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Aiken, A and Rehman, AM (2023). MBIRA - Mortality from Bacterial Infections Resistant to Antibiotics study - underlying data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003168.
Asio, J, Watera, C, Namuwenge, N, Kirungi, W, Musinguzi, J, Mugagga, K, Busobozi, R, Tusiime, BJ, Lutalo, T, Mbidde, EK and Kaleebu, P (2020). Population-based monitoring of HIV drug resistance early warning indicators in Uganda: A nationally representative survey following revised WHO recommendations: S1 Data. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0230451.s001
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
Brunn, A and Waage, J (2024). Data extraction results for a scoping review on AMR in food crops. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003087.
Cameron, DW, Panesar, P, Jones, A, Aldous, A, Kranzer, K, Halpin, E, Fifer, H, Macrae, B, Curtis, C and Pollara, G (2016). Attitudes and Behaviours to Antimicrobial Prescribing following introduction of a Smartphone App. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0154202.s004
Cerdeira, L, Dyson, ZA and Holt, KE (2023). typhoidgenomics/TyphiNET: New release. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.5281/zenodo.5338903
Cerdeira, L, Sharma, V, Maranga, M, Carey, M, Dyson, ZA and Holt, KE (2024). amrnet/amrnet: AMRnet-v1.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10810218
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
Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Accession numbers and data for S. Typhi sequences used in this study. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s005
Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Excluded repeat and phage regions in PNG MDUST348 2.1.7.2 completed reference sequence. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s006
Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Outgroups used for phylogenetic tree rooting. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s007
Emes, ET and Naylor, N (2023). Trescovia/AHHME. [Data Collection]. Github. https://github.com/Trescovia/AHHME
Evangelopoulos, D, Prosser, GA, Rodgers, A, Dagg, BM, Khatri, B, Ho, MM, Gutierrez, MG and Cortes, T (2019). Comparative fitness analysis of D-cycloserine resistant mutants reveals both fitness-neutral and high-fitness cost genotypes. [Data Collection]. Nature Communications. https://doi.org/10.1038/s41467-019-12074-z
Guevara, PD, Maes, M, Thanh, DP, Duarte, C, Rodriguez, EC, Montaño, LA, Dan, THN, Nguyen, TNT, Carey, ME, Campos, J, Chinen, I, Perez, E and Baker, S (2021). Profile of the organisms selected for sequencing. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0009755.s001
Holt, KE, Dyson, ZA, Hawkey, J and flashton2003 (2024). typhoidgenomics/genotyphi. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4707613
Holt, KE and Hawkey, J (2024). interpretAMR/AMRrules. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.12724318
Holt, KE and Wyres, K (2018). Klebsiella ecology and genome plasticity compared to E. coli and Gram negative ESKAPE pathogens. [Data Collection]. University of Melbourne, Australia. https://doi.org/10.4225/49/5ac3670f83717
Kim, C, Abbas, KM and vaccine-impact (2023). vaccine-impact/vaccine_amr. [Data Collection]. Github. https://github.com/vaccine-impact/vaccine_amr
Knight, G (2019). gwenknight/empiricprescribing. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3418998
Leclerc, QJ (2022). qleclerc/mrsa_phage_dynamics. [Data Collection]. Github. https://github.com/qleclerc/mrsa_phage_dynamics
Leclerc, QJ (2023). qleclerc/phage_antibiotic_dynamics. [Data Collection]. Github.
Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App all datasets. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9821996.v1
Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App drug breakdown. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9822077.v1
Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App drug breakdown (groups). [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9822104.v1
Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App economic data. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9822122.v1
Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App species breakdown. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9822179.v1
Lehri, B, Navoly, G, Willcocks, S, Huong, L and Stabler, RA (2022). Campylobacter coli strain, whole genome shotgun sequencing project. [Data Collection]. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/nuccore/JAKGTW000000000
London School of Hygiene & Tropical Medicine (2019). Comparing antimicrobial resistance prediction pipelines from bacterial whole genome sequencing data: An inter-laboratory study. [Data Collection]. European Nucleotide Archive. https://www.ebi.ac.uk/ena/data/view/PRJEB34513
London School of Hygiene & Tropical Medicine (2023). Data for: "Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana". [Data Collection]. NCBI Sequence Read Archive. https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA1052100
Lubell, Y, Mills, A, Whitty, CJ and Staedke, SG (2010). Model S1 - An Economic Evaluation of Home Management of Malaria in Uganda: An Interactive Markov Model. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0012439.s001
Ngufor, C, Critchley, J, Fagbohoun, J, N'guessan, R, Todjinou, D and Rowland, M (2016). Experimental hut data. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0162210.s001
Olaru, ID (2020). Evaluation of the InTray and Compact Dry culture systems for the diagnosis of urinary tract infections - ARGUS study dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001997.
Olaru, I (2021). ARGUS clinical and bacteriological outcomes dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002110.
Pickering, H, Hart, JD, Burr, S, Stabler, R, Maleta, K, Kalua, K, Bailey, RL and Holland, MJ (2022). Additional file 1 of Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.17982643.v1
Rahman, SIA, Dyson, ZA, Klemm, EJ, Khanam, F, Holt, KE, Chowdhury, EK, Dougan, G and Qadri, F (2020). Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0008036
Simpson, KMJ, Mor, SM, Ward, MP, Collins, J, Flint, J, Hill-Cawthorne, GA and El Ghany, MA (2020). Dataset for "Genomic characterisation of Salmonella enterica serovar Wangata isolates obtained from different sources reveals low genomic diversity". [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0229697.s002
Spadar, A (2022). AntonS-bio/entropy. [Data Collection]. GitHub. https://github.com/AntonS-bio/entropy
Thiha, N, Chinnakali, P, Harries, AD, Shwe, M, Balathandan, TP, Thein Than Tun, S, Das, M, Tin, HH, Yi, Y, Babin, FX, Lwin, TT and Clevenbergh, PA (2016). S1 Data for: "Is There a Need for Viral Load Testing to Assess Treatment Failure in HIV-Infected Patients Who Are about to Change to Tenofovir-Based First-Line Antiretroviral Therapy? Programmatic Findings from Myanmar". [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0160616.s001
Tsang, KK (2020). karatsang/rulesbased_logisticregression. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3988479
Ugarte-Ruiz, M, Domínguez, L, Corcionivoschi, N, Wren, BW, Dorrell, N and Gundogdu, O (2018). Exploring the oxidative, antimicrobial and genomic properties of Campylobacter jejuni strains isolated from poultry. [Data Collection]. Research in Veterinary Science. https://doi.org/10.1016/j.rvsc.2018.06.016
Waterlow, N and Knight, G (2024). gwenknight/ecdc_data_age_sex. [Data Collection]. Github. https://github.com/gwenknight/ecdc_data_age_sex
van Kleef, E, Luangasanatip, N, Bonten, MJ and Cooper, BS (2017). R code: why sensitive bacteria are resistant to hospital infection control. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.1045530