Heinz, E, Pearse, O, Zuza, A, Bilima, S, Msefula, C, Musicha, P, Siyabu, P, Tewesa, E, Graf, FE, Lester, R, Lissauer, S, Cornick, J, Lewis, JM, Kawaza, K, Thomson, NR and Feasey, NA (2024). 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. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.26716636.v1

Dorman, M, Thomson, NR and Campos, J (2021). Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.14384225.v1

Fennell, TG, Blackwell, GA, Thomson, NR and Dorman, MJ (2021). gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae. [Data Collection]. Microbiology Society. https://doi.org/10.6084/m9.figshare.14398688.v1

Fennell, TG, Blackwell, GA, Thomson, NR and Dorman, MJ (2021). Supporting data for "chiA and gbpA genes are not uniformly distributed amongst diverse Vibrio cholerae". [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.13169189

Dorman, M, Thomson, NR and Campos, J (2021). Supporting data for "Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection". [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.13636577.v1

Dorman, MJ, Domman, D, Poklepovich, T, Tolley, C, Zolezzi, G, Kane, L, Viñas, MR, Panagópulo, M, Moroni, M, Binsztein, N, Caffer, MI, Clare, S, Dougan, G, Salmond, GPC, Parkhill, J, Campos, J and Thomson, NR (2020). Supporting data for "Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae". [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.11310131.v1

Wyres, KL, Nguyen, TNT, Lam, MMC, Judd, LM, van Vinh Chau, N, Dance, DAB, Ip, M, Karkey, A, Ling, CL, Miliya, T, Newton, PN, Lan, NPH, Sengduangphachanh, A, Turner, P, Veeraraghavan, B, Vinh, PV, Vongsouvath, M, Thomson, NR, Baker, S and Holt, KE (2020). Data for, "Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia.". [Data Collection]. Monash University. https://doi.org/10.26180/5c67982956721

Heinz, E, Brindle, R, Morgan-McCalla, A, Peters, K and Thomson, N (2019). Supporting data for: "Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors". [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.7867760.v1

Dorman, MJ, Domman, D, Uddin, MI, Sharmin, S, Hassan Afrad, M, Begum, YA, Qadri, F and Thomson, NR (2019). Supporting data for 'High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139'. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6480266.v1

Dorman, MJ, Kane, L, Domman, D, Turnbull, JD, Cormie, C, Fazal, M, Goulding, DA, Russell, JE, Alexander, S and Thomson, NR (2019). Additional materials from The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One. [Data Collection]. The Royal Society. https://doi.org/10.6084/m9.figshare.7951289.v1

Wailan​, AM, Coll, F, Heinz, E, Tonkin-Hill, G, Corander, J, Feasey, NA and Thomson, NR (2019). rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. [Data Collection]. Microbial Genomics. https://doi.org/10.1099/mgen.0.000264

Musicha, P, Msefula, CL, Mather, AE, Chaguza, C, Cain, AK, Peno, C, Kallonen, T, Khonga, M, Denis, B, Gray, KJ, Heyderman, RS, Thomson, NR, Everett, DB and Feasey, NA (2019). Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. [Data Collection]. Journal of Antimicrobial Chemotherapy. https://doi.org/10.1093/jac/dkz032

Boinett, CJ, Cain, AK, Hawkey, J, Do Hoang, NT, Khanh, NNT, Thanh, DP, Dordel, J, Campbell, JI, Lan, NPH, Mayho, M, Langridge, GC, Hadfield, J, Chau, NVV, Thwaites, GE, Parkhill, J, Thomson, NR, Holt, KE and Baker, S (2019). Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. [Data Collection]. Microbial genomics. https://doi.org/10.1099/mgen.0.000246

Domman, D, Chowdhury, F, Khan, AI, Dorman, MJ, Mutreja, A, Uddin, MI, Paul, A, Begum, YA, Charles, RC, Calderwood, SB, Bhuiyan, TR, Harris, JB, LaRocque, RC, Ryan, ET, Qadri, F and Thomson, NR (2018). Dhaka household cholera dataset. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6062804.v1

Domman, D, Quilici, M, Dorman, MJ, Njamkepo, E, Mutreja, A, Mather, AE, Delgado, G, Morales-Espinosa, R, Grimont, PAD, Lizárraga-Partida, ML, Bouchier, C, Aanensen, DM, Kuri-Morales, P, Tarr, CL, Dougan, G, Parkhill, J, Campos, J, Cravioto, A, Weill, F and Thomson, NR (2017). Integrated view of Vibrio cholerae in the Americas. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.5427253.v1

Weill, F, Domman, D, Njamkepo, E, Tarr, C, Rauzier, J, Fawal, N, Keddy, KH, Salje, H, Moore, S, Mukhopadhyay, AK, Bercion, R, Luquero, FJ, Ngandjio, A, Dosso, M, Monakhova, E, Garin, B, Bouchier, C, Pazzani, C, Mutreja, A, Grunow, R, Sidikou, F, Bonte, L, Breurec, S, Damian, M, Njanpop-Lafourcade, B, Sapriel, G, Page, A, Hamze, M, Henkens, M, Chowdhury, G, Mengel, M, Koeck, J, Fournier, J, Dougan, G, Grimont, PAD, Parkhill, J, Holt, KE, Piarroux, R, Ramamurthy, T, Quilici, M and Thomson, NR (2017). Genomic history of the seventh pandemic of cholera in Africa. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.5314822.v3

The, HC, Florez de Sessions, P, Jie, S, Pham Thanh, D, Thompson, CN, Nguyen Ngoc Minh, C, Chu, CW, Tran, T, Thomson, NR, Thwaites, GE, Rabaa, MA, Hibberd, M and Baker, S (2017). Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. [Data Collection]. Gut microbes. https://doi.org/10.1080/19490976.2017.1361093

Chung The, H, Rabaa, MA, Pham Thanh, D, Ruekit, S, Wangchuk, S, Dorji, T, Pem Tshering, K, Nguyen Thi Nguyen, T, Voong Vinh, P, Ha Thanh, T, Nguyen Ngoc Minh, C, Turner, P, Sar, P, Thwaites, G, Holt, KE, Thomson, NR, Bodhidatta, L, Mason, CJ and Baker, S (2015). The introduction and establishment of fluoroquinolone resistant Shigella sonnei into Bhutan. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.1610693.v1

Reuter, S, Corander, J, de Been, M, Harris, S, Cheng, L, Hall, M, Thomson, NR and McNally, A (2015). Directional gene flow and ecological separation in Yersinia enterocolitica. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.1482060.v1

Vehkala, M, Shubin, M, Connor, TR, Thomson, N and Corander, J (2015). Data from: Novel R pipeline for analyzing Biolog phenotypic microarray data. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.r98g7

Lindgreen, S, Umu, SU, Lai, AS, Eldai, H, Liu, W, McGimpsey, S, Wheeler, NE, Biggs, PJ, Thomson, NR, Barquist, L, Poole, AM and Gardner, PP (2014). Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1003907

Bronowski, C, Fookes, MC, Gilderthorp, R, Ashelford, KE, Harris, SR, Phiri, A, Hall, N, Gordon, MA, Wain, J, Hart, CA, Wigley, P, Thomson, NR and Winstanley, C (2013). Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0002557

Arnvig, KB, Comas, I, Thomson, NR, Houghton, J, Boshoff, HI, Croucher, NJ, Rose, G, Perkins, TT, Parkhill, J, Dougan, G and Young, DB (2011). Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1002342.s008

Perkins, TT, Kingsley, RA, Fookes, MC, Gardner, PP, James, KD, Yu, L, Assefa, SA, He, M, Croucher, NJ, Pickard, DJ, Maskell, DJ, Parkhill, J, Choudhary, J, Thomson, NR and Dougan, G (2009). A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi. [Data Collection]. PLOS Genetics. https://doi.org/10.1371/journal.pgen.1000569

Carver, T, Thomson, N, Bleasby, A, Berriman, M and Parkhill, J (2009). DNAPlotter: circular and linear interactive genome visualization. [Data Collection]. Github. http://sanger-pathogens.github.io/Artemis/DNAPlotter/

Vernikos, GS, Thomson, NR and Parkhill, J (2007). Genetic flux over time in the Salmonella lineage. [Data Collection]. Genome Biology. https://doi.org/10.1186/gb-2007-8-6-r100

Young, JPW, Crossman, LC, Johnston, AW, Thomson, N, Ghazoui, ZF, Hull, KH, Wexler, M, Curson, AR, Todd, JD, Poole, PS, Mauchline, TH, East, AK, Quail, MA, Churcher, C, Arrowsmith, C, Cherevach, I, Chillingworth, T, Clarke, K, Cronin, A, Davis, P, Fraser, A, Hance, Z, Hauser, H, Jagels, K, Moule, S, Mungall, K, Norbertczak, H, Rabbinowitsch, E, Sanders, M, Simmonds, M, Whitehead, S and Parkhill, J (2006). The genome of Rhizobium leguminosarum has recognizable core and accessory components. [Data Collection]. Genome Biology. https://doi.org/10.1186/gb-2006-7-4-r34