Item Type Date Title No Grouping

A

Additional file 2 of Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations. (2024) Heinz, Eva, Pearse, Oliver, Zuza, Allan, Bilima, Sithembile, Msefula, Chisomo, Musicha, Patrick, Siyabu, Patriciah, Tewesa, Edith, Graf, Fabrice E., Lester, Rebecca, Lissauer, Samantha, Cornick, Jennifer, Lewis, Joseph M., Kawaza, Kondwani, Thomson, Nicholas R., Feasey, Nicholas A.

Additional materials from The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One. (2019) Dorman, Matthew J, Kane, Leanne, Domman, Daryl, Turnbull, Jake D, Cormie, Claire, Fazal, Mohammed-Abbas, Goulding, David A, Russell, Julie E, Alexander, Sarah, Thomson, Nicholas R.

Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. (2017) The, Hao Chung, Florez de Sessions, Paola, Jie, Song, Pham Thanh, Duy, Thompson, Corinne N, Nguyen Ngoc Minh, Chau, Chu, Collins Wenhan, Tran, Tuan-Anh, Thomson, Nicholas R, Thwaites, Guy E, Rabaa, Maia A, Hibberd, Martin, Baker, Stephen

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi. (2009) Perkins, Timothy T., Kingsley, Robert A., Fookes, Maria C., Gardner, Paul P., James, Keith D., Yu, Lu, Assefa, Samuel A., He, Miao, Croucher, Nicholas J., Pickard, Derek J., Maskell, Duncan J., Parkhill, Julian, Choudhary, Jyoti, Thomson, Nicholas R., Dougan, Gordon

C

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. (2019) Boinett, Christine J., Cain, Amy K., Hawkey, Jane, Do Hoang, Nhu Tran, Khanh, Nhu Nguyen Thi, Thanh, Duy Pham, Dordel, Janina, Campbell, James I., Lan, Nguyen Phu Huong, Mayho, Matthew, Langridge, Gemma C., Hadfield, James, Chau, Nguyen Van Vinh, Thwaites, Guy E., Parkhill, Julian, Thomson, Nicholas R., Holt, Kathryn E., Baker, Stephen

D

Data for, "Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia.". (2020) Wyres, Kelly L., Nguyen, To N. T., Lam, Margaret M. C., Judd, Louise M., van Vinh Chau, Nguyen, Dance, David A. B., Ip, Margaret, Karkey, Abhilasha, Ling, Clare L., Miliya, Thyl, Newton, Paul N., Lan, Nguyen Phu Huong, Sengduangphachanh, Amphone, Turner, Paul, Veeraraghavan, Balaji, Vinh, Phat Voong, Vongsouvath, Manivanh, Thomson, Nicholas R., Baker, Stephen, Holt, Kathryn E.

Dhaka household cholera dataset. (2018) Domman, Daryl, Chowdhury, Fahima, Khan, Ashraful I., Dorman, Matthew J., Mutreja, Ankur, Uddin, Muhammad Ikhtear, Paul, Anik, Begum, Yasmin A., Charles, Richelle C., Calderwood, Stephen B., Bhuiyan, Taufiqur R., Harris, Jason B., LaRocque, Regina C., Ryan, Edward T., Qadri, Firdausi, Thomson, Nicholas R.

Directional gene flow and ecological separation in Yersinia enterocolitica. (2015) Reuter, Sandra, Corander, Jukka, de Been, Mark, Harris, Simon, Cheng, Lu, Hall, Miquette, Thomson, Nicholas R., McNally, Alan

Data from: Novel R pipeline for analyzing Biolog phenotypic microarray data. (2015) Vehkala, Minna, Shubin, Mikhail, Connor, Thomas R, Thomson, Nick, Corander, Jukka folder_zip

DNAPlotter: circular and linear interactive genome visualization. (2009) Carver, Tim, Thomson, Nick, Bleasby, Alan, Berriman, Matthew, Parkhill, Julian

G

Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection. (2021) Dorman, Matthew, Thomson, Nicholas R., Campos, Josefina

gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae. (2021) Fennell, Thea G., Blackwell, Grace A., Thomson, Nicholas R., Dorman, Matthew J.

Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. (2019) Musicha, Patrick, Msefula, Chisomo L, Mather, Alison E, Chaguza, Chrispin, Cain, Amy K, Peno, Chikondi, Kallonen, Teemu, Khonga, Margaret, Denis, Brigitte, Gray, Katherine J, Heyderman, Robert S, Thomson, Nicholas R, Everett, Dean B, Feasey, Nicholas A

Genomic history of the seventh pandemic of cholera in Africa. (2017) Weill, François-Xavier, Domman, Daryl, Njamkepo, Elisabeth, Tarr, Cheryl, Rauzier, Jean, Fawal, Nizar, Keddy, Karen H., Salje, Henrik, Moore, Sandra, Mukhopadhyay, Asish K., Bercion, Raymond, Luquero, Francisco J., Ngandjio, Antoinette, Dosso, Mireille, Monakhova, Elena, Garin, Benoit, Bouchier, Christiane, Pazzani, Carlo, Mutreja, Ankur, Grunow, Roland, Sidikou, Fati, Bonte, Laurence, Breurec, Sébastien, Damian, Maria, Njanpop-Lafourcade, Berthe-Marie, Sapriel, Guillaume, Page, Anne-Laure, Hamze, Monzer, Henkens, Myriam, Chowdhury, Goutam, Mengel, Martin, Koeck, Jean-Louis, Fournier, Jean-Michel, Dougan, Gordon, Grimont, Patrick A. D., Parkhill, Julian, Holt, Kathryn E., Piarroux, Renaud, Ramamurthy, Thandavarayan, Quilici, Marie-Laure, Thomson, Nicholas R.

Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi. (2013) Bronowski, Christina, Fookes, Maria C., Gilderthorp, Ruth, Ashelford, Kevin E., Harris, Simon R., Phiri, Amos, Hall, Neil, Gordon, Melita A., Wain, John, Hart, Charles A., Wigley, Paul, Thomson, Nicholas R., Winstanley, Craig

Genetic flux over time in the Salmonella lineage. (2007) Vernikos, Georgios S, Thomson, Nicholas R., Parkhill, Julian

I

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.

R

Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. (2014) Lindgreen, Stinus, Umu, Sinan Uğur, Lai, Alicia Sook-Wei, Eldai, Hisham, Liu, Wenting, McGimpsey, Stephanie, Wheeler, Nicole E., Biggs, Patrick J., Thomson, Nick R., Barquist, Lars, Poole, Anthony M., Gardner, Paul P.

S

Supporting data for "chiA and gbpA genes are not uniformly distributed amongst diverse Vibrio cholerae". (2021) Fennell, Thea G., Blackwell, Grace A., Thomson, Nicholas R., Dorman, Matthew J.

Supporting data for "Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection". (2021) Dorman, Matthew, Thomson, Nicholas R., Campos, Josefina

Supporting data for "Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae". (2020) Dorman, Matthew J., Domman, Daryl, Poklepovich, Tomás, Tolley, Charlotte, Zolezzi, Gisella, Kane, Leanne, Viñas, María Rosa, Panagópulo, Marcela, Moroni, Miriam, Binsztein, Norma, Caffer, María Inés, Clare, Simon, Dougan, Gordon, Salmond, George P. C., Parkhill, Julian, Campos, Josefina, 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

Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis. (2011) Arnvig, Kristine B., Comas, Iñaki, Thomson, Nicholas R., Houghton, Joanna, Boshoff, Helena I., Croucher, Nicholas J., Rose, Graham, Perkins, Timothy T., Parkhill, Julian, Dougan, Gordon, Young, Douglas B.

T

The introduction and establishment of fluoroquinolone resistant Shigella sonnei into Bhutan. (2015) Chung The, Hao, Rabaa, Maia A., Pham Thanh, Duy, Ruekit, Sirigade, Wangchuk, Sonam, Dorji, Tshering, Pem Tshering, Kinzang, Nguyen Thi Nguyen, To, Voong Vinh, Phat, Ha Thanh, Tuyen, Nguyen Ngoc Minh, Chau, Turner, Paul, Sar, Poda, Thwaites, Guy, Holt, Kathryn E., Thomson, Nicholas R., Bodhidatta, Ladaporn, Mason, Carl Jeffries, Baker, Stephen

The genome of Rhizobium leguminosarum has recognizable core and accessory components. (2006) Young, J Peter W, Crossman, Lisa C, Johnston, Andrew WB, Thomson, Nick, Ghazoui, Zara F, Hull, Katherine H, Wexler, Margaret, Curson, Andrew RJ, Todd, Jonathan D, Poole, Philip S, Mauchline, Tim H, East, Alison K, Quail, Michael A, Churcher, Carol, Arrowsmith, Claire, Cherevach, Inna, Chillingworth, Tracey, Clarke, Kay, Cronin, Ann, Davis, Paul, Fraser, Audrey, Hance, Zahra, Hauser, Heidi, Jagels, Kay, Moule, Sharon, Mungall, Karen, Norbertczak, Halina, Rabbinowitsch, Ester, Sanders, Mandy, Simmonds, Mark, Whitehead, Sally, Parkhill, Julian