aurora, Thomson, Nicholas R., Berger, Cedric N., Frankel, Gad and Young, V. B. 2016. The Type III secretion system effector SeoC of salmonella enterica subsp. salamae and S. enterica subsp. arizonae ADP-Ribosylates Src and Inhibits Opsonophagocytosis. Infection and Immunity 84 (12) , pp. 3618-3628. 10.1128/IAI.00704-16

Connor, Thomas R., Loman, Nicholas J., Thompson, Simon, Smith, Andy, Southgate, Joel, Poplawski, Radoslaw, Bull, Matthew J., Richardson, Emily, Ismail, Matthew, Elwood-Thompson, Simon, Kitchen, Christine, Guest, Martyn, Bakke, Marius, Sheppard, Samuel K. and Pallen, Mark J. 2016. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microbial Genomics 2 (9) , 000086. 10.1099/mgen.0.000086

Ryan, Edward T., Karlsson, Stefan L., Thomson, Nicholas, Mutreja, Ankur, Connor, Thomas Richard, Sur, Dipika, Ali, Mohammad, Clemens, John, Dougan, Gordon, Holmgren, Jan and Lebens, Michael 2016. Retrospective analysis of serotype switching of Vibrio cholerae O1 in a cholera endemic region Shows it is a non-random process. PLOS Neglected Tropical Diseases 10 (10) , e0005044. 10.1371/journal.pntd.0005044

Wong, Vanessa K., Baker, Stephen, Connor, Thomas R., Pickard, Derek, Page, Andrew J., Dave, Jayshree, Murphy, Niamh, Holliman, Richard, Sefton, Armine, Millar, Michael, Dyson, Zoe A., Dougan, Gordon, Holt, Kathryn E., Parkhill, Julian, Feasey, Nicholas A., Kingsley, Robert A., Thomson, Nicholas R., Keane, Jacqueline A., Weill, François- Xavier, Le Hello, Simon, Hawkey, Jane, Edwards, David J., Harris, Simon R., Cain, Amy K., Hadfield, James, Hart, Peter J., Thieu, Nga Tran Vu, Klemm, Elizabeth J., Breiman, Robert F., Watson, Conall H., Edmunds, W. John, Kariuki, Samuel, Gordon, Melita A., Heyderman, Robert S., Okoro, Chinyere, Jacobs, Jan, Lunguya, Octavie, 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, Dongol, Sabina, Basnyat, Buddha, Arjyal, Amit, Mulholland, E. Kim, Campbell, James I., Dufour, Muriel, Bandaranayake, Don, Toleafoa, Take N., Singh, Shalini Pravin, Hatta, Mochammad, Newton, Paul N., Dance, David, Davong, Viengmon, Onsare, Robert S., Isaia, Lupeoletalalelei, 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, Mather, Alison E. and Amos, Ben 2016. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature Communications 7 , -. 10.1038/ncomms12827

International Typhoid Consortium, , Wong, Vanessa K., Baker, Stephen, Holt, Kathryn E., Okoro, Chinyere, Pickard, Derek J., Marks, Florian, Page, Andrew J., Olanipekun, Grace, Munir, Huda, Alter, Roxanne, Fey, Paul D., Feasey, Nicholas A., Weill, Francois-Xavier, Le Hello, Simon, Hart, Peter J., Kariuki, Samuel, Breiman, Robert F., Gordon, Melita, Heyderman, Robert S., Jacobs, Jan, Lunguya, Octavie, Onsare, Robert S., Msefula, Chisomo, MacLennan, Calman A., Keddy, Karen H., Smith, Anthony M., De Pinna, Elizabeth, Nair, Satheesh, Amos, Ben, Dougan, Gordon, Obaro, Stephen, Ryan, Edward T. and Connor, Thomas Richard 2016. Molecular surveillance identifies multiple transmissions of typhoid in West Africa. PLOS Neglected Tropical Diseases 10 (9) , e0004781. 10.1371/journal.pntd.0004781

Baker, Kate S., Dallman, Timothy J., Behar, Adi, Weill, François-Xavier, Gouali, Malika, Sobel, Jeremy, Fookes, Maria, Valinsky, Lea, Gal-Mor, Ohad, Connor, Thomas Richard, Nissan, Israel, Bertrand, Sophie, Parkhill, Julian, Jenkins, Claire, Cohen, Dani and Thomson, Nicholas R. 2016. Travel- and community-based transmission of multidrug-resistant Shigella sonnei lineage among international Orthodox Jewish communities. Emerging Infectious Diseases 22 (9) , p. 1545. 10.3201/eid2209.151953

Connor, Thomas, Owen, Sian V., Langridge, Gemma, Connell, Steve, Nair, Sasheeth, Reuter, Sandra, Dallman, Timothy J., Corander, Jukka, Tabing, Kristine C., Le Hello, Simon, Fookes, Maria, Doublet, Benoit, Zhou, Zhemin, Feltwell, Theresa, Ellington, Matthew J., Herrera, Silvia, Gilmour, Matthew, Cloeckaer, Axel, Achtman, Mark, Parkhill, Julian, Wain, John, De Pinna, Elizabeth, Weill, François-Xavier, Peters, Tansy and Thomson, Nick 2016. What's in a name? Species wide whole genome sequencing resolves invasive and non-invasive Salmonella Paratyphi B. mBio 7 (4) , e00527-16. 10.1128/mBio.00527-16

Laugel, Bruno, Lloyd, Angharad, Meermeier, Erin W., Crowther, Michael D., Connor, Thomas, Dolton, Garry Michael, Miles, John James, Burrows, Scott R., Gold, Marielle C., Lewinsohn, David M. and Sewell, Andrew K. 2016. Engineering of isogenic cells deficient for MR1 with a CRISPR/Cas9 lentiviral system: tools to study microbial antigen processing and presentation to human MR1-restricted T cells. Journal of Immunology 197 (3) , pp. 971-982. 10.4049/jimmunol.1501402

Petrovska, Liljana, Mather, Alison E., AbuOun, Manal, Branchu, Priscilla, Harris, Simon R., Connor, Thomas Richard, Hopkins, K.L., Underwood, A., Lettini, Antonia A., Page, Andrew, Bagnall, Mary, Wain, John, Parkhill, Julian, Dougan, Gordon, Davies, Robert and Kingsley, Robert A. 2016. Microevolution of Monophasic Salmonella Typhimurium during epidemic, United Kingdom, 2005-2010. Emerging infectious diseases 22 (4) , 617. 10.3201/eid2204.150531

Connor, Thomas R., Barker, Clare R., Baker, Kate S., Weill, François-Xavier, Talukder, Kaisar Ali, Smith, Anthony M., Baker, Stephen, Gouali, Malika, Pham Thanh, Duy, Azmi, Ishrat Jahan, Dias da Silveira, Wanderley, Semmler, Torsten, Wieler, Lothar H., Jenkins, Claire, Cravioto, Alejandro, Faruque, Shah M., Parkhill, Julian, Kim, Dong Wook, Keddy, Karen H. and Thomson, Nicholas R. 2015. Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife 4 , e07335. 10.7554/eLife.07335

Baker, Kate S, Dallman, Timothy J., Ashton, Philip M, Day, Martin, Hughes, Gwenda, Crook, Paul D, Gilbart, Victoria L., Zittermann, Sandra, Allen, Vanessa G., Howden, Benjamin P., Tomita, Takehiro, Valcanis, Mary, Harris, Simon R., Connor, Thomas Richard, Sintchenko, Vitali, Howard, Peter, Brown, Jeremy D., Petty, Nicola K., Gouali, Malika, Thanh, Duy Pham, Keddy, Karen H., Smith, Anthony M, Talukder, Kaisar A, Faruque, Shah M., Parkhill, Julian, Baker, Stephen, Weill, François-Xavier, Jenkins, Claire and Thomson, Nicholas R 2015. Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. The Lancet Infectious Diseases 15 (8) , pp. 913-921. 10.1016/S1473-3099(15)00002-X

Holt, Kathryn E., Wertheim, Heiman, Zadoks, Ruth N., Baker, Stephen, Whitehouse, Chris A., Dance, David, Jenney, Adam, Connor, Thomas R., Hsu, Li Yang, Severin, Juliëtte, Brisse, Sylvain, Cao, Hanwei, Wilksch, Jonathan, Gorrie, Claire, Schultz, Mark B., Edwards, David J., Nguyen, Kinh Van, Nguyen, Trung Vu, Dao, Trinh Tuyet, Mensink, Martijn, Minh, Vien Le, Nhu, Nguyen Thi Khanh, Schultsz, Constance, Kuntaman, Kuntaman, Newton, Paul N., Moore, Catrin E., Strugnell, Richard A. and Thomson, Nicholas R. 2015. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health. Proceedings of the National Academy of Sciences of the United States of America 112 (27) , E3574-E3581. 10.1073/pnas.1501049112

Okoro, Chinyere K., Barquist, Lars, Connor, Thomas Richard, Harris, Simon R., Clare, Simon, Stevens, Mark P., Arends, Mark J., Hale, Christine, Kane, Leanne, Pickard, Derek J., Hill, Jennifer, Harcourt, Katherine, Parkhill, Julian, Dougan, Gordon and Kingsley, Robert A. 2015. Correction: Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from Sub-Saharan Africa. PLOS Neglected Tropical Diseases 9 (6) , e0003848. 10.1371/journal.pntd.0003848

Okoro, Chinyere K., Barquist, Lars, Connor, Thomas Richard, Harris, Simon R., Clare, Simon, Stevens, Mark P., Arends, Mark J., Hale, Christine, Kane, Leanne, Pickard, Derek J., Hill, Jennifer, Harcourt, Katherine, Parkhill, Julian, Dougan, Gordon and Kingsley, Robert A. 2015. Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from Sub-Saharan Africa. PLOS Neglected Tropical Diseases 9 (3) , e0003611. 10.1371/journal.pntd.0003611

Vehkala, Minna, Shubin, Mikhail, Connor, Thomas Richard, Thomson, Nicholas R. and Corander, Jukka 2015. Novel R pipeline for analyzing biolog phenotypic microarray data. PLoS ONE 10 (3) , e0118392. 10.1371/journal.pone.0118392

Croucher, Nicholas J., Page, Andrew J., Connor, Thomas R., Delaney, Aidan J., Keane, Jacqueline A., Bentley, Stephen D., Parkhill, Julian and Harris, Simon R. 2015. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Research 43 (3) , e15. 10.1093/nar/gku1196

Jones, Lim Stephen, Carvalho, Maria, Toleman, Mark Alexander Howard, White, Peter, Connor, Thomas Richard, Mushtaq, Ammara, Weeks, Janis Lesley, Kumarasamy, Karthikeyan K., Raven, Katherine E., Török, M. Estée, Peacock, Sharon J., Howe, Robin A. and Walsh, Timothy Rutland 2015. Characterization of plasmids in extensively drug-resistant acinetobacter strains isolated in India and Pakistan. Antimicrobial Agents and Chemotherapy 59 (2) , pp. 923-929. 10.1128/AAC.03242-14

Langridge, Gemma C., Fookes, Maria, Connor, Thomas R., Feltwell, Theresa, Feasey, Nicholas, Parsons, Bryony N., Seth-Smith, Helena M. B., Barquist, Lars, Stedman, Anna, Humphrey, Tom, Wigley, Paul, Peters, Sarah E., Maskell, Duncan J., Corander, Jukka, Chabalgoity, Jose A., Barrow, Paul, Parkhill, Julian, Dougan, Gordon and Thomson, Nicholas R. 2015. Patterns of genome evolution that have accompanied host adaptation in Salmonella. Proceedings of the National Academy of Sciences 112 (3) , pp. 863-868. 10.1073/pnas.1416707112

Hall, Miquette, Chattaway, Marie A., Reuter, Sandra, Savin, Cyril, Strauch, Eckhard, Carniel, Elisabeth, Connor, Thomas Richard, Van Damme, Inge, Rajakaruna, Lakshani, Rajendram, Dunstan, Jenkins, Claire, Thomson, Nicholas R., McNally, Alan and Ledeboer, N. A. 2015. Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels. Journal of Clinical Microbiology 53 (1) , pp. 35-42. 10.1128/JCM.02395-14

Connor, Thomas Richard and Southgate, Joel 2015. Automated cloud brokerage based upon continuous real-time benchmarking. Presented at: 2015 IEEE/ACM 8th International Conference on Utility and Cloud Computing, Limassol, Cyprus, 7 - 0 December 2015.

Knetsch, C. W., Connor, Thomas Richard, Mutreja, A., van Dorp, S. M., Sanders, I. M., Browne, H. P., Harris, D., Lipman, L., Keessen, E. C. and Corver, J. 2014. Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011. Eurosurveillance 19 (45) , 20954.

von Mentzer, Astrid, Connor, Thomas R., Wieler, Lothar H., Semmler, Torsten, Iguchi, Atsushi, Thomson, Nicholas R., Rasko, David A., Joffre, Enrique, Corander, Jukka, Pickard, Derek, Wiklund, Gudrun, Svennerholm, Ann-Mari, Sjöling, Åsa and Dougan, Gordon 2014. Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nature Genetics 46 (12) , pp. 1321-1326. 10.1038/ng.3145

Lamelas, A., Harris, S. R., Roltgen, K., Dangy, J.-P., Hauser, J., Kingsley, R. A., Connor, Thomas Richard, Sie, A., Hodgson, A., Dougan, G., Parkhill, J., Bentley, S. D. and Pluschke, G. 2014. Emergence of a new epidemic Neisseria meningitidis serogroup A clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion. mBio 5 (5) , e01974-14. 10.1128/mBio.01974-14

Reuter, Sandra, Connor, Thomas R., Barquist, Lars, Walker, Danielle, Feltwell, Theresa, Harris, Simon R., Fookes, Maria, Hall, Miquette E., Petty, Nicola K., Fuchs, Thilo M., Corander, Jukka, Dufour, Muriel, Ringwood, Tamara, Savin, Cyril, Bouchier, Christiane, Martin, Liliane, Miettinen, Minna, Shubin, Mikhail, Riehm, Julia M., Laukkanen-Ninios, Riikka, Sihvonen, Leila M., Siitonen, Anja, Skurnik, Mikael, Falcao, Juliana Pfrimer, Fukushima, Hiroshi, Scholz, Holger C., Prentice, Michael B., Wren, Brendan W., Parkhill, Julian, Carniel, Elisabeth, Achtman, Mark, McNally, Alan and Thomson, Nicholas R. 2014. Parallel independent evolution of pathogenicity within the genus Yersinia. Proceedings of the National Academy of Sciences 111 (18) , pp. 6768-6773. 10.1073/pnas.1317161111

Sheppard, Samuel K., Cheng, Lu, Méric, Guillaume, de Haan, Caroline P. A., Llarena, Ann-Katrin, Marttinen, Pekka, Vidal, Ana, Ridley, Anne, Clifton-Hadley, Felicity, Connor, Thomas Richard, Strachan, Norval J. C., Forbes, Ken, Colles, Frances M., Jolley, Keith A., Bentley, Stephen D., Maiden, Martin C. J., Hänninen, Marja-Liisa, Parkhill, Julian, Hanage, William P. and Corander, Jukka 2014. Cryptic ecology among host generalist Campylobacter jejuniin domestic animals. Molecular Ecology 23 (10) , pp. 2442-2451. 10.1111/mec.12742

Shepheard, Marcus A., Fleming, Vicki M., Connor, Thomas Richard, Corander, Jukka, Feil, Edward J., Fraser, Christophe and Hanage, William P. 2013. Historical zoonoses and other changes in host tropism of staphylococcus aureus, identified by phylogenetic analysis of a population dataset. PLoS ONE 8 (5) , e62369. 10.1371/journal.pone.0062369

Cheng, Lu, Connor, Thomas Richard, Siren, J., Aanensen, D. M. and Corander, J. 2013. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Molecular Biology and Evolution 30 (5) , pp. 1224-1228. 10.1093/molbev/mst028

Dziva, F., Hauser, H., Connor, Thomas Richard, van Diemen, P. M., Prescott, G., Langridge, G. C., Eckert, S., Chaudhuri, R. R., Ewers, C., Mellata, M., Mukhopadhyay, S., Curtiss, R., Dougan, G., Wieler, L. H., Thomson, N. R., Pickard, D. J. and Stevens, M. P. 2013. Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms. Infection and Immunity 81 (3) , pp. 838-849. 10.1128/IAI.00585-12

McDonnell, J., Dallman, T., Atkin, S., Turbitt, D. A., Connor, Thomas Richard, Grant, K. A., Thomson, N. R. and Jenkins, C. 2013. Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK. Epidemiology and Infection 141 (12) , pp. 2568-2575. 10.1017/S0950268813000137

Kingsley, R. A., Kay, S., Connor, Thomas Richard, Barquist, L., Sait, L., Holt, K. E., Sivaraman, K., Wileman, T., Goulding, D., Clare, S., Hale, C., Seshasayee, A., Harris, S., Thomson, N. R., Gardner, P., Rabsch, W., Wigley, P., Humphrey, T., Parkhill, J. and Dougan, G. 2013. Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. mBio 4 (5) , e00565-13. 10.1128/mBio.00565-13

Mather, A. E., Reid, S. W. J., Maskell, D. J., Parkhill, J., Fookes, M. C., Harris, S. R., Brown, D. J., Coia, J. E., Mulvey, M. R., Gilmour, M. W., Petrovska, L., de Pinna, E., Kuroda, M., Akiba, M., Izumiya, H., Connor, Thomas Richard, Suchard, M. A., Lemey, P., Mellor, D. J., Haydon, D. T. and Thomson, N. R. 2013. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science 341 (6153) , pp. 1514-1517. 10.1126/science.1240578

He, Miao, Miyajima, Fabio, Roberts, Paul, Ellison, Louise, Pickard, Derek J., Martin, Melissa J., Connor, Thomas Richard, Harris, Simon R., Fairley, Derek, Bamford, Kathleen B., D'Arc, Stephanie, Brazier, J. S., Brown, Derek, Coia, John E., Douce, Gill, Gerding, Dale, Kim, Hee Jung, Koh, Tse Hsien, Kato, Haru, Senoh, Mitsutoshi, Louie, Tom, Michell, Stephen, Butt, Emma, Peacock, Sharon J., Brown, Nick M., Riley, Tom, Songer, Glen, Wilcox, Mark, Pirmohamed, Munir, Kuijper, Ed, Hawkey, Peter, Wren, Brendan W., Dougan, Gordon, Parkhill, Julian and Lawley, Trevor D. 2012. Emergence and global spread of epidemic healthcare-associated Clostridium difficile [Letter]. Nature Genetics 45 (1) , pp. 109-113. 10.1038/ng.2478

Okoro, Chinyere K., Kingsley, Robert A., Connor, Thomas Richard, Harris, Simon R., Parry, Christopher M., Al-Mashhadani, Manar N., Kariuki, Samuel, Msefula, Chisomo L., Gordon, Melita A., de Pinna, Elizabeth, Wain, John, Heyderman, Robert S., Obaro, Stephen, Alonso, Pedro L., Mandomando, Inacio, MacLennan, Calman A., Tapia, Milagritos D., Levine, Myron M., Tennant, Sharon M., Parkhill, Julian and Dougan, Gordon 2012. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nature Genetics 44 (11) , pp. 1215-1221. 10.1038/ng.2423

Lawley, Trevor D., Clare, Simon, Walker, Alan W., Stares, Mark D., Connor, Thomas Richard, Raisen, Claire, Goulding, David, Rad, Roland, Schreiber, Fernanda, Brandt, Cordelia, Deakin, Laura J., Pickard, Derek J., Duncan, Sylvia H., Flint, Harry J., Clark, Taane G., Parkhill, Julian and Dougan, Gordon 2012. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing clostridium difficile disease in mice. PLoS Pathogens 8 (10) , e1002995. 10.1371/journal.ppat.1002995

Quail, Michael, Smith, Miriam E., Coupland, Paul, Otto, Thomas D., Harris, Simon R., Connor, Thomas Richard, Bertoni, Anna, Swerdlow, Harold P. and Gu, Yong 2012. A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics 13 (1) , 341. 10.1186/1471-2164-13-341

Corander, Jukka, Connor, Thomas Richard, O'Dwyer, Cliona A., Kroll, J. Simon and Hanage, William Paul 2012. Population structure in the Neisseria, and the biological significance of fuzzy species. Journal of The Royal Society Interface 9 (71) , pp. 1208-1215. 10.1098/rsif.2011.0601

Murchison, Elizabeth P., Schulz-Trieglaff, Ole B., Ning, Zemin, Alexandrov, Ludmil B., Bauer, Markus J., Fu, Beiyuan, Hims, Matthew, Ding, Zhihao, Ivakhno, Sergii, Stewart, Caitlin, Ng, Bee Ling, Wong, Wendy, Aken, Bronwen, White, Simon, Alsop, Amber, Becq, Jennifer, Bignell, Graham R., Cheetham, R. Keira, Cheng, William, Connor, Thomas Richard, Cox, Anthony J., Feng, Zhi-Ping, Gu, Yong, Grocock, Russell J., Harris, Simon R., Khrebtukova, Irina, Kingsbury, Zoya, Kowarsky, Mark, Kreiss, Alexandre, Luo, Shujun, Marshall, John, McBride, David J., Murray, Lisa, Pearse, Anne-Maree, Raine, Keiran, Rasolonjatovo, Isabelle, Shaw, Richard, Tedder, Philip, Tregidgo, Carolyn, Vilella, Albert J., Wedge, David C., Woods, Gregory M., Gormley, Niall, Humphray, Sean, Schroth, Gary, Smith, Geoffrey, Hall, Kevin, Searle, Stephen M.J., Carter, Nigel P., Papenfuss, Anthony T., Futreal, P. Andrew, Campbell, Peter J., Yang, Fengtang, Bentley, David R., Evers, Dirk J. and Stratton, Michael R. 2012. Genome sequencing and analysis of the Tasmanian Devil and its transmissible cancer. Cell 148 (4) , pp. 780-791. 10.1016/j.cell.2011.11.065

Connor, Thomas Richard, Corander, Jukka and Hanage, William Paul 2012. Population subdivision and the detection of recombination in non-typable Haemophilus influenzae. Microbiology 158 (12) , pp. 2958-2964. 10.1099/mic.0.063073-0

Marttinen, Pekka, Hanage, William Paul, Croucher, Nicholas J., Connor, Thomas Richard, Harris, Simon R., Bentley, Stephen D. and Corander, Jukka 2011. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Research 40 (1) , e6. 10.1093/nar/gkr928

Mutreja, Ankur, Kim, Dong Wook, Thomson, Nicholas R., Connor, Thomas Richard, Lee, Je Hee, Kariuki, Samuel, Croucher, Nicholas J., Choi, Seon Young, Harris, Simon R., Lebens, Michael, Niyogi, Swapan Kumar, Kim, Eun Jin, Ramamurthy, T., Chun, Jongsik, Wood, James L. N., Clemens, John D., Czerkinsky, Cecil, Nair, G. Balakrish, Holmgren, Jan, Parkhill, Julian and Dougan, Gordon 2011. Evidence for several waves of global transmission in the seventh cholera pandemic [Letter]. Nature 477 (7365) , pp. 462-465. 10.1038/nature10392

Fookes, Maria, Schroeder, Gunnar N., Langridge, Gemma C., Blondel, Carlos J., Mammina, Caterina, Connor, Thomas Richard, Seth-Smith, Helena, Vernikos, Georgios S., Robinson, Keith S., Sanders, Mandy, Petty, Nicola K., Kingsley, Robert A., Bäumler, Andreas J., Nuccio, Sean-Paul, Contreras, Inés, Santiviago, Carlos A., Maskell, Duncan, Barrow, Paul, Humphrey, Tom, Nastasi, Antonino, Roberts, Mark, Frankel, Gad, Parkhill, Julian, Dougan, Gordon and Thomson, Nicholas R. 2011. Salmonella bongori provides insights into the evolution of the Salmonellae. PLoS Pathogens 7 (8) , e1002191. 10.1371/journal.ppat.1002191

Cheng, Lu, Connor, Thomas Richard, Aanensen, David M., Spratt, Brian G. and Corander, Jukka 2011. Bayesian semi-supervised classification of bacterial samples using MLST databases. BioMed Central Bioinformatics 12 (1) , 302. 10.1186/1471-2105-12-302

Hanage, William Paul, Fraser, Christophe, Tang, Jing, Connor, Thomas Richard and Corander, Jukka 2009. Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science 324 (5933) , pp. 1454-1457. 10.1126/science.1171908

Turner, Katherine M. E., Hanage, William P., Fraser, Christophe, Connor, Thomas Richard and Spratt, Brian G. 2007. Assessing the reliability of eBURST using simulated populations with known ancestry. BMC Microbiology 7 (1) , pp. 30-43. 10.1186/1471-2180-7-30

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