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Article

Abongomera, G; Cook, A; Musiime, V; Chabala, C; Lamorde, M; Abach, J; Thomason, M; ... CHAPAS-3 trial Team, .; + view all (2016) Improved adherence to antiretroviral therapy observed among HIV-infected children whose caregivers had positive beliefs in medicine in Sub-Saharan Africa. AIDS and Behavior 10.1007/s10461-016-1582-8. Green open access
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Abouyannis, Michael; Esmail, Hanif; Hamaluba, Mainga; Ngama, Mwanajuma; Mwangudzah, Hope; Mumba, Noni; Yeri, Betty; ... Walker, Ann; + view all (2022) A global core outcome measurement set for snakebite clinical trials. The Lancet Global Health , 11 (2) e296-e300. 10.1016/S2214-109X(22)00479-X. Green open access
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AbuOun, M; Jones, H; Stubberfield, E; Gilson, D; Shaw, L; Hubbard, A; Chau, K; ... Anjum, M; + view all (2021) A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage. Microbial Genomics , 7 (10) , Article 000630. 10.1099/mgen.0.000630. Green open access
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Adams, ER; Ainsworth, M; Anand, R; Andersson, MI; Auckland, K; Baillie, JK; Barnes, E; ... Whitehouse, J; + view all (2020) Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel [version 1; peer review: awaiting peer review]. Wellcome Open Research , 5 p. 139. 10.12688/wellcomeopenres.15927.1. Green open access
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Alkhmees, M; Van den Bruel, A; Hayward, G; Blanker, MH; Walker, AS; Holtman, GA; (2024) Trends in C-Reactive Protein testing: a retrospective cohort study in paediatric ambulatory care settings. BMJ Open , 14 (6) , Article e081658. 10.1136/bmjopen-2023-081658. Green open access
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AMR-X Collaborators; (2024) System-wide approaches to antimicrobial therapy and antimicrobial resistance in the UK: the AMR-X framework. The Lancet Microbe , 5 (5) e500-e507. 10.1016/S2666-5247(24)00003-X. Green open access
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Anyanwu, P; Pouwels, K; Walker, A; Moore, M; Butler, C; Majeed, A; Holmes, A; ... Costelloe, C; + view all (2020) Do variations in primary care practice characteristics explain the effect of a financial incentive scheme on antibiotic prescribing? A longitudinal study of the Quality Premium intervention in NHS England. BJGP Open , 4 (3) , Article bjgpopen20X101052. 10.3399/bjgpopen20X101052. Green open access
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Arenas-Pinto, A; Thompson, J; Musoro, G; Musana, H; Lugemwa, A; Kambugu, A; Mweemba, A; ... Paton, NI; + view all (2016) Peripheral neuropathy in HIV patients in sub-Saharan Africa failing first-line therapy and the response to second-line ART in the EARNEST trial. Journal of Neurovirology , 22 (1) pp. 104-113. 10.1007/s13365-015-0374-7. Green open access
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Arrigoni, Francesca IF; Spyer, Moira; Hunter, Patricia; Alber, Dagmar; Kityo, Cissy; Hakim, James; Matubu, Allen; ... EARNEST trial team; + view all (2023) Impact of sub-optimal HIV viral control on activated T cells. AIDS , 37 (6) pp. 913-923. 10.1097/QAD.0000000000003488. Green open access
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Ayoubkhani, Daniel; Bermingham, Charlotte; Pouwels, Koen B; Glickman, Myer; Nafilyan, Vahe; Zaccardi, Francesco; Khunti, Kamlesh; ... Walker, Ann; + view all (2022) Changes in the trajectory of Long Covid symptoms following COVID-19 vaccination: community-based cohort study. BMJ: British Medical Journal (In press). Green open access
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Ayoubkhani, Daniel; Bosworth, Matthew L; King, Sasha; Pouwels, Koen B; Glickman, Myer; Nafilyan, Vahé; Zaccardi, Francesco; ... Walker, A Sarah; + view all (2022) Risk of Long Covid in people infected with SARS-CoV-2 after two doses of a COVID-19 vaccine: community-based, matched cohort study. Open Forum Infectious Diseases 10.1093/ofid/ofac464. (In press). Green open access
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Ayoubkhani, Daniel; Zaccardi, Francesco; Pouwels, Koen B; Walker, Ann; Houston, Donald; Alwan, Nisreen A; Martin, Josh; ... Nafilyan, Vahe; + view all (2024) Employment outcomes of people with Long Covid symptoms: community-based cohort study. European Journal of Public Health , 34 (3) pp. 489-496. 10.1093/eurpub/ckae034. Green open access
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Batty, EM; Wong, TH; Trebes, A; Argoud, K; Attar, M; Buck, D; Ip, CL; ... Piazza, P; + view all (2013) A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One , 8 (6) , Article e66129. 10.1371/journal.pone.0066129. Green open access
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Bekker, Adrie; Panjasawatwong, Navarat; Hill, Louise F; Stohr, Wolfgang; Walker, Sarah; Ellis, Sally; Dramowski, Angela; ... NeoSep Study Team; + view all (2025) Pharmacokinetics and safety of fosfomycin and flomoxef administered as part of neonatal sepsis treatment (NeoSep1 Part 1). Antimicrobial Agents and Chemotherapy (In press). Green open access
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Bermingham, Charlotte; Morgan, Jasper; Ayoubkhani, Daniel; Glickman, Myer; Islan, Hazrul; Sheikh, Aziz; Sterne, Jonathan; ... Nafilyan, Vahe; + view all (2022) Estimating the effectiveness of first dose of COVID-19 vaccine against mortality in England: a quasi-experimental study. American Journal of Epidemiology , 97 (4) pp. 470-480. 10.1002/ajh.26478. Green open access
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Bielicki, J; Sharland, M; Heath, P; Walker, A; Agarwal, R; Turner, P; Cromwell, D; (2020) Evaluation of the coverage of three antibiotic regimens for neonatal sepsis in the 1 hospital setting across Asian countries. JAMA Network Open , 3 (2) , Article e1921124. 10.1001/jamanetworkopen.2019.21124. Green open access
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Bienczak, A; Cook, A; Wiesner, L; Mulenga, V; Kityo, C; Kekitiinwa, A; Walker, AS; ... Denti, P; + view all (2016) Effect of diurnal variation, CYP2B6 genotype and age on the pharmacokinetics of nevirapine in African children. Journal of Antimicrobial Chemotherapy , 72 (1) pp. 190-199. 10.1093/jac/dkw388. Green open access
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Bienczak, A; Cook, A; Wiesner, L; Olagunju, A; Mulenga, V; Kityo, C; Kekitiinwa, A; ... Denti, P; + view all (2016) The impact of genetic polymorphisms on the pharmacokinetics of efavirenz in African children. British Journal of Clinical Pharmacology , 82 (1) pp. 185-198. 10.1111/bcp.12934. Green open access
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Bienczak, A; Denti, P; Cook, A; Wiesner, L; Mulenga, V; Kityo, C; Kekitiinwa, A; ... McIlleron, H; + view all (2016) Plasma efavirenz exposure, sex, and age predict virological response in HIV-infected African children. JAIDS Journal of Acquired Immune Deficiency Syndromes , 73 (2) pp. 161-168. 10.1097/QAI.0000000000001032. Green open access
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Bienczak, A; Denti, P; Cook, A; Wiesner, L; Mulenga, V; Kityo, C; Kekitiinwa, A; ... McIlleron, H; + view all (2017) Determinants of virological outcome and adverse events in African children treated with paediatric nevirapine fixed-dose-combination tablets. AIDS , 31 (7) pp. 905-915. 10.1097/QAD.0000000000001376. Green open access
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Birrell, Paul J; Blake, Joshua; Kandiah, Joel; Alexopoulos, Angelos; van Leeuwen, Edwin; Pouwels, Koen; Ghosh, Sanmitra; ... De Angelis, Daniela; + view all (2025) Real-time modelling of the SARS-CoV-2 pandemic in England 2020-2023: a challenging data integration. Journal of the Royal Statistical Society: Statistics in Society Series A , Article qnaf030. 10.1093/jrsssa/qnaf030. (In press).

Borek, AJ; Campbell, A; Dent, E; Moore, M; Butler, CC; Holmes, A; Walker, A; ... Tonkin-Crine, S; + view all (2021) Development of an intervention to support the implementation of evidence-based strategies for optimising antibiotic prescribing in general practice. Implementation Science Communications (In press). Green open access
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Borek, Aleksandra; Edwards, George; Santillo, Marta; Wanat, Marta; Glogowska, Margaret; Butler, Christopher C; Walker, Ann; ... Tonkin-Crine, Sarah; + view all (2023) Re-examining advice to complete antibiotic courses: a qualitative study with clinicians and patients. BJGP Open 10.3399/BJGPO.2022.0170. Green open access
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Borek, Aleksandra; Ledda, Alice; Pouwels, Koen; Butler, Chris; Hayward, Gail; Walker, Ann; Robotham, Julie; (2024) Stop antibiotics when you feel better? Opportunities, challenges and research directions. JAC-Antimicrobial Resistance , 6 (5) , Article dlae147. 10.1093/jacamr/dlae147. Green open access
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Borek, A; Anthierens, S; Allison, R; McNulty, C; Anyanwu, PE; Costelloe, C; Walker, A; (2020) Social and contextual influences on antibiotic prescribing and antimicrobial stewardship: A qualitative study with Clinical Commissioning Group and general practice professionals. Antibiotics , 9 (12) , Article 859. 10.3390/antibiotics9120859. Green open access
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Borek, A; Anthierens, S; Allison, R; McNulty, C; Lecky, D; Costelloe, C; Holmes, A; ... Tonkin-Crine, S; + view all (2020) How did a Quality Premium financial incentive influence antibiotic prescribing in primary care? Views of Clinical Commissioning Group and general practice professionals. Journal of Antimicrobial Chemotherapy , 75 (9) pp. 2681-2688. 10.1093/jac/dkaa224. Green open access
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Borek, A; Campbell, A; Dent, E; Butler, CC; Holmes, A; Moore, M; Walker, A; ... Tonkin-Crine, S; + view all (2021) Implementing interventions to reduce antibiotic use: A qualitative study in high-prescribing practices. BMC Family Practice , 22 (25) 10.1186/s12875-021-01371-6. Green open access
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Bosworth, Matthew L; Shenhuy, Boran; Walker, A Sarah; Nafilyan, Vahé; Alwan, Nisreen A; O'Hara, Margaret E; Ayoubkhani, Daniel; (2023) Risk of new-onset Long Covid following reinfection with SARS-CoV-2: community-based cohort study. Open Forum Infectious Diseases , Article ofad493. 10.1093/ofid/ofad493. (In press). Green open access
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Bourke, C; Gough, E; Pimundu, G; Shonhai, A; Berejena, C; Terry, L; Baumard, L; ... Prendergast, AJ; + view all (2019) Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation. Science Translational Medicine , 11 (486) , Article eaav0537. 10.1126/scitranslmed.aav0537. Green open access
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Bown, Abbie; Peto, Tim; Sweed, Angela; Catton, Matthew; Nelthorpe-Cowne, Joshua; Benford, Tracy; LFD laboratory team, .; ... Vipond, Richard; + view all (2025) Laboratory evaluation of 185 commercial assays for detecting SARS-CoV-2: the UK response for mass testing. EClinicalMedicine , Article 103416. 10.1016/j.eclinm.2025.103416. (In press). Green open access
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Buchanan, J; Roope, L; Morrell, L; Pouwels, K; Robotham, J; Abel, L; Crook, D; ... Wordsworth, S; + view all (2021) Preferences for Medical Consultations from Online Providers: Evidence from a Discrete Choice Experiment in the United Kingdom. Applied Health Economics and Health Policy 10.1007/s40258-021-00642-8. (In press). Green open access
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Buckell, John; Jones, Joel; Matthews, Philippa; Diamond, Ian; Rourke, Emma; Studley, Ruth; Cook, Duncan; ... Pouwels, Koen B; + view all (2023) COVID-19 vaccination, risk-compensatory behaviours, and contacts in the UK. Scientific Reports , 13 , Article 8441. 10.1038/s41598-023-34244-2. Green open access
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Budgell, EP; Davies, T; Donker, T; Hopkins, S; Wyllie, D; Peto, TEA; Gill, M; ... Walker, AS; + view all (2021) Impact of hospital antibiotic use on patient-level risk of death among 36,124,372 acute and medical admissions in England. Journal of Infection 10.1016/j.jinf.2021.12.029. (In press). Green open access
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Burman, WJ; Cotton, MF; Gibb, DM; Walker, AS; Vernon, AA; Donald, PR; (2008) Ensuring the involvement of children in the evaluation of new tuberculosis treatment regimens. PLOS MEDICINE , 5 (8) , Article e176. 10.1371/journal.pmed.0050176. Green open access
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Bush, S; Connor, T; Peto, T; Crook, D; Walker, A; (2020) Evaluation of methods for detecting human reads in microbial sequencing datasets. Microbial Genomics , 6 (7) 10.1099/mgen.0.000393. Green open access
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Bush, S; Foster, D; Eyre, D; Clark, E; de Maio, N; Shaw, L; Stoesser, N; ... Walker, A; + view all (2020) Genomic diversity affects the accuracy of bacterial SNP calling pipelines. GigaScience , 9 (2) , Article giaa007. 10.1093/gigascience/giaa007. Green open access
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Bwakura-Dangarembizi, M; Amadi, B; Bourke, CD; Robertson, RC; Mwapenya, B; Chandwe, K; Kapoma, C; ... Prendergast, AJ; + view all (2019) Health Outcomes, Pathogenesis and Epidemiology of Severe Acute Malnutrition (HOPE-SAM): rationale and methods of a longitudinal observational study. BMJ Open , 9 (1) , Article e023077. 10.1136/bmjopen-2018-023077. Green open access
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Bwakura-Dangarembizi, M; Kendall, L; Bakeera-Kitaka, S; Nahirya-Ntege, P; Keishanyu, R; Nathoo, K; Spyer, MJ; ... Antiretroviral Research for Watoto (ARROW) Trial Team; + view all (2014) A randomized trial of prolonged co-trimoxazole in HIV-infected children in Africa. New England Journal of Medicine , 370 (1) 41 - 53. 10.1056/NEJMoa1214901. Green open access
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Bwakura-Dangarembizi, M; Musiime, V; Szubert, AJ; Prendergast, AJ; Gomo, ZA; Thomason, MJ; Musarurwa, C; ... Nathoo, K; + view all (2015) Prevalence of Lipodystrophy and Metabolic Abnormalities in HIV-infected African Children after 3 Years on First-line Antiretroviral Therapy. Pediatr Infect Dis J , 34 (2) e23 - e31. 10.1097/INF.0000000000000491. Green open access
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Campbell, Anne; Borek, Aleksandra; McLeod, Monsey; Tonkin-Crine, Sarah; Pouwels, Koen B; Roope, Laurence; Hayhoe, Benedict; ... Holmes, Alison; + view all (2023) Impact of the COVID-19 pandemic on antimicrobial stewardship support for general practices in England: a qualitative interview study. British Journal of General Practice Open , 7 (3) , Article BJGPO.2022.0193. 10.3399/BJGPO.2022.0193. Green open access
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Cane, Jennifer; Sanderson, Nicholas; Barnett, Sophie; Vaughan, Ali; Pott, Megan; Kapel, Natalia; Morgan, Marcus; ... Eyre, David W; + view all (2024) Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022–23. Journal of Infection , 88 (6) , Article 106164. 10.1016/j.jinf.2024.106164. Green open access
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Carter, Joshua; Walker, Timothy M; Walker, Ann; Whitfield, Michael G; Morlock, Glenn P; Lynch, Charlotte I; Adlard, Dylan; ... Fowler, Philip W; + view all (2024) Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches. JAC-Antimicrobial Resistance , 6 (2) , Article dlae037. 10.1093/jacamr/dlae037. Green open access
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Chau, Kevin; Barker, Louise; Budgell, Eric P; Vihta, Karina-Doris; Sims, N; Kasprzyk-Hordern, Barbara; Hariss, E; ... Stoesser, Nicole; + view all (2022) Systematic review of wastewater surveillance of antimicrobial resistance in human populations. Environment International , 162 , Article 107171. 10.1016/j.envint.2022.107171. Green open access
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Chau, Kevin K; Goodall, T; Bowes, M; Walker, Ann; Easterbrook, K; Brett, H; Hughes, J; ... Stoesser, Nicole; + view all (2023) High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent. Microbial Genomics , 9 (5) , Article 000983. 10.1099/mgen.0.000983. Green open access
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Chimhini, G; Chimhuya, S; Madzudzo, L; Heys, M; Crehan, C; Robertson, V; Ferrand, R; ... Fitzgerald, F; + view all (2020) Auditing use of antibiotics in Zimbabwean neonates. Infection Prevention in Practice , 2 (2) , Article 100046. 10.1016/j.infpip.2020.100046. Green open access
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Chintoloa, Elizabeth; Connon, Roisin; George, Elizabeth; Chagaluka, George; M'baya, Bridon; Walker, Sarah; Kennedy, Neil; (2025) Cardiac Output Measurement in Malawian children aged 2 months to 12 years hospitalised with severe anaemia (COM-TRACT). International Health (In press).

Clements, MN; Russell, N; Bielicki, JA; Ellis, S; Gastine, S; Hsia, Y; Standing, JF; ... Sharland, M; + view all (2021) Global antibiotic dosing strategies in hospitalised children: Characterising variation and implications for harmonisation of international guidelines. PLoS One , 16 (5) , Article e0252223. 10.1371/journal.pone.0252223. Green open access
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Connon, Roisin; Olupot-Olupot, Peter; Pistorius, Arthur MA; Okiror, William; Ssenyondo, Tony; Muhindo, Rita; Uyoga, Sophie; ... Maitland, Kathryn; + view all (2024) Azithromycin in severe malaria bacterial co-infection in African children (TABS-PKPD): a Phase II randomised controlled trial. BMC Medicine , 22 , Article 516. 10.1186/s12916-024-03712-5. Green open access
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Connon, R; George, EC; Olupot-Olupot, P; Kiguli, S; Chagaluka, G; Alaroker, F; Opoka, RO; ... TRACT trial group; + view all (2021) Incidence and predictors of hospital readmission in children presenting with severe anaemia in Uganda and Malawi: a secondary analysis of TRACT trial data. BMC Public Health , 21 (1) , Article 1480. 10.1186/s12889-021-11481-6. Green open access
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Constantinides, B; Chau, KK; Quan, TP; Rodger, G; Andersson, MI; Jeffery, K; Lipworth, S; ... Stoesser, N; + view all (2020) Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. Microbial Genomics 10.1099/mgen.0.000391. (In press). Green open access
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Cooke, Graham; Le Manh, Hung; Flower, Barnaby; McCabe, Leanne; Vu Thi Kim, Hang; Vo Thi, Thu; Dang Trong, Thuan; ... Walker, Ann Sarah; + view all (2025) Treatment Options to Support the Elimination of Hepatitis C: an open label, factorial randomised controlled trial. The Lancet , 405 pp. 1769-1780. Green open access
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Cooke, GS; Pett, SL; McCabe, L; Jones, C; Gilson, R; Verma, S; Ryder, SD; ... Walker, A; + view all (2021) Variable short duration treatment versus standard treatment, with and without adjunctive ribavirin, for chronic hepatitis C: the STOP-HCV-1 non-inferiority, factorial RCT. Efficacy and Mechanism Evaluation , 8 (17) 10.3310/eme08170. Green open access
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Cooke, GS; Walker, SA; Barnes, E; Thwaites, G; Van Vinh Chau, N; (2025) HCV response-guided therapy: is shorter always better? – Authors' reply. Lancet , 406 (10519) p. 2540. 10.1016/S0140-6736(25)01902-6.

Cooke, GS; Pett, S; McCabe, L; Jones, C; Gilson, R; Verma, S; Ryder, SD; ... Walker, AS; + view all (2021) Strategic treatment optimization for HCV (STOPHCV1): a randomised controlled trial of ultrashort duration therapy for chronic hepatitis C. Wellcome Open Research , 6 , Article 93. 10.12688/wellcomeopenres.16594.2. Green open access
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Cooke, GS; Pett, S; McCabe, L; Jones, C; Gilson, R; Verma, S; Ryder, SD; ... Walker, AS; + view all (2021) Strategic treatment optimization for HCV (STOPHCV1): a randomised controlled trial of ultrashort duration therapy for chronic hepatitis C [version 1; peer review: awaiting peer review]. Wellcome Open Research , 6 , Article 93. 10.12688/wellcomeopenres.16594.1. Green open access
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Cregan, Jack; Nsonwu, Olisaeloka; Chudasama, Dimple; Hopkins, Susan; Muller-Pebody, Berit; Hope, Russell; Brown, Colin; ... Walker, A Sarah; + view all (2025) The potential of a centrally-implemented system for national surveillance of bloodstream infections in England, compared to current local surveillance, 2023-2024. Journal of Hospital Infection 10.1016/j.jhin.2025.11.041. (In press). Green open access
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Cregan, Jack; Nsonwu, Olisaeloka; Chudasama, Dimple; Hopkins, Susan; Muller-Pebody, Berit; Hope, Russell; Walker, Ann; (2025) Case ascertainment of a potential centrally-implemented, automated system for national surveillance of healthcare-associated infections in England 2016-2023. Eurosurveillance (In press).

Crook, Derrick W; Rodrigues, Camilla; Ismail, Nazir Ahmed; Mistry, Nerges; Iqbal, Zamin; Merker, Matthias; Moore, David; ... coinvestigators; + view all (2022) Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms. PLoS Biology , 20 (8) , Article e3001755. 10.1371/journal.pbio.3001755. Green open access
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Crook, AM; Turkova, A; Musiime, V; Bwakura-Dangarembizi, M; Bakeera-Kitaka, S; Nahirya-Ntege, P; Thomason, M; ... ARROW Trial Team; + view all (2016) Tuberculosis incidence is high in HIV-infected African children but is reduced by co-trimoxazole and time on antiretroviral therapy. BMC Medicine , 14 (50) pp. 1-11. 10.1186/s12916-016-0593-7. Green open access
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Cross, Elizabeth LA; Hayward, Gail N; Llewelyn, Martin J; Walker, A Sarah; (2025) External validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score and the added impact of acute clinical response: a prospective cohort study. BMC Infectious Diseases (In press).

Cross, Elizabeth LA; Llewelyn, Martin J; Walker, Ann; Hayward, Gail N; (2025) Comparing thermal imaging and non-contact infrared thermometers for monitoring skin temperature in a prospective cohort with lower limb cellulitis. BMJ Open (In press). Green open access
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Cross, Elizabeth LA; Quan, T Phuong; Hayward, Gail N; Walker, A Sarah; Llewelyn, Martin J; (2024) Development and validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score. Journal of Infection , 88 (2) pp. 103-111. 10.1016/j.jinf.2023.12.007. Green open access
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Cross, ELA; Jordan, H; Godfrey, R; Onakpoya, IJ; Shears, A; Fidler, K; Peto, TEA; ... Llewelyn, MJ; + view all (2020) Route and duration of antibiotic therapy in acute cellulitis: A systematic review and meta-analysis of the effectiveness and harms of antibiotic treatment. Journal of Infection , 81 (4) pp. 521-531. 10.1016/j.jinf.2020.07.030. Green open access
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Cross, ELA; Sivyer, KA; Islam, J; Santillo, M; Mowbray, F; Peto, TEA; Walker, A; ... Llewelyn, M; + view all (2019) Adaptation and implementation of the ARK (Antibiotic Review Kit) Intervention to safely and substantially reduce antibiotic use in hospitals: A feasibility study. Journal of Hospital Infection , 103 (3) pp. 268-275. 10.1016/j.jhin.2019.07.017. Green open access
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CRyPTIC Consortium, .; Walker, Ann Sarah; (2022) Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis. European Respiratory Journal , 60 (4) , Article 2200239. 10.1183/13993003.00239-2022. Green open access
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CRyPTIC consortium and on behalf of the 100,000 Genomes Project, .; (2018) Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. New England Journal of Medicine , 379 (15) 10.1056/NEJMoa1800474. Green open access
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Davies, Timothy J; Swann, Jeremy; Sheppard, Anna E; Pickford, Hayleah; Lipworth, Samuel; AbuOun, Manal; Ellington, Matthew J; ... Stoesser, Nicole; + view all (2023) Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli. Microbial Genomics , 9 (12) , Article 001151. 10.1099/mgen.0.001151. Green open access
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Davies, K; Mawer, D; Walker, A; Berry, C; Planche, T; Stanley, P; Goldenberg, S; ... Wilcox, MH; + view all (2020) An analysis of C.difficile Environmental Contamination During and Following Treatment for C.difficile Infection. Open Forum Infectious Diseases , 7 (11) , Article ofaa362. /10.1093/ofid/ofaa362. Green open access
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Davies, TJ; Stoesser, N; Sheppard, A; Abuoun, M; Fowler, P; Swann, J; Quan, TP; ... Walker, A; + view all (2020) Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli. Antimicrobial Agents and Chemotherapy , 64 (6) , Article e02026-19. 10.1128/AAC.02026-19. Green open access
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De Maio, N; Shaw, LP; Hubbard, A; George, S; Sanderson, ND; Swann, J; Wick, R; ... Stoesser, N; + view all (2019) Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. Microbial Genomics , 5 (9) 10.1099/mgen.0.000294. Green open access
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de Silva, D; Peters, J; Cole, K; Cole, MJ; Cresswell, F; Dean, G; Dave, J; ... Eyre, DW; + view all (2016) Whole-genome sequencing to determine Neisseria gonorrhoeae transmission: an observational study. The Lancet Infectious Diseases , 16 (11) pp. 1295-1303. 10.1016/S1473-3099(16)30157-8. Green open access
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Decraene, V; Phan, HTT; George, R; Wyllie, DH; Akinremi, O; Aiken, Z; Cleary, P; ... TRACE Investigators’ Group, .; + view all (2018) A Large, Refractory Nosocomial Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Escherichia coli Demonstrates Carbapenemase Gene Outbreaks Involving Sink Sites Require Novel Approaches to Infection Control. Antimicrobial Agents and Chemotherapy , 62 (12) , Article e01689-18. 10.1128/AAC.01689-18. Green open access
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Didelot, X; Eyre, DW; Cule, M; Ip, CLC; Ansari, MA; Griffiths, D; Vaughan, A; ... Harding, RM; + view all (2012) Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biology , 13 (12) , Article R118. 10.1186/gb-2012-13-12-r118. Green open access
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Dingle, Kate E; Freeman, Jane; Didelot, Xavier; Quan, T Phuong; Eyre, David W; Swann, Jeremy; Spittal, William; ... Crook, Derrick; + view all (2023) Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in ‘Epidemic’ Lineages of Multi Drug-Resistant Clostridioides difficile. mBio , 14 (2) 10.1128/mbio.00243-23. Green open access
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Dingle, K; Didelot, X; Quan, P; Eyre, DW; Stoesser, N; Marwick, C; Coia, J; ... Crook, D; + view all (2019) A role for tetracycline selection in recent evolution of the agriculture-associated Clostridium difficile PCR-ribotype 078. mBio , 10 (2) , Article e02790-18. 10.1128/mBio.02790-18. Green open access
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Dingle, KE; Didelot, X; Quan, TP; Eyre, DW; Stoesser, N; Golubchik, T; Harding, RM; ... Crook, DW; + view all (2017) Effects of control interventions on Clostridium difficile infection in England: an observational study. Lancet Infectious Diseases , 17 (4) pp. 411-421. 10.1016/S1473-3099(16)30514-X. Green open access
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Dingle, KE; Elliott, B; Robinson, E; Griffiths, D; Eyre, DW; Stoesser, N; Vaughan, A; ... Didelot, X; + view all (2013) Evolutionary History of the Clostridium difficile Pathogenicity Locus. Genome Biology and Evolution , 6 (1) , Article evt204. 10.1093/gbe/evt204. Green open access
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Dingle, KE; Griffiths, D; Didelot, X; Evans, J; Vaughan, A; Kachrimanidou, M; Stoesser, N; ... Crook, DW; + view all (2011) Clinical Clostridium difficile: clonality and pathogenicity locus diversity. PLoS One , 6 (5) , Article e19993. 10.1371/journal.pone.0019993. Green open access
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Donker, T; Henderson, KL; Hopkins, KL; Dodgson, AR; Thomas, S; Crook, DW; Peto, TEA; ... Robotham, JV; + view all (2017) The relative importance of large problems far away versus small problems closer to home: insights into limiting the spread of antimicrobial resistance in England. BMC Medicine , 15 , Article 86. 10.1186/s12916-017-0844-2. Green open access
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Donker, T; Smieszek, T; Henderson, KL; Johnson, AP; Walker, AS; Robotham, JV; (2017) Measuring distance through dense weighted networks: The case of hospital-associated pathogens. PLoS Computational Biology , 13 (8) , Article e1005622. 10.1371/journal.pcbi.1005622. Green open access
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Donker, T; Smieszek, T; Henderson, KL; Walker, TM; Hope, R; Johnson, AP; Woodford, N; ... Robotham, JV; + view all (2019) Using hospital network-based surveillance for antimicrobial resistance as a more robust alternative to self-reporting. PLOS ONE , 14 (7) , Article e0219994. 10.1371/journal.pone.0219994. Green open access
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Eyre, DW; Lumley, SF; Wei, J; Cox, S; James, T; Justice, A; Jesuthasan, G; ... Jeffery, K; + view all (2021) Quantitative SARS-CoV-2 anti-spike responses to Pfizer–BioNTech and Oxford–AstraZeneca vaccines by previous infection status. Clinical Microbiology and Infection , 27 (10) 1516.e7-1516.e14. 10.1016/j.cmi.2021.05.041. Green open access
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Eyre, DW; Taylor, D; Purver, M; Chapman, D; Fowler, T; Pouwels, KB; Walker, A; (2022) Effect of Covid-19 Vaccination on Transmission of Alpha and Delta Variants. The New England Journal of Medicine , 386 pp. 744-756. 10.1056/NEJMoa2116597. Green open access
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Eyre, DW; Cule, ML; Griffiths, D; Crook, DW; Peto, TE; Walker, AS; Wilson, DJ; (2013) Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. PLoS Computational Biology , 9 (5) , Article e1003059. 10.1371/journal.pcbi.1003059. Green open access
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Eyre, DW; Davies, KA; Davis, G; Fawley, WN; Dingle, KE; De Maio, N; Karas, A; ... Wilcox, MH; + view all (2018) Two Distinct Patterns of Clostridium difficile Diversity Across Europe Indicating Contrasting Routes of Spread. Clinical Infectious Diseases , 67 (7) pp. 1035-1044. 10.1093/cid/ciy252. Green open access
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Eyre, DW; De Silva, D; Cole, K; Peters, J; Cole, MJ; Grad, YH; Demczuk, W; ... Paul, J; + view all (2017) WGS to predict antibiotic MICs for Neisseria gonorrhoeae. Journal of Antimicrobial Chemotherapy , 72 (7) pp. 1937-1947. 10.1093/jac/dkx067. Green open access
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Eyre, DW; Didelot, X; Buckley, AM; Freeman, J; Moura, I; Crook, D; Peto, TEA; ... Dingle, KE; + view all (2019) Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage. EBioMedicine , 43 pp. 347-355. 10.1016/j.ebiom.2019.04.038. Green open access
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Eyre, DW; Fawley, WN; Rajgopal, A; Settle, C; Mortimer, K; Goldberg, SD; Dawson, S; ... Walker, AS; + view all (2017) Comparison of control of Clostridium difficile infection in six English hospitals using whole-genome sequencing. Clinical Infectious Diseases , 65 (3) pp. 433-441. 10.1093/cid/cix338. Green open access
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Eyre, DW; Griffiths, D; Vaughan, A; Golubchik, T; Acharya, M; O'Connor, L; Crook, DW; ... Peto, TE; + view all (2013) Asymptomatic Clostridium difficile Colonisation and Onward Transmission. PLoS One , 8 (11) , Article e78445. 10.1371/journal.pone.0078445. Green open access
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Eyre, DW; Laager, M; Walker, AS; Cooper, BS; Wilson, DJ; CDC Modeling Infectious Diseases in Healthcare Program (MInD-Hea; (2021) Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission. PLOS Computational Biolology , 17 (1) , Article e1008417. 10.1371/journal.pcbi.1008417. Green open access
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Eyre, DW; Peto, TEA; Crook, DW; Walker, AS; Wilcox, MH; (2019) Hash-based core genome multi-locus sequencing typing for Clostridium difficile. Journal of Clinical Microbiology 10.1128/JCM.01037-19. (In press). Green open access
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Eyre, DW; Shaw, R; Adams, H; Cooper, T; Crook, DW; Griffin, R-M; Mannion, P; ... Craine, N; + view all (2019) Whole-genome sequencing to determine the extent of Clostridium difficile transmission in a high incidence setting in North Wales in 2015. Journal of Antimicrobial Chemotherapy , 74 (4) pp. 1092-1100. 10.1093/jac/dky523. Green open access
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Eyre, DW; Sheppard, AE; Madder, H; Moir, I; Moroney, R; Quan, TP; Griffiths, D; ... Jeffery, KM; + view all (2018) A Candida auris outbreak and its control in an intensive care setting. New England Journal of Medicine , 379 pp. 1322-1331. 10.1056/NEJMoa1714373. Green open access
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Eyre, DW; Walker, AS; Freeman, J; Baines, SD; Fawley, WN; Chilton, CH; Griffiths, D; ... Wilcox, MH; + view all (2013) Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease. PLoS One , 8 (5) , Article e63540. 10.1371/journal.pone.0063540. Green open access
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Farmer, R; Daniel, R; Ford, D; Cook, A; Musiime, V; Bwakura-Dangarembizi, M; Gibb, D; ... Walker, A; + view all (2020) Marginal Structural Models for repeated measures where intercept and slope are correlated: An application exploring the benefit of nutritional supplements on weight gain in HIV-infected children initiating antiretroviral therapy. PLoS One , 15 (7) , Article e0233877. 10.1371/journal.pone.0233877. Green open access
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Farmer, RE; Kounali, D; Walker, AS; Savovic, J; Richards, A; May, MT; Ford, D; (2018) Application of causal inference methods in the analyses of randomised controlled trials: a systematic review. Trials , 19 , Article 23. 10.1186/s13063-017-2381-x. Green open access
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Fawcett, N; Young, B; Peto, L; Quan, TP; Gillot, R; Wu, J; Middlemass, C; ... Sandoe, JAT; + view all (2019) ‘Caveat emptor’: the cautionary tale of endocarditis and the potential pitfalls of clinical coding 1 data: an electronic health records study. BMC Medicine , 17 (169) 10.1186/s12916-019-1390-x. Green open access
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Fawcett, NK; Jones, N; Quan, TP; Mistry, V; Crook, DW; Peto, TEA; Walker, AS; (2016) Antibiotic use and clinical outcomes in the acute setting under management by an Infectious Diseases Acute Physician versus other clinical teams: a cohort study. BMJ Open , 6 (8) , Article e010969. 10.1136/bmjopen-2015-010969. Green open access
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Fillekes, Q; Kendall, L; Kitaka, S; Mugyenyi, P; Musoke, P; Ndigendawani, M; Bwakura-Dangarembizi, M; ... ARROW Trial Team; + view all (2014) Pharmacokinetics of Zidovudine Dosed Twice Daily According to World Health Organization Weight Bands in Ugandan HIV-infected Children. Pediatric Infectious Disease Journal , 33 (5) 495 - 498. 10.1097/INF.0000000000000143. Green open access
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Fillekes, Q; Muro, EP; Chunda, C; Aitken, S; Kisanga, ER; Kankasa, C; Thomason, MJ; ... Burger, DM; + view all (2013) Effect of 7 days of phenytoin on the pharmacokinetics of and the development of resistance to single-dose nevirapine for perinatal HIV prevention: a randomized pilot trial. Journal of Antimicrobial Chemotherapy , 68 (11) pp. 2609-2615. 10.1093/jac/dkt246. Green open access
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Finney, JM; Walker, AS; Peto, TE; Wyllie, DH; (2011) An efficient record linkage scheme using graphical analysis for identifier error detection. BMC Medical Informatics and Decision Making , 11 , Article 7. 10.1186/1472-6947-11-7. Green open access
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Fitzgerald, FC; Lhomme, E; Harris, K; Kenny, J; Doyle, R; Kityo, C; Shaw, LP; ... CHAPAS-3 Trial Team; + view all (2019) Microbial translocation does not drive immune activation in Ugandan children with HIV. Journal of Infectious Diseases , 219 (1) pp. 89-100. 10.1093/infdis/jiy495. Green open access
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Fizpatrick, JM; Biswas, J; Edgeworth, JD; Islam, J; Jenkins, N; Judge, R; Lavery, AJ; ... Llewelyn, MJ; + view all (2016) Gram-negative bacteraemia; a multi-centre prospective evaluation of empiric antibiotic therapy and outcome in English acute hospitals. Clinical Microbiology and Infection , 22 (3) pp. 244-251. 10.1016/j.cmi.2015.10.034. Green open access
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Flower, B; McCabe, L; Ngoc, CL; Hung, LM; Phuong, LT; Trong, TD; Thi, TV; ... Cooke, GS; + view all (2021) High cure rates for HCV genotype 6 in advanced liver fibrosis with 12 weeks sofosbuvir and daclatasvir: The Vietnam SEARCH Study. Open Forum Infectious Diseases , 8 (7) , Article ofab267. 10.1093/ofid/ofab267. Green open access
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Flower, Barnaby; Hung, Le Manh; Mccabe, Leanne; Ansari, M Azim; Le Ngoc, Chau; Vo Thi, Thu; Vu Thi Kim, Hang; ... Cooke, Graham S; + view all (2023) Efficacy of ultra-short, response-guided sofosbuvir and daclatasvir therapy for hepatitis C in a single-arm mechanistic pilot study. eLife , 12 , Article e81801. 10.7554/elife.81801. Green open access
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Flower, Barnaby; Nguyen Thi Ngoc, Phuong; McCabe, Leanne; Le Ngoc, Chau; Vo Thi, Thu; Thi Kim, Hang Vu; Dang Trong, Thuan; ... Day, Jeremy N; + view all (2023) Rise in alanine aminotransferase after HCV treatment is a highly sensitive screen for treatment failure. Clinical Liver Disease , 21 (5) pp. 138-142. 10.1097/CLD.0000000000000055. Green open access
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Folgori, L; Lutsar, I; Standing, JF; Walker, A; Roilides, E; Zaoutis, T; Jafri, H; ... Sharland, M; + view all (2019) Standardising neonatal and paediatric antibiotic clinical trial design and conduct: the PENTA-ID network view. BMJ Open , 9 (12) , Article e032592. 10.1136/bmjopen-2019-032592. Green open access
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Ford, DJ; Robins, J; Petersen, M; Gibb, DM; Gilks, CF; Mugyenyi, P; Grosskurth, H; ... Walker, AS; + view all (2015) The impact of different CD4 monitoring and switching strategies on mortality in HIV-infected African adults on antiretroviral therapy; an application of dynamic marginal structural models. American Journal of Epidemiology , 182 (7) 10.1093/aje/kwv083. Green open access
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Fowler, Philip; Wright, Carla; Spiers, Helen; Zhu, Tingting; Baeten, Elizabeth ML; Hoosdally, Sarah W; Gilbertoni Cruz, Ana L; ... CRyPTIC Consortium; + view all (2022) A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates. eLife , 11 , Article e75046. 10.7554/eLife.75046. Green open access
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Fowler, PW; Cole, K; Gordon, NC; Kearns, AM; Llewelyn, MJ; Peto, TEA; Crook, DW; (2018) Robust prediction of resistance to trimethoprim in Staphylococcus aureus. Cell Chemical Biology , 25 (3) 339-349.e4. 10.1016/j.chembiol.2017.12.009. Green open access
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Gaughan, Charlotte; Braunholtz, David; Massie, Leanne; Khera, Tarnjit; Birrell, Paul; Blake, Joshua; De Angelis, Daniela; ... Walker, Sarah; + view all (2025) The cumulative incidence and infection hospitalisation risk of SARS-CoV-2 by variant; a longitudinal study in England. American Journal of Epidemiology (In press).

George, EC; Uyoga, S; M'baya, B; Kyeyune Byabazair, D; Kiguli, S; Olupot-Olupot, P; Opoka, R; ... Maitland, K; + view all (2022) Whole blood versus red cell concentrates for children with severe anaemia: a secondary analysis of the Transfusion and Treatment of African Children (TRACT) trial. The Lancet Haematology , 10 (1) e360-e368. 10.1016/S2214-109X(21)00565-9. Green open access
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George, E; Kiguli, S; Olupot Olupot, P; Opoka, R; Engoru, C; Akech, S; Nyeko, R; ... Walker, A; + view all (2019) Mortality risk over time after early fluid resuscitation in African children. Critical Care , 23 , Article 377. 10.1186/s13054-019-2619-y. Green open access
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George, EC; Walker, AS; Kiguli, S; Olupot-Olupot, P; Opoka, RO; Engoru, C; Akech, SO; ... Babiker, AG; + view all (2015) Predicting mortality in sick African children: the FEAST Paediatric Emergency Triage (PET) Score. BMC Medicine , 13 , Article 174. 10.1186/s12916-015-0407-3. Green open access
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George, S; Xu, Y; Rodger, G; Morgan, M; Sanderson, N; Hoosdally, SJ; Thulborn, S; ... Dingle, K; + view all (2020) DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples. Journal of Clinical Microbiology , 58 , Article e00670-20. 10.1128/JCM.00670-20. Green open access
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Ghafari, Mahan; Hall, Matthew; Golubchik, Tanya; Ayoubkhani, Daniel; House, Thomas; MacIntyre-Cockett, George; Fryer, Helen R; ... Lythgoe, Katrina; + view all (2024) Prevalence of persistent SARS-CoV-2 in a large community surveillance study. Nature , 626 pp. 1094-1101. 10.1038/s41586-024-07029-4. Green open access
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Ghafari, Mahan; Kemp, Steven A; Hall, Matthew; Clarke, Joseph; Ferretti, Luca; Thomson, Laura; Studley, Ruth; ... Lythgoe, Katrina; + view all (2025) SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study. The Lancet Microbe , 6 (9) , Article 101154. 10.1016/j.lanmic.2025.101154. Green open access
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Gibb, DM; Kizito, H; Russell, EC; Chidziva, E; Zalwango, E; Nalumenya, R; Spyer, M; ... DART trial team, The; + view all (2012) Pregnancy and infant outcomes among HIV-infected women taking long-term ART with and without tenofovir in the DART trial. PLoS Medicine , 9 (5) , Article e1001217. 10.1371/journal.pmed.1001217. Green open access
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Gilks, CF; Walker, AS; Munderi, P; Kityo, C; Reid, A; Katabira, E; Goodall, RL; ... Team, DARTT; + view all (2013) Single CD4 Test with 250 Cells/Mm(3) Threshold Predicts Viral Suppression in HIV-Infected Adults Failing First-Line Therapy by Clinical Criteria. PLOS ONE , 8 (2) , Article ARTN e57580. 10.1371/journal.pone.0057580. Green open access
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Gordon, NC; Pichon, B; Golubchik, T; Wilson, DJ; Paul, J; Blanc, DS; Cole, K; ... Kearns, AM; + view all (2017) Whole Genome Sequencing reveals the contribution of long-term carriers in Staphylococcus aureus outbreak investigation. Journal of Clinical Microbiology , 55 (7) pp. 2188-2197. 10.1128/JCM.00363-17. Green open access
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Grady, C; Touloumi, G; Walker, AS; Smolskis, M; Sharma, S; Babiker, AG; Pantazis, N; ... START Informed Consent Substudy Group, .; + view all (2017) A randomized trial comparing concise and standard consent forms in the START trial. PLoS ONE , 12 (4) , Article e0172607. 10.1371/journal.pone.0172607. Green open access
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Gu, Qingze; Jones, Nicola; Drennan, Philip; Peto, Tim EA; Walker, Ann; Eyre, David W; (2022) Assessment of an institutional guideline for vancomycin dosing and identification of predictive factors associated with dose and drug trough levels. Journal of Infection , 85 (4) pp. 382-389. 10.1016/j.jinf.2022.06.029. Green open access
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Gu, Qingze; Wei, Jia; Yoon, Chang Ho; Yuan, Kevin; Jones, Nicola; Brent, Andrew; Llewelyn, Martin; ... Walker, A Sarah; + view all (2024) Distinct patterns of vital sign and inflammatory marker responses in adults with suspected bloodstream infection. Journal of Infection , 88 (5) , Article 106156. 10.1016/j.jinf.2024.106156. Green open access
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Gu, Qingze; Yuan, Kevin; Wei, Jia; Yoon, Chang Ho; Danielsen, Anders S; Luk, Augustine; Eyre, David; (2025) Interplay between C-reactive protein responses and antibiotic prescribing in people with suspected infection. BMC Infectious Diseases (In press).

Haberer, JE; Cook, A; Walker, AS; Ngambi, M; Ferrier, A; Mulenga, V; Kityo, C; ... Bangsberg, DR; + view all (2011) Excellent Adherence to Antiretrovirals in HIV plus Zambian Children Is Compromised by Disrupted Routine, HIV Nondisclosure, and Paradoxical Income Effects. PLOS ONE , 6 (4) , Article e18505. 10.1371/journal.pone.0018505. Green open access
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Hakim, J; Musiime, V; Szubert, AJ; Mallewa, J; Siika, A; Agutu, C; Walker, S; ... Gibb, DM; + view all (2017) Enhanced Prophylaxis plus Antiretroviral Therapy for Advanced HIV Infection in Africa. New England Journal of Medicine , 377 (3) pp. 233-245. 10.1056/NEJMoa1615822. Green open access
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Hakim, JG; Thompson, J; Kityo, C; Hoppe, A; Kambugu, A; van Oosterhout, JJ; Lugemwa, A; ... Europe Africa Research Network for Evaluation of Second-line The; + view all (2017) Lopinavir plus nucleoside reverse-transcriptase inhibitors, lopinavir plus raltegravir, or lopinavir monotherapy for second-line treatment of HIV (EARNEST): 144-week follow-up results from a randomised controlled trial. Lancet Infectious Diseases , 18 (1) pp. 47-57. 10.1016/S1473-3099(17)30630-8. Green open access
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Harrison, Rebecca E; Hamada, Ahmed; Haswell, Nujcharee; Groves, Aigul; Vihta, Karina Doris; Cella, Kerry; Garner, Sarah; ... Seale, Anna C; + view all (2023) Cycle Threshold Values as Indication of Increasing SARS-CoV-2 New Variants, England, 2020–2022. Emerging Infectious Diseases , 29 (10) pp. 2024-2031. 10.3201/eid2910.230030. Green open access
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Hasse, B; Walker, AS; Fehr, J; Furrer, H; Hoffmann, M; Battegay, M; Calmy, A; ... Study, SHIVC; + view all (2014) Co-Trimoxazole Prophylaxis Is Associated with Reduced Risk of Incident Tuberculosis in Participants in the Swiss HIV Cohort Study. Antimicrobial Agents and Chemotherapy , 58 (4) 2363 - 2368. 10.1128/AAC.01868-13. Green open access
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Herbeć, A; Chimhini, G; Pacareu, JR; Sithole, K; Rickli, F; Chimhuya, S; Manyau, S; ... Fitzgerald, F; + view all (2020) Barriers and facilitators to infection prevention and control in a neonatal unit in Zimbabwe – a theory-driven qualitative study to inform design of a behaviour change intervention. Journal of Hospital Infection , 106 (4) pp. 804-811. 10.1016/j.jhin.2020.09.020. Green open access
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Hill, LF; Clements, MN; Turner, MA; Dona, D; Lutsar, I; Jacqz-Aigrain, E; Heath, PT; ... Sharland, M; + view all (2022) An optimised versus standard dosing regimen of vancomycin in infants with Gram-1 positive sepsis (NeoVanc): a multi-centre randomised, open-label, phase IIb, non-inferiority trial. The Lancet Child & Adolescent Health , 6 (1) pp. 49-59. 10.1016/S2352-4642(21)00305-9. Green open access
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Hill, Louise; Obiero, Christina; Bekker, Adrie; Walker, Ann; Bielick, Julia; Sharland, Michael; Schiavone, Francesca; (2025) Safety reporting in neonatal clinical trials: reflections towards optimal, globally relevant approaches. Trials , 26 , Article 46. 10.1186/s13063-025-08723-y. Green open access
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Honda, Trenton; Vazquez-Montes, Maria DLA; Fanshawe, Thomas; Stoesser, Nicole; Butler, Christopher C; Walker, Ann; Hayward, Gail; (2025) The impact of inter-infection time on antimicrobial resistance profiles in women with multiple urinary tract infections over time. Journal of Antimicrobial Chemotherapy , 80 (8) pp. 2234-2240. 10.1093/jac/dkaf194. Green open access
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Hoppe, A; Guilano, M; Lugemwa, A; Thompson, J; Floridia, M; Walker, AS; Senoga, I; ... Paton, NI; + view all (2017) HIV-1 viral load and resistance in genital secretions in patients taking protease-inhibitor-based second-line therapy in Africa. Antiviral Therapy 10.3851/IMP3200. (In press). Green open access
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HORNE, R; Glendinning, E; King, K; Chalder, T; Sabin, C; Walker, A; Campbell, L; ... Cooper, V; + view all (2019) Protocol of a two arm randomised, multi-centre, 12-month controlled trial: Evaluating the impact of a Cognitive Behavioural Therapy (CBT)-based intervention Supporting UPtake and Adherence to antiretrovirals (SUPA) in adults with HIV. BMC Public Health , 19 , Article 905. 10.1186/s12889-019-6893-z. Green open access
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House, T; Riley, H; Pellis, L; Pouwels, KB; Bacon, S; Eidukas, A; Jahanshahi, K; ... Walker, A; + view all (2021) Inferring risks of coronavirus transmission from community household data. Statistical Methods in Medical Research (In press). Green open access
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Islam, J; Ashiru-Oredope, D; Budd, E; Howard, P; Walker, AS; Hopkins, S; Llewelyn, MJ; (2018) A national quality incentive scheme to reduce antibiotic overuse in hospitals: evaluation of perceptions and impact. Journal of Antimicrobial Chemotherapy , 73 (6) pp. 1708-1713. 10.1093/jac/dky041. Green open access
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Jackson, Niall; Woods, Jessica; Watkinson, Peter; Brent, Andrew; Peto, Tim; Walker, Ann; Eyre, David W; (2023) The quality of vital signs measurements and value preferences in electronic medical records varies by hospital, specialty, and patient demographics. Scientific Reports , 13 , Article 3858. 10.1038/s41598-023-30691-z. Green open access
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Kakaraskoska Boceska, Biljana; Vilken, Tuba; Xavier, Basil Britto; Kostyanev, Tomislav; Lin, Qiang; Lammens, Christine; Ellis, Sally; ... Goossens, Herman; + view all (2024) Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries. Nature Communications , 15 , Article 3947. 10.1038/s41467-024-48296-z. Green open access
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Kambugu, A; Thompson, J; Hakim, J; Tumukunde, D; van Oosterhout, JJ; Mwebaze, R; Hoppe, A; ... EARNEST Trial Team; + view all (2016) Neurocognitive Function at the First-Line Failure and on the Second-Line Antiretroviral Therapy in Africa: Analyses From the EARNEST Trial. JAIDS Journal of Acquired Immune Deficiency Syndromes , 71 (5) pp. 506-513. 10.1097/QAI.0000000000000898. Green open access
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Katrina, Lythgoe; Golubchik, Tanya; Hall, Matthew; House, Thomas; Cahuantzi, Roberto; MacIntyre-Cockett, George; Fryer, Helen; ... Bonsall, David; + view all (2023) Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey. Proceedings of the Royal Society B: Biological Sciences , 290 (2009) , Article 20231284. 10.1098/rspb.2023.1284. Green open access
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Kekitiinwa, A; Musiime, V; Thomason, MJ; Mirembe, G; Lallement, M; Nakalanzi, S; Baptiste, D; ... Judd, A; + view all (2016) Acceptability of lopinavir/r pellets (minitabs), tablets and syrups in HIV-infected children. Antiviral Therapy , 21 (7) pp. 579-585. 10.3851/IMP3054. Green open access
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Kekitiinwa, A; Szubert, AJ; Spyer, M; Katuramu, R; Musiime, V; Mhute, T; Bakeera-Kitaka, S; ... ARROW Trial Team, .; + view all (2017) Virologic Response to First-Line Efavirenz- or Nevirapine-Based Anti-Retroviral Therapy in HIV-Infected African Children. Pediatric Infectious Disease Journal , 36 (6) pp. 588-594. 10.1097/INF.0000000000001505. Green open access
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Kelly, C; Mwandumba, HC; Heyderman, RS; Jambo, K; Kamng'ona, R; Chammudzi, M; Sheha, I; ... Khoo, S; + view all (2019) HIV-Related Arterial Stiffness in Malawian Adults Is Associated With the Proportion of PD-1–Expressing CD8⁺ T Cells and Reverses With Antiretroviral Therapy. Journal of Infectious Diseases , 219 (12) pp. 1948-1958. 10.1093/infdis/jiz015. Green open access
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Kelly, C; Tinago, W; Alber, D; Hunter, P; Luckhurst, N; Connolly, J; Arrigoni, F; ... Khoo, S; + view all (2020) Inflammatory Phenotypes Predict Changes in Arterial Stiffness following ART Initiation. Clinical Infectious Diseases 10.1093/cid/ciaa186. (In press). Green open access
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Kityo, C; Szubert, A; Siika, A; Heyderman, R; Bwakura-Dangarembizi, M; Lugemwa, A; Mwaringa, S; ... Pett, S; + view all (2018) Raltegravir-intensified initial antiretroviral therapy in advanced HIV in Africa: a randomized controlled trial. PLoS Medicine , 15 (12) , Article e1002706. 10.1371/journal.. Green open access
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Kityo, C; Thompson, J; Nankya, I; Hoppe, A; Ndashimye, E; Warambwa, C; Mambule, I; ... Paton, N; + view all (2017) HIV drug resistance mutations in non-B subtypes after prolonged virological failure on NNRTI-based first-line regimens in sub-Saharan Africa. JAIDS: Journal of Acquired Immune Deficiency Syndromes , 75 (2) e45-e54. 10.1097/QAI.0000000000001285. Green open access
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Kiwuwa-Muyingo, S; Kikaire, B; Mambule, I; Musana, H; Musoro, G; Gilks, CF; Levin, J; (2014) Prevalence, incidence and predictors of peripheral neuropathy in African adults with HIV infection within the DART trial. AIDS , 28 (17) pp. 2579-2588. 10.1097/QAD.0000000000000447. Green open access
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Kiwuwa-Muyingo, S; Oja, H; Walker, AS; Ilmonen, P; Levin, J; Mambule, I; Reid, A; ... DART Trial Team, The; + view all (2013) Dynamic logistic regression model and population attributable fraction to investigate the association between adherence, missed visits and mortality: a study of HIV-infected adults surviving the first year of ART. BMC Infectious Diseases , 13 , Article 395. 10.1186/1471-2334-13-395. Green open access
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Kizny Gordon, A; Phan, HTT; Lipworth, S; Cheong, E; Gottlieb, T; George, S; Peto, T; ... Stoesser, N; + view all (2020) Genomic Dynamics of Species and Mobile Genetic Elements in a Prolonged blaIMP-4-associated Carbapenemase Outbreak in an Australian Hospital. Journal of Antimicrobial Chemotherapy , 75 (4) pp. 873-882. 10.1093/jac/dkz526. Green open access
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Kizny-Gordon, A; Mathers, AJ; Cheong, EYL; Gottlieb, T; Kotay, S; Walker, AS; Peto, TEA; ... Stoesser, N; + view all (2017) Is the hospital water environment a reservoir for carbapenem-resistant organisms causing hospital-acquired infections? A systematic review of the literature. Clinical Infectious Diseases , 64 (10) pp. 1435-1444. 10.1093/cid/cix132. Green open access
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Klein, N; Sefe, D; Mosconi, I; Zanchetta, M; Castro, H; Jacobsen, M; Jones, H; ... Paediatric European Network for Treatment of AIDS (PENTA) 11 Tri, The; + view all (2013) The Immunological and Virological Consequences of Planned Treatment Interruptions in Children with HIV Infection. PLoS One , 8 (10) , Article e76582. 10.1371/journal.pone.0076582. Green open access
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Kong, LY; Wilson, JD; Moura, IB; Fawley, W; Walker, A; Kelly, L; Eyre, DW; (2021) Utility of Whole Genome Sequencing in Assessing and Enhancing Partner Notification of Neisseria gonorrhoeae Infection. Sexually Transmitted Diseases , 48 (10) pp. 773-780. 10.1097/OLQ.0000000000001419. Green open access
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Kong, LY; Eyre, D; Corbeil, J; Raymond, F; Walker, AS; Wilcox, MH; Crook, DW; ... Loo, VG; + view all (2019) Clostridium difficile: Investigating Transmission Patterns Between Infected and Colonized Patients Using Whole Genome Sequencing. Clinical Infectious Diseases , 68 (2) pp. 204-209. 10.1093/cid/ciy457. Green open access
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Kotay, Shireen; Parikh, Hardik I; Gweon, Hyun S; Barry, Katie; Stoesser, Nicole; Walker, Sarah; Crook, Derrick W; ... Mathers, Amy J; + view all (2026) Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance. npj Antimicrobials and Resistance (In press).

Kouchaki, S; Yang, Y; Lapachelle, A; Walker, TM; Walker, A; CRyPTIC Consortium; Peto, T; ... Clifton, DA; + view all (2020) Multi-Label Random Forest Model for Tuberculosis Drug Resistance Classification and Mutation Ranking. Frontiers in Microbiology 10.3389/fmicb.2020.00667. (In press). Green open access
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Kouchaki, S; Yang, Y; Walker, T; Walker, AS; Wilson, DJ; Peto, TEA; Crook, D; ... CRyPTIC consortium, .; + view all (2019) Application of machine learning techniques to tuberculosis drug resistance analysis. Bioinformatics , 35 (13) pp. 2276-2282. 10.1093/bioinformatics/bty949. Green open access
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Kulasegaran-Shylini, Raghavendran; Bown, Abbie; Collinge, Tom; Sienkiewicz, Alex; Eyre, David W; Crook, Derrick; Walker, Sarah; ... Fowler, Tom; + view all (2025) Evaluation of SARS-CoV-2 lateral flow device sensitivity: a comparison of systematic laboratory assessments with manufacturer-reported sensitivity. EClinicalMedicine , 87 , Article 103454. 10.1016/j.eclinm.2025.103454. Green open access
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Lara, AM; Kigozi, J; Amurwon, J; Muchabaiwa, L; Wakaholi, BN; Mota, REM; Walker, AS; ... Team, DARTT; + view all (2012) Cost Effectiveness Analysis of Clinically Driven versus Routine Laboratory Monitoring of Antiretroviral Therapy in Uganda and Zimbabwe. PLoS One , 7 (4) , Article e33672. 10.1371/journal.pone.0033672. Green open access
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Larsen, Tim; Bosworth, Matthew L; Ayoubkhani, Daniel; Schofield, Ryan; Ali, Raghib; Khunti, Kamlesh; Walker, Ann; ... Nafilyan, Vahé; + view all (2023) Inequalities in SARS-CoV-2 case rates by ethnicity, religion, measures of socioeconomic position, English proficiency, and self-reported disability: cohort study of 39 million people in England during the alpha and delta waves. BMC Medicine , 2 (1) , Article e000187. 10.1136/bmjmed-2022-000187. Green open access
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Lee, Kim May; Turner, Rebecca M; Thwaites, Guy; Walker, A Sarah; White, Ian R; (2023) The Personalised Randomized Controlled Trial: Evaluation of a new trial design. Statistics in Medicine , 42 (8) pp. 1156-1170. 10.1002/sim.9663. Green open access
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Lee, L; Rozmanowski, S; Pang, M; Charlett, A; Anderson, C; Hughes, G; Barnard, M; ... Eyre, D; + view all (2021) Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity by Viral Load, S Gene Variants and Demographic Factors, and the Utility of Lateral Flow Devices to Prevent Transmission. Clinical Infectious Diseases 10.1093/cid/ciab421. (In press). Green open access
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Lewandowski, K; Xu, Y; Pullan, ST; Lumley, S; Foster, D; Sanderson, N; Vaughan, A; ... Matthews, P; + view all (2019) Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples. Journal of Clinical Microbiology , 58 (1) , Article e00963-19. 10.1128/JCM.00963-19. Green open access
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Lewis, J; Payne, H; Walker, AS; Otwombe, K; Gibb, DM; Babiker, AG; Panchia, R; ... Callard, RE; + view all (2017) Thymic output and CD4 T-cell reconstitution in HIV-infected children on early and interrupted antiretroviral treatment: evidence from the CHER trial. Frontiers in Immunology , 8 , Article 1162. 10.3389/fimmu.2017.01162. Green open access
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Li, HK; Rombach, I; Zambellas, R; Walker, A; McNally, M; Atkins, B; Stubbs, D; ... Scarborough, M; + view all (2019) Oral versus Intravenous Antibiotics for Bone and Joint Infection. The New England Journal of Medicine , 380 (5) pp. 425-436. 10.1056/NEJMoa1710926. Green open access
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Lipworth, S; Hough, N; Weston, N; Muller-Pebody, B; Phin, N; Myers, R; Chapman, S; ... Walker, TM; + view all (2021) Epidemiology of Mycobacterium abscessus in England: an observational study. The Lancet Microbe , 2 (10) e498-e507. 10.1016/S2666-5247(21)00128-2. Green open access
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Lipworth, S; Vihta, K-D; Chau, K; Barker, L; Goerge, S; Kavanagh, J; Davies, T; ... Stoesser, N; + view all (2021) Ten year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK. Genomic Medicine , 13 , Article 144. 10.1186/s13073-021-00947-2. (In press). Green open access
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Lipworth, Sam; Vihta, Karina-Doris; Davies, Tim; Wright, Sarah; Tabirao, Merline; Chau, Kevin; Vaughan, Alison; ... Stoesser, Nicole; + view all (2022) Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria. Communications Medicine , 2 , Article 101. 10.1038/s43856-022-00161-0. Green open access
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Lipworth, Samuel; Chau, Kevin; Oakley, Sarah; Barrett, Lucinda; Crook, Derrick; Tim, Peto; Walker, Ann; (2025) Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli, an observational study. The Lancet Microbe , 6 (11) , Article 101183. 10.1016/j.lanmic.2025.101183. Green open access
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Lipworth, Samuel; Crook, Derrick; Walker, Ann; Peto, Tim; Stoesser, Nicole; (2024) Exploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli: an observational analysis. The Lancet Microbe , 5 (11) , Article 100913. 10.1016/S2666-5247(24)00152-6. Green open access
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Lipworth, Samuel; Matlock, William; Shaw, Liam; Vihta, Karina-Doris; Rodger, Gillian; Chau, Kevin; Barker, Leanne; ... Stoesser, Nicole; + view all (2024) The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies. Nature Communications , 15 , Article 1612. 10.1038/s41467-024-45761-7. Green open access
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Lipworth, S; Pickford, H; Sanderson, N; Chau, KK; Kavanagh, J; Barker, L; Vaughan, A; ... Walker, A; + view all (2020) Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies. Microbial Genomics , 6 (11) 10.1099/mgen.0.000453. Green open access
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Lipworth, S; Vihta, K-D; Chau, KK; Kavanagh, J; Davies, T; George, S; Barker, L; ... Stoesser, N; + view all (2021) Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections. Clinical Infectious Diseases 10.1093/cid/ciab006. (In press). Green open access
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Llewelyn, Martin; Budgell, Eric; Peto, Tim; Walker, Ann; (2022) Antibiotic Review Kit for Hospitals (ARK-Hospital): a stepped wedge cluster randomised controlled trial. Lancet Infectious Diseases 10.1016/S1473-3099(22)00508-4. (In press). Green open access
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Llewelyn, Martin J; Budgell, Eric P; Pouwels, Koen B; Morrell, Liz; Roope, Laurence SJ; Sivyer, Katy; Santillo, Marta; ... Walker, Sarah; + view all (2025) Optimising antibiotic “review and revise” in acute/general medical inpatients: the Antibiotic Review Kit in Hospitals (ARK-Hospital) research programme including a stepped-wedge cluster-randomised trial. NIHR Journals Library (In press).

Llewelyn, MJ; Fitzpatrick, JM; Darwin, E; Tonkin-Crine, S; Gorton, C; Paul, J; Peto, TEA; ... Walker, AS; + view all (2017) The antibiotic course has had its day. BMJ , 358 , Article j3418. 10.1136/bmj.j3418. Green open access
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Lumley, SF; Richens, N; Lees, E; Cregan, J; Kalimeris, E; Oakley, S; Morgan, M; ... Matthews, PC; + view all (2022) Changes in paediatric respiratory infections at a UK teaching hospital 2016–2021; impact of the SARS-CoV-2 pandemic. Journal of Infection , 84 (1) p. 4047. 10.1016/j.jinf.2021.10.022. Green open access
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Lumley, SF; O'Donnell, D; Stoesser, NE; Matthews, PC; Howarth, A; Hatch, SB; Marsden, BD; ... Oxford University Hospitals Staff Testing Group, .; + view all (2021) Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers. The New England Journal of Medicine , 384 pp. 533-540. 10.1056/NEJMoa2034545. Green open access
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Lumley, SF; Wei, J; O'Donnell, D; Stoesser, N; Matthews, P; Howarth, A; Hatch, S; ... Eyre, D; + view all (2021) The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers. Clinical Infectious Diseases (In press). Green open access
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Maitland, K; Obonyo, N; Hamaluba, M; Ogoda, E; Mogaka, C; Williams, TN; Newton, C; ... George, EC; + view all (2024) A Phase I trial of Non-invasive Ventilation and seizure prophylaxis with levetiracetam In Children with Cerebral Malaria Trial (NOVICE-M Trial) [version 1; peer review: 2 approved]. Wellcome Open Research , 9 , Article 281. 10.12688/wellcomeopenres.21403.1. Green open access
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Maitland, K; Kiguli, S; Olupot-Olupot, P; Engoru, C; Mallewa, M; Goncalves, PS; Opoka, RO; ... Walker, AS; + view all (2019) Immediate Transfusion in African Children with Uncomplicated Severe Anemia. New England Journal Of Medicine , 381 (5) pp. 407-419. 10.1056/NEJMoa1900105. Green open access
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Maitland, K; Kiguli, S; Olupot-Olupot, P; Opoka, RO; Chimalizeni, Y; Alaroker, F; Uyoga, S; ... George, EC; + view all (2021) Transfusion management of severe anaemia in African children: a consensus algorithm. British Journal of Haematology 10.1111/bjh.17429. (In press). Green open access
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Maitland, K; Olupot-Olupot, P; Kiguli, S; Chagaluka, G; Alaroker, F; Opoka, RO; Mpoya, A; ... Walker, AS; + view all (2019) Transfusion Volume for Children with Severe Anemia in Africa. New England Journal Of Medicine , 381 pp. 420-431. 10.1056/NEJMoa1900100. Green open access
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Maitland, K; Olupot-Olupot, P; Kiguli, S; Chagaluka, G; Alaroker, F; Opoka, RO; Mpoya, A; ... Walker, A; + view all (2019) Co-trimoxazole or multivitamin multimineral supplement for post-discharge outcomes after severe anaemia in African children: a randomised controlled trial. The Lancet Global Health , 7 (10) e1435-e1447. 10.1016/S2214-109X(19)30345-6. Green open access
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Mallewa, J; Szubert, AJ; Mugyenyi, P; Chidziva, E; Thomason, MJ; Chepkorir, P; Abongomera, G; ... REALITY trial team, .; + view all (2018) Effect of ready-to-use supplementary food on mortality in severely immunocompromised HIV-infected individuals in Africa initiating antiretroviral therapy (REALITY): an open-label, parallel-group, randomised controlled trial. The Lancet HIV , 5 (5) e231-e240. 10.1016/S2352-3018(18)30038-9. Green open access
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Martin, J; Phan, HTT; Findlay, J; Stoesser, N; Pankhurst, L; Navickaite, I; De Maio, N; ... Wilcox, MH; + view all (2017) Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission. Journal of Antimicrobial Chemotherapy , 72 (11) pp. 3025-3034. 10.1093/jac/dkx264. Green open access
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Martin, JSH; Eyre, DW; Fawley, WN; Griffiths, D; Davies, K; Mawer, DPC; Peto, TEA; ... Wilcox, MH; + view all (2018) Patient and Strain Characteristics Associated With Clostridium difficile Transmission and Adverse Outcomes. Clinical Infectious Diseases , 67 (9) pp. 1379-1387. 10.1093/cid/ciy302. Green open access
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Mason, A; Foster, D; Bradley, P; Golubchik, T; Doumith, M; Gordon, NC; Pichon, B; ... Peto, T; + view all (2018) Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole-Genome Sequences. Journal of Clinical Microbiology , 56 (9) , Article e01815-17. 10.1128/JCM.01815-17. Green open access
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Mathers, AJ; Crook, D; Vaughan, A; Barry, K; Vegesana, K; Stoesser, N; Parikh, HI; ... Sheppard, AE; + view all (2019) Klebsiella quasipneumoniae provides a window into carbapenemase gene transfer, plasmid rearrangements and patient interactions with the hospital environment. Antimicrobial Agents and Chemotherapy , 63 (6) , Article e02513-18. 10.1128/AAC.02513-18. Green open access
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Mathers, Amy; Li, Thomas; He, Qijan; Narendra, Sharvari; Stoesser, Nicole; Eyre, David; Walker, Ann; ... Reidys, Christian; + view all (2024) Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir. npj Antimicrobials and Resistance , 2 , Article 50. 10.1038/s44259-024-00069-w. Green open access
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Mathers, A; Stoesser, N; Chai, W; Carroll, J; Barry, K; Cheruvanky, A; Sebra, R; ... Sheppard, A; + view all (2017) Chromosomal Integration of the Klebsiella pneumoniae carbapenemase gene (blaKPC) in Klebsiella Species: Elusive but not Rare. Antimicrobial Agents and Chemotherapy , 61 (3) , Article e01823-16. 10.1128/AAC.01823-16. Green open access
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Mathers, A; Vesegana, K; German Mesner, I; Ainsworth, J; Pannone, A; Crook, D; Sifri, C; ... Eyre, D; + view all (2020) Risk factors for Klebsiella pneumoniae carbapenemase (KPC) gene acquisition and clinical outcomes across multiple bacterial species. Journal of Hospital Infection , 104 (4) pp. 456-468. 10.1016/j.jhin.2020.01.005. Green open access
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Matlock, William; Rodger, Gillian; Pritchard, Emma; Colpus, Matthew; Kapel, Natalia; Barrett, Lucinda; Morgan, Marcus; ... Stoesser, Nicole; + view all (2025) Escherichia coli phylogeny drives co-amoxiclav resistance through variable expression of TEM-1 beta-lactamase. Nature Communications , 16 , Article 8669. 10.1038/s41467-025-63714-6. Green open access
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Matlock, W; Chau, KK; AbuOun, M; Stubberfield, E; Barker, L; Kavanagh, J; Pickford, H; ... Shaw, L; + view all (2021) Genomic network analysis of environmental and livestock F-type 1 plasmid populations. The ISME Journal 10.1038/s41396-021-00926-w. (In press). Green open access
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Matlock, W; Lipworth, S; Constantinides, B; Peto, T; Walker, A; Crook, D; Hopkins, S; ... Stoesser, N; + view all (2021) Flanker: a tool for comparative genomics of gene flanking regions. Microbial Genomics (In press). Green open access
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Mawer, DPC; Eyre, DW; Griffiths, D; Fawley, WN; Martin, JSH; Quan, TP; Peto, TEA; ... Wilcox, MH; + view all (2017) Contribution to Clostridium difficile transmission of symptomatic patients with toxigenic strains who are fecal toxin negative. Clinical Infectious Diseases , 64 (9) pp. 1163-1170. 10.1093/cid/cix079. Green open access
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McCabe, L; White, IR; Chau, NVV; Barnes, E; Pett, SL; Cooke, GS; Walker, AS; (2020) The design and statistical aspects of VIETNARMS: a strategic post-licensing trial of multiple oral direct-acting antiviral hepatitis C treatment strategies in Vietnam. Trials , 21 (1) , Article 413. 10.1186/s13063-020-04350-x. Green open access
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Mead, S; Burnell, M; Lowe, J; Thompson, A; Lukic, A; Porter, MC; Carswell, C; ... Collinge, J; + view all (2016) Clinical Trial Simulations Based on Genetic Stratification and the Natural History of a Functional Outcome Measure in Creutzfeldt-Jakob Disease. JAMA Neurology , 73 (4) pp. 447-455. 10.1001/jamaneurol.2015.4885. Green open access
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Moore, Matthew P; Wilcox, Mark H; Walker, Ann; Eyre, David; (2022) K-mer based prediction of Clostridioides difficile relatedness and ribotypes. Microbial Genomics , 8 , Article 000804. 10.1099/mgen.0.000804. Green open access
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Morrell, L; Buchanan, J; Roope, LSJ; Pouwels, K; Butler, CC; Hayhoe, B; Tonkin-Crine, S; ... Wordsworth, S; + view all (2021) Public preferences for delayed or immediate antibiotic prescriptions in UK primary care: A choice experiment. PLoS Medicine , 18 (8) , Article e1003737. 10.1371/journal.pmed.1003737. Green open access
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Morrell, L; Buchanan, J; Roope, LSJ; Pouwels, KB; Butler, CC; Hayhoe, B; Moore, M; ... Wordsworth, S; + view all (2020) Delayed antibiotic prescription by general practitioners in the UK: a stated-choice study. Antibiotics (In press). Green open access
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Mowbray, F; Sivyer, K; Santillo, M; Jones, N; Peto, T; Walker, A; Llewelyn, MJ; (2020) Patient engagement with antibiotic messaging in secondary care: a qualitative feasibility study of the ‘review & revise’ experience. Pilot and Feasibility Studies , 6 , Article 43. 10.1186/s40814-020-00590-5. Green open access
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Mpoya, A; Kiguli, S; Olupot-Olupot, P; Opoka, RO; Engoru, C; Mallewa, M; Chimalizeni, Y; ... Maitland, K; + view all (2015) Transfusion and Treatment of severe anaemia in African children (TRACT): a study protocol for a randomised controlled trial. Trials , 16 (593) 10.1186/s13063-015-1112-4. Green open access
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Mramba, L; Ngari, M; Mwangome, M; Muchai, L; Bauni, E; Walker, AS; Gibb, DM; ... Berkley, JA; + view all (2017) A Growth Reference for Mid Upper Arm Circumference for Age among School Age Children and Adolescents, with Validation for Mortality in Two Cohorts. BMJ , 358 10.1136/bmj.j3423. Green open access
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Mulenga, V; Musiime, V; Kekitiinwa, A; Cook, AD; Abongomera, G; Kenny, J; Chabala, C; ... CHAPAS-3 trial team, .; + view all (2015) Abacavir, zidovudine, or stavudine as paediatric tablets for African HIV-infected children (CHAPAS-3): an open-label, parallel-group, randomised controlled trial. Lancet Infectious Diseases , 16 pp. 169-179. 10.1016/S1473-3099(15)00319-9. Green open access
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Musiime, Victor; Bwakura-Dangarembizi, Mutsa; Szubert, Alexander J; Mumbiro, Vivian; Mujuru, Hilda A; Kityo, Cissy M; Lugemwa, Abbas; ... CHAPAS-4 Trial Team; + view all (2025) Second-Line Antiretroviral Therapy for Children Living with HIV in Africa. New England Journal of Medicine , 392 (19) pp. 1917-1932. 10.1056/NEJMoa2404597. Green open access
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Musiime, V; Kasirye, P; Naidoo-James, B; Nahirya-Ntege, P; Mhute, T; Cook, A; Mugarura, L; ... Walker, AS; + view all (2016) Once- versus twice-daily abacavir and lamivudine in African children: the randomised controlled ARROW Trial. AIDS , 30 (11) pp. 1761-1770. 10.1097/QAD.0000000000001116. Green open access
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Musoke, P; Szubert, AJ; Musiime, V; Nathoo, K; Nahirya-Ntege, P; Mutasa, K; Williams, DE; ... Gibb, DM; + view all (2015) Single-dose nevirapine exposure does not affect response to antiretroviral therapy in HIV-infected African children aged below 3 years. AIDS , 29 (13) pp. 1623-1632. 10.1097/QAD.0000000000000749. Green open access
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Nafilyan, V; Dolby, T; Razieh, C; Gaughan, C; Morgan, J; Ayoubkhani, D; Walker, A; ... Yates, T; + view all (2021) Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study. BMJ Open , 11 , Article e053402. 10.1136/bmjopen-2021-053402. Green open access
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Naghavi, M; Vollset, SE; Ikuta, KS; Swetschinski, LR; Gray, AP; Wool, EE; Robles Aguilar, G; ... Aziz, S; + view all (2024) Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050. The Lancet , 404 (10459) pp. 1199-1226. 10.1016/S0140-6736(24)01867-1. Green open access
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Nambiar, K; Siefert, H; Rieg, S; Kern, WV; Scarborough, M; Gordon, NC; Kim, BN; ... Kaasch, A; + view all (2018) Survival following Staphylococcus aureus bloodstream infection; a prospective multinational cohort study assessing the impact of place of care. Journal of Infection , 77 (6) pp. 516-525. 10.1016/j.jinf.2018.08.015. Green open access
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Obiero, Christina W; Williams, Phoebe; Murunga, Sheila; Thitiri, Johnstone; Omollo, Raymond; Walker, Ann Sarah; Egondi, Thaddaeus; ... NeoFosfo Study Group; + view all (2022) Randomised controlled trial of fosfomycin in neonatal sepsis: pharmacokinetics and safety in relation to sodium overload. Archives of Disease in Childhood , 107 (9) 10.1136/archdischild-2021-322483. Green open access
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Olson, A; Walker, AS; Suthar, AB; Sabin, C; Bucher, H; Jarriin, I; Moreno, S; ... Ford, D; + view all (2016) Limiting cumulative HIV viremia copy years by early treatment reduces risk of AIDS and death. Journal of Acquired Immune Deficiency Syndromes , 73 (1) pp. 100-108. 10.1097/QAI.0000000000001029. Green open access
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Olupot-Olupot, Peter; Connon, Roisin; Kiguli, Sarah; Opoka, Robert O; Alaroker, Florence; Uyoga, Sophie; Nakuya, Margret; ... Maitland, Kathryn; + view all (2022) A predictive algorithm for identifying children with sickle cell anemia among children admitted to hospital with severe anemia in Africa. American Journal of Hematology , 97 (5) pp. 527-536. 10.1002/ajh.26492. Green open access
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Olupot-Olupot, P; Okiror, W; Mnjalla, H; Muhindo, R; Uyoga, S; Mpoya, A; Williams, TN; ... Maitland, K; + view all (2021) Pharmacokinetics and pharmacodynamics of azithromycin in severe malaria bacterial co-infection in African children (TABS-PKPD): a protocol for a Phase II randomised controlled trial [version 1; peer review: awaiting peer review]. Wellcome Open Research , 6 , Article 161. 10.12688/wellcomeopenres.16968.1. Green open access
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Onakpoya, IJ; Walker, AS; Tan, P; Spencer, EA; Gbinigie, OA; Cook, J; Llewelyn, MJ; (2018) Overview of systematic reviews assessing the evidence for shorter versus longer duration antibiotic treatment for bacterial infections in secondary care. PLOS ONE , 13 (3) , Article e0194858. 10.1371/journal.pone.0194858. Green open access
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Ordóñez-Mena, J; Fanshawe, TR; Foster, D; Andersson, M; Oakley, S; Stoesser, N; Walker, A; (2022) Frequencies and patterns of microbiology test requests from primary care in Oxfordshire, UK, 2008-2018: a retrospective cohort study of electronic health records to inform point of care testing. BMJ Open , 11 , Article e048527. 10.1136/bmjopen-2020-048527. Green open access
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Orlek, Alex; Anjum, Muna F; Mather, Alison E; Stoesser, Nicole; Walker, Ann; (2023) Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis. Scientific Reports , 13 , Article 2500. 10.1038/s41598-023-29530-y. Green open access
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Orlek, A; Phan, H; Sheppard, A; Doumith, M; Ellington, M; Peto, T; Crook, DW; ... Stoesser, N; + view all (2017) Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids. Plasmid , 91 pp. 42-52. 10.1016/j.plasmid.2017.03.002. Green open access
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Orlek, A; Phan, H; Sheppard, AE; Doumith, M; Ellington, M; Peto, TEA; Crook, D; ... Stoesser, N; + view all (2017) A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database. Data in Brief , 12 pp. 423-426. 10.1016/j.dib.2017.04.024. Green open access
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Orlek, A; Stoesser, N; Anjum, M; Doumith, M; Ellington, M; Peto, T; Crook, DW; ... Sheppard, A; + view all (2017) Plasmid classification in an era of whole-genome sequencing: application in studies of antibiotic resistance epidemiology. Frontiers in Microbiology , 8 , Article 182. 10.3389/fmicb.2017.00182. Green open access
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Pansa, P; Hsia, Y; Bielicki, J; Lutsar, I; Walker, AS; Sharland, M; Folgori, L; (2018) Evaluating Safety Reporting in Paediatric Antibiotic Trials, 2000–2016: A Systematic Review and Meta-Analysis. Drugs , 78 (2) pp. 231-244. 10.1007/s40265-017-0850-x. Green open access
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Parikh, SM; Obuku, EA; Walker, SA; Semeere, AS; Auerbach, BJ; Hakim, JG; Mayanja-Kizza, H; ... DART Trial Team, The; + view all (2013) Clinical differences between younger and older adults with HIV/AIDS starting antiretroviral therapy in Uganda and Zimbabwe: a secondary analysis of the DART trial. PLoS One , 8 (10) , Article e76158. 10.1371/journal.pone.0076158. Green open access
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Park, SC; Parikh, H; Vegesana, K; Stoesser, N; Barry, KE; Kotay, SM; Dudley, S; ... Mathers, AJ; + view all (2020) Risk Factors Associated with Carbapenemase-Producing Enterobacterales (CPE) Positivity in the Hospital Wastewater Environment. Applied and Environmental Microbiology , 86 (24) , Article e01715-20. 10.1128/AEM.01715-20. Green open access
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Paton, NI; Kityo, C; Hoppe, A; Reid, A; Kambugu, A; Lugemwa, A; van Oosterhout, JJ; ... Mugyenyi, P; + view all (2014) Assessment of second-line antiretroviral regimens for HIV therapy in Africa. The New England Journal of Medicine , 371 234 - 247. 10.1056/NEJMoa1311274. Green open access
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Paton, NI; Kityo, C; Thompson, J; Nankya, I; Bagenda, L; Hoppe, A; Hakim, JG; ... Walker, AS; + view all (2017) Nucleoside reverse-transcriptase inhibitor cross-resistance and outcomes from second-line antiretroviral therapy in the public health approach: an observational analysis within the randomised, open-label, EARNEST trial. The Lancet HIV , 4 (8) e341-e348. 10.1016/S2352-3018(17)30065-6. Green open access
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Peto, Leon; Fawcett, Nicola; Kamfose, Musaiwale; Scarborough, Claire; Peniket, Andy; Danby, robert; Peto, Tim; ... Walker, Ann; + view all (2025) The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study. eLife 10.7554/eLife.97751.2. (In press). Green open access
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Peto, L; Fawcett, NJ; Crook, DW; Peto, T; Llewelyn, MJ; Walker, A; (2019) Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae. PLoS ONE , 14 (11) , Article e0222831. 10.1371/journal.pone.0222831. Green open access
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Pett, SL; Spyer, M; Haddow, L; Nhema, R; Benjamin, L; Najjuka, G; Bilima, S; ... Walker, A; + view all (2021) Benefits of enhanced infection prophylaxis at antiretroviral therapy initiation by cryptococcal antigen status. AIDS , 35 (4) pp. 585-594. 10.1097/QAD.0000000000002781. Green open access
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Phan, HTT; Stoesser, N; Maciuca, IE; Toma, F; Szekely, E; Flonta, M; Hubbard, ATM; ... Timofte, D; + view all (2018) Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania. Journal of Antimicrobial Chemotherapy , 73 (3) pp. 672-679. 10.1093/jac/dkx456. Green open access
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Phillips, PP; Morris, TP; Walker, AS; (2015) DOOR/RADAR: A Gateway Into the Unknown? [Letter]. Clinical Infectious Diseases 10.1093/cid/civ1002. Green open access
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Picat, MQ; Lewis, J; Musiime, V; Prendergast, A; Nathoo, K; Kekitiinwa, A; Nahirya Ntege, P; ... ARROW Trial Team, The; + view all (2013) Predicting Patterns of Long-Term CD4 Reconstitution in HIV-Infected Children Starting Antiretroviral Therapy in Sub-Saharan Africa: A Cohort-Based Modelling Study. PLoS Med , 10 (10) , Article e1001542. 10.1371/journal.pmed.1001542. Green open access
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Pople, Diane; Kypraios, Theodore; Donker, Tjibbe; Stoesser, Nicole; Seale, Anna C; George, Ryan; Dodgson, Andrew; ... Robotham, Julie; + view all (2023) Model-based evaluation of admission screening strategies for the detection and control of carbapenemase-producing Enterobacterales in the English hospital setting. BMC Medicine , 21 , Article 492. 10.1186/s12916-023-03007-1. Green open access
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Post, FA; Szubert, AJ; Prendergast, AJ; Johnston, V; Lyall, H; Fitzgerald, F; Musiime, V; ... Pett, SL; + view all (2018) Causes and Timing of Mortality and Morbidity Among Late Presenters Starting Antiretroviral Therapy in the REALITY Trial. Clinical Infectious Diseases , 66 (S2) S132-S139. 10.1093/cid/cix1141. Green open access
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Pouwels, KB; Pritchard, E; Matthews, PC; Stoesser, N; Eyre, DW; Vihta, K-D; House, T; ... Walker, AS; + view all (2021) Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK. Nature Medecine 10.1038/s41591-021-01548-7. (In press). Green open access
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Pouwels, Koen; Eyre, David W; House, Thomas; Aspey, Ben; Matthews, Philippa; Stoesser, Nicole; Newton, John N; ... Walker, Ann; + view all (2024) Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification. Nature Communications , 15 , Article 5340. 10.1038/s41467-024-49201-4. Green open access
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Pouwels, K; Hopkins, S; Llewelyn, M; Walker, A; McNulty, C; Robotham, JV; (2019) Duration of antibiotic treatment for common infections in English primary care: cross sectional analysis and comparison with guidelines. BMJ , 364 , Article 1440. 10.1136/bmj.l440. Green open access
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Pouwels, K; House, T; Pritchard, E; Robotham, JV; Birrell, PJ; Gelman, A; Vihta, K-D; ... Walker, A; + view all (2021) Community prevalence of SARS-CoV-2 in England from April to November, 2020: results from the ONS Coronavirus Infection Survey. The Lancet Public Health , 6 (1) e30-e38. 10.1016/S2468-2667(20)30282-6. Green open access
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Pouwels, K; Yin, M; Butler, C; Cooper, B; Wordsworth, S; Walker, A; Robotham, JV; (2019) Optimising trial designs for identifying appropriate antibiotic treatment durations. BMC Medicine , 17 , Article 115. 10.1186/s12916-019-1348-z. Green open access
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Pouwels, KB; Roope, LSJ; Buchanan, J; Morrell, L; Tonkin-Crine, S; Peters, M; Jones, LF; ... Wordsworth, S; + view all (2020) Awareness of Appropriate Antibiotic Use in Primary Care for Influenza-Like Illness: Evidence of Improvement from UK Population-Based Surveys. Antibiotics , 9 (10) , Article 690. 10.3390/antibiotics9100690. Green open access
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Prendergast, A; Szubert, A; Berejena, C; Pimundu, G; Pala, P; Shonhai, A; Musiime, V; ... Klein, N; + view all (2016) Baseline inflammatory biomarkers identify subgroups of HIV-infected African children with differing responses to antiretroviral therapy. Journal of Infectious Diseases , 214 (2) pp. 226-236. 10.1093/infdis/jiw148. Green open access
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Prendergast, AJ; Berejena, C; Pimundu, G; Shonhai, A; Bwakura-Dangarembizi, M; Musiime, V; Szubert, AJ; ... Walker, AS; + view all (2019) Inflammatory biomarkers in HIV-infected children hospitalized for severe malnutrition in Uganda and Zimbabwe. AIDS , 33 (9) pp. 1485-1490. 10.1097/QAD.0000000000002231. Green open access
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Prendergast, AJ; Bwakura-Dangarembizi, M; Mugyenyi, P; Lutaakome, J; Kekitiinwa, A; Thomason, MJ; Gibb, DM; (2016) Reduced bacterial skin infections in HIV-infected African children randomized to long-term cotrimoxazole prophylaxis. AIDS , 30 (18) pp. 2823-2829. 10.1097/QAD.0000000000001264. Green open access
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Prendergast, AJ; Szubert, AJ; Pimundu, G; Berejena, C; Pala, P; Shonhai, A; Hunter, P; ... Klein, N; + view all (2021) The impact of viraemia on inflammatory biomarkers and CD4 cell subpopulations in HIV-infected children in sub-Saharan Africa. AIDS , 35 (10) pp. 1537-1548. 10.1097/QAD.0000000000002916. (In press). Green open access
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Prendergast, AJ; Szubert, AJ; Spyer, MJ; Musiime, V; Musoke, P; Bwakura-Dangarembizi, M; Nahirya-Ntege, P; ... Walker, AS; + view all (2017) Virological response and resistance among HIV-infected children receiving long-term antiretroviral therapy without virological monitoring in Uganda and Zimbabwe: Observational analyses within the randomised ARROW trial. PLOS Medicine , 14 (11) , Article e1002432. 10.1371/journal.pmed.1002432. Green open access
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Price, JR; Cole, K; Bexley, A; Kostiou, V; Eyre, DW; Golubchik, T; Wilson, D; ... Paul, J; + view all (2017) Transmission of Staphylococcus aureus between healthcare workers, the environment and patients in an intensive care unit: a whole-genome sequencing based longitudinal cohort study. Lancet Infectious Diseases , 17 (2) pp. 207-214. 10.1016/S1473-3099(16)30413-3. Green open access
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Pritchard, E; Fawcett, N; Quan, TP; Crook, D; Peto, TEA; Walker, A; (2021) Combining Charlson and Elixhauser scores with varying lookback predicated mortality better than using individual scores. Journal of Clinical Epidemiology , 130 pp. 32-41. 10.1016/j.jclinepi.2020.09.020. Green open access
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Pritchard, E; Jones, J; Vihta, K-D; Stoesser, N; Matthews, PC; Eyre, DW; House, T; ... Walker, A; + view all (2022) Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance. The Lancet Regional Health - Europe , 13 , Article 100282. 10.1016/j.lanepe.2021.100282. (In press). Green open access
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Pritchard, E; Matthews, PC; Stoesser, N; Eyre, DW; Gethings, O; Vihta, K; Jones, J; ... Pouwels, K; + view all (2021) Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom. Nature Medicine , 27 pp. 1370-1378. 10.1038/s41591-021-01410-w. Green open access
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Pritchard, Emma; Vihta, Karina; Eyre, David W; Hopkins, Susan; Peto, Tim EA; Matthews, Philippa; Stoesser, Nicole; ... COVID-19 Infection Survey Team; + view all (2024) Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar. American Journal of Epidemiology , 193 (12) pp. 1848-1860. 10.1093/aje/kwae091. Green open access
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Pritchard, Emma; Vihta, Karina-Doris; Lipworth, Samuel; Pouwels, Koen B; Stoesser, Nicole; Hope, Russell; Muller-Pebody, Berit; ... Walker, A Sarah; + view all (2025) An electronic health record-wide association study to identify populations at increased risk of E. coli bacteraemia. Journal of Infection , 91 (4) , Article 106612. 10.1016/j.jinf.2025.106612. Green open access
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Quan, T Phuong; Eyre, David W; Shadwell, Stephanie; West, Daniel; Hopkins, Susan; Chudasama, Dimple; Muller-Pebody, Berit; ... Walker, A Sarah; + view all (2025) Timeliness of a potential automated system for national surveillance of healthcare-associated infections in England. Journal of Hospital Infection 10.1016/j.jhin.2025.04.008. (In press).

Quan, T Phuong; Lacey, Ben; Peto, Tim EA; Walker, A Sarah; (2023) Health record hiccups—5,526 real-world time series with change points labelled by crowdsourced visual inspection. GigaScience , 12 , Article giad060. 10.1093/gigascience/giad060. Green open access
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Quan, P; Muller-Pebody, B; Fawcett, N; Young, B; MINAJI, M; Sandoe, J; Hopkins, S; ... Walker, A; + view all (2020) Investigation of the impact of the NICE guidelines regarding antibiotic prophylaxis during invasive dental procedures on the incidence of infective endocarditis in England: an Electronic Health Records study. BMC Medicine (In press). Green open access
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Quan, TP; Bawa, Z; Foster, D; Walker, T; del Ojo Elias, C; Rathod, P; MMM Informatics Group; ... Smith, EG; + view all (2018) Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping. Journal of Clinical Microbiology , 56 (2) , Article e01480-17. 10.1128/JCM.01480-17. Green open access
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Quan, TP; Fawcett, NJ; Wrightson, JM; Finney, J; Wyllie, D; Jeffery, K; Jones, N; ... Infections in Oxfordshire Research Database (IORD); + view all (2016) Increasing burden of community-acquired pneumonia leading to hospitalisation, 1998-2014. Thorax , 71 (6) pp. 535-542. 10.1136/thoraxjnl-2015-207688. Green open access
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Quan, TP; Hope, R; Clarke, T; Moroney, R; Butcher, L; Knight, P; Crook, D; ... Walker, AS; + view all (2018) Using linked electronic health records to report healthcare-associated infections. PLoS ONE , 13 (11) , Article e0206860. 10.1371/journal.pone.0206860. Green open access
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Quartagno, M; Carpenter, JR; Walker, AS; Clements, M; Parmar, MKB; (2020) The DURATIONS randomised trial design: Estimation targets, analysis methods and operating characteristics. Clinical Trials 10.1177/1740774520944377. (In press). Green open access
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Quartagno, M; Walker, AS; Babiker, AG; Turner, RM; Parmar, MKB; Copas, A; White, IR; (2020) Handling an uncertain control group event risk in non-inferiority trials: non-inferiority frontiers and the power-stabilising transformation. Trials , 21 , Article 145. 10.1186/s13063-020-4070-4. Green open access
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Quartagno, M; Walker, AS; Carpenter, J; Phillips, P; Parmar, M; (2018) Rethinking non-inferiority: a practical trial design for optimising treatment duration. Clinical Trials , 15 (5) pp. 477-488. 10.1177/1740774518778027. Green open access
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Read, Daniel S; Gweon, H Soon; Bowes, Michael J; Anjum, Muna F; Crook, Derrick; Chau, Kevin; Shaw, Liam P; ... Stoesser, Nicole; + view all (2024) Dissemination and Persistence of Antimicrobial Resistance (AMR) along the Wastewater-River Continuum. Water Research , 264 , Article 122204. 10.1016/j.watres.2024.122204. Green open access
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Revill, PA; Walker, S; Mabugu, T; Nathoo, KJ; Mugyenyi, P; Kekitinwa, A; Munderi, P; ... Gibb, DM; + view all (2015) Opportunities for improving the efficiency of paediatric HIV treatment programmes. AIDS , 29 (2) 201 - 210. 10.1097/QAD.0000000000000518. Green open access
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Revill, PA; Walker, S; Sculpher, MJ; Mabugu, T; Nathoo, KJ; Bwakura-Dangarembizi, M; Mugyenyi, P; ... Gibb, DM; + view all (2015) Opportunities for improving the efficiency of paediatric HIV treatment programmes. AIDS , 29 (2) 201 - 210. 10.1097/QAD.0000000000000518. Green open access
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Riitho, Victor; Connon, Roisin; Gwela, Agnes; Namusanje, Joseph; Nhema, Ruth; Siika, Abraham; Bwakura-Dangarembizi, Mutsa; ... REALITY Trial Team, .; + view all (2024) Biomarkers of mortality in adults and adolescents with advanced HIV in sub-Saharan Africa. Nature Communications , 15 , Article 5492. 10.1038/s41467-024-49317-7. Green open access
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Rodger, G; Chau, K; Aranega-Bou, P; Roohi, A; Moore, G; Hopkins, KL; Hopkins, S; ... Stoesser, N; + view all (2024) A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing. Journal of Hospital Infection , 144 pp. 128-136. 10.1016/j.jhin.2023.11.021. Green open access
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Rodger, G; Chau, KK; Aranega Bou, P; Moore, G; Roohi, A; The SinkBug Consortium; Walker, AS; (2025) Survey of healthcare-associated sink infrastructure, and sink trap antibiotic residues and biochemistry, in twenty-nine UK hospitals. Journal of Hospital Infection , 159 pp. 140-147. 10.1016/j.jhin.2025.02.002. Green open access
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Rooney, C; Sheppard, AE; Clark, E; Davies, K; Hubbard, ATM; Sebra, R; Crook, DW; ... Chilton, C; + view all (2019) Dissemination of multiple carbapenem resistance genes in an in-vitro gut model simulating the human colon. Journal of Antimicrobial Chemotherapy , 74 (7) pp. 1876-1883. 10.1093/jac/dkz106. Green open access
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Roope, Laurence SJ; Morrell, Liz; Buchanan, James; Ledda, Alice; Adler, Amanda I; Jit, Mark; Walker, A Sarah; ... STEPUP team; + view all (2024) Overcoming challenges in the economic evaluation of interventions to optimise antibiotic use. Communications Medicine , 4 , Article 101. 10.1038/s43856-024-00516-9. Green open access
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Roope, L; Tonkin-Crine, S; Herd, N; Michie, S; Pouwels, K; Castro-Sanchez, E; Sallis, A; ... Wordsworth, S; + view all (2020) Reducing expectations for antibiotics in primary care: a randomised experiment to test the response to fear based messages about antimicrobial resistance. BMC Medicine , 18 , Article 110. 10.1186/s12916-020-01553-6. Green open access
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Roope, LSJ; Buchanan, J; Morrell, L; Pouwels, K; Sivyer, K; Mowbray, F; Abel, L; ... Wordsworth, S; + view all (2020) Why do hospital prescribers continue antibiotics when it is safe to stop? Results of a choice experiment survey. BMC Medicine , 18 , Article 196. Green open access
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Roope, LSJ; Smith, RD; Pouwels, KB; Buchanan, J; Abel, L; Eibich, P; Butler, C; ... Wordsworth, S; + view all (2019) The challenge of antimicrobial resistance: What economics can contribute. Science , 364 (6435) , Article eaau4679. 10.1126/science.aau4679. Green open access
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Roope, LSJ; Tonkin-Crine, S; Butler, CC; Crook, D; Peto, T; Peters, M; Walker, AS; (2018) Reducing demand for antibiotic prescriptions: evidence from an online survey of the general public on the interaction between preferences, beliefs and information, United Kingdom, 2015. Eurosurveillance , 23 (25) pp. 13-23. 10.2807/1560-7917.ES.2018.23.25.1700424. Green open access
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Ross, JM; Badje, A; Rangaka, M; Walker, A; Shapiro, A; Thomas, K; Anglaret, X; ... Barnabas, R; + view all (2021) Isoniazid Preventive Therapy Added to ART to Prevent TB: An Individual Participant Data Meta-Analysis. The Lancet HIV , 8 (1) e8-e15. 10.1016/s2352-3018(20)30299-x. Green open access
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Ross, LL; Walker, AS; Lou, Y; Tenorio, AR; Gibb, DM; Double, J; Gilks, C; ... Shaefer, MS; + view all (2019) Changes over time in creatinine clearance and comparison of emergent adverse events for HIV-positive adults receiving standard doses (300 mg/day) of lamivudine-containing antiretroviral therapy with baseline creatinine clearance of 30–49 vs ≥50 mL/min. PLoS One , 14 (11) , Article e0225199. 10.1371/journal.pone.0225199. Green open access
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Russell, Neal; Clements, Michelle N; Azmery, Kazi S; Bekker, Adrie; Bielicki, Julia; Dramowski, Angela; Ellis, Sally; ... Sharland, Michael; + view all (2024) Safety and efficacy of whole-body chlorhexidine gluconate cleansing with or without emollient in hospitalised neonates (NeoCHG): a multicentre, randomised, open-label, factorial pilot trial. EClinicalMedicine , 69 , Article 102463. Green open access
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Russell, Neal J; Stöhr, Wolfgang; Plakkal, Nishad; Cook, Aislinn; Berkley, James A; Adhisivam, Bethou; Agarwal, Ramesh; ... Sharland, Mike; + view all (2023) Patterns of antibiotic use, pathogens, and prediction of mortality in hospitalized neonates and young infants with sepsis: A global neonatal sepsis observational cohort study (NeoOBS). PLoS Medicine , 20 (6) , Article e1004179. 10.1371/journal.pmed.1004179. Green open access
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Santillo, M; Sivyer, K; Krusche, A; Mowbray, F; Jones, N; Peto, TEA; Walker, A; ... Yardley, L; + view all (2019) Intervention planning for ARK (Antibiotic Review Kit): a digital and behavioural intervention to safely review and reduce antibiotic prescriptions in acute and general medicine. Journal of Antimicrobial Chemotherapy , 74 (11) pp. 3362-3370. 10.1093/jac/dkz333. Green open access
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Scarborough, M; Li, HK; Rombach, I; Zambellas, R; Walker, AS; McNally, M; Atkins, B; ... Bejon, P; + view all (2019) Oral versus intravenous antibiotics for bone and joint infections: the OVIVA non-inferiority RCT. Health Technology Assessment , 23 (38) 1-+. 10.3310/hta23380. Green open access
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Schlackow, I; Walker, AS; Dingle, K; Griffiths, D; Oakley, S; Finney, J; Vaughan, A; ... Wyllie, DH; + view all (2012) Surveillance of infection severity: a registry study of laboratory diagnosed Clostridium difficile. PLoS Med , 9 (7) , Article e1001279. 10.1371/journal.pmed.1001279. Green open access
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Schomaker, Michael; Denti, Paolo; Bienczak, Andrzej; Burger, David; Diaz, Ivan; Gibb, Diana; Walker, Ann; (2024) Determining Targets for Antiretroviral Drug Concentrations: a Causal Framework Illustrated with Pediatric Efavirenz Data from the CHAPAS-3 Trial. Pharmacoepidemiology and Drug Safety , 33 (12) , Article e70051. 10.1002/pds.70051. Green open access
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Schweitzer, V; Van Heilj, I; Van Werkhoven, CH; Islam, J; Hendriks-Spoor, K; Bielicki, J; Bonten, MJM; ... Llewelyn, MJ; + view all (2019) The quality of studies evaluating antimicrobial stewardship interventions: a systematic review. Clinical Microbiology and Infection , 25 (5) pp. 555-561. 10.1016/j.cmi.2018.11.002. Green open access
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Schweitzer, V; van Werkhoven, CH; Rodriguez Bano, J; Bielicki, J; Harbarth, S; Hulscher, M; Huttner, B; ... Llewelyn, MJ; + view all (2019) Optimizing design of research to evaluate antibiotic stewardship interventions: consensus recommendations of a multinational working group. Clinical Microbiology and Infection , 26 (1) pp. 41-50. 10.1016/j.cmi.2019.08.017. Green open access
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Seale, AC; Koech, AC; Sheppard, AE; Barsosio, HC; Langat, J; Anyango, E; Mwakio, S; ... Berkley, JA; + view all (2016) Maternal colonisation with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya. Nature Microbiology , Article 16067. 10.1038/nmicrobiol.2016.67. Green open access
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Shaw, L; Harjunmaa, U; Doyle, R; Mulewa, S; Charlie, D; Maleta, K; Callard, R; ... Klein, N; + view all (2016) Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: A Cross-Sectional Cohort Study in Malawi. Applied and Enviromental Microbiology , 82 (19) pp. 6057-6067. 10.1128/AEM.01756-16. Green open access
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Shaw, LP; Bassam, H; Barnes, CP; Walker, AS; Klein, N; Balloux, F; (2019) Modelling microbiome recovery after antibiotics using a stability landscape framework. The ISME Journal , 13 (7) pp. 1845-1856. 10.1038/s41396-019-0392-1. Green open access
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Shaw, LP; Chau, KK; Kavanagh, J; AbuOun, M; Stubberfield, E; Gweon, HS; Barker, L; ... REHAB consortium; + view all (2021) Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. Science Advances , 7 (15) , Article eabe3868. 10.1126/sciadv.abe3868. Green open access
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Sheppard, A; Stoesser, N; German-Mesner, I; Vegesana, K; Walker, AS; Crook, D; Mathers, A; (2018) TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data. Microbial Genomics , 4 10.1099/mgen.0.000232. Green open access
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Sheppard, A; Stoesser, N; Wilson, D; Sebra, R; Kasarkis, A; Anson, L; Giess, A; ... Mathers, A; + view all (2016) Nested Russian Doll-like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC. Antimicrobial Agents and Chemotherapy , 60 (6) pp. 3767-3778. 10.1128/AAC.00464-16. Green open access
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sheppard, A; Vaughan, A; Jones, N; Turner, P; Turner, C; Efstratiou, A; Patel, D; ... Seale, AC; + view all (2016) Capsular typing method for Streptococcus agalactiae using whole genome sequence data. Journal of Clinical Microbiology , 54 (5) pp. 1388-1390. 10.1128/JCM.03142-15. Green open access
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Sheppard, AE; Stoesser, N; Sebra, R; Kasarskis, A; Deikus, G; Anson, L; Walker, AS; ... Mathers, AJ; + view all (2016) Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193. Genome Announcements , 4 (1) , Article e01649-15. 10.1128/genomeA.01649-15. Green open access
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Shi, Y; Thompson, J; Walker, A; PATON, NI; Cheung, YB; (2019) Mapping the Medical Outcomes Study HIV Health Survey (MOS-HIV) to the EuroQoL 5 Dimension (EQ-5D-3L) utility index. Health and Quality of Life Outcomes , 17 , Article 83. 10.1186/s12955-019-1135-8. Green open access
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Siika, A; McCabe, L; Bwakura-Dangarembizi, M; Kityo, C; Mallewa, J; Berkley, J; Maitland, K; ... Gibb, DM; + view all (2018) Late presentation with HIV in Africa: phenotypes, risk and risk stratification in the REALITY trial. Clinical Infectious Diseases , 66 (S2) S140-S146. 10.1093/cid/cix1142. Green open access
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Soon, HG; Shaw, LP; Swann, J; De Maio, N; AbuOun, M; Niehus, R; Hubbard, ATM; ... Stoesser, N; + view all (2019) The impact of sequencing depth on the 1 inferred taxonomic composition and AMR gene content of metagenomic samples. Environmental Microbiome , 14 (7) 10.1186/s40793-019-0347-1. Green open access
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Stoesser, N; George, R; Aiken, Z; Phan, HTT; Lipworth, S; Quan, TP; Mathers, AJ; ... TRACE Investigators’ Group, .; + view all (2024) Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting. JAC-Antimicrobial Resistance , 6 (5) , Article dlae140. 10.1093/jacamr/dlae140. Green open access
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Stoesser, N; Eyre, DW; Quan, TP; Godwin, H; Pill, G; Mbuvi, E; Vaughan, A; ... Walker, AS; + view all (2017) Epidemiology of Clostridium difficile in infants in Oxfordshire, UK: risk factors for colonization and carriage, and genetic overlap with regional C. difficile infection strains. PLoS ONE , 12 (8) , Article e0182307. 10.1371/journal.pone.0182307. Green open access
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Stoesser, N; Phan, HTT; Seale, A; Aiken, Z; Thomas, S; Smith, M; Wyllie, D; ... Walker, A; + view all (2020) Genomic epidemiology of complex, multi-species, plasmid-borne blaKPC carbapenemase in Enterobacterales in the UK, 2009-2014. Antimicrobial Agents and Chemotherapy , 64 (5) , Article e02244-19. 10.1128/AAC.02244-19. Green open access
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Stoesser, N; Sheppard, AE; Moore, CE; Golubchik, T; Parry, CM; Nget, P; Saroeun, M; ... Walker, AS; + view all (2015) Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses. Journal of Clinical Microbiology , 53 (7) pp. 2122-2131. 10.1128/JCM.00378-15. Green open access
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Stoesser, N; Sheppard, AE; Pankhurst, L; De Maio, N; Moore, CE; Sebra, R; Turner, P; ... Modernizing Medical Microbiology Informatics Group (MMMIG); + view all (2016) Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131. mBio , 7 (2) 10.1128/mBio.02162-15. Green open access
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Stoesser, N; Sheppard, AE; Peirano, G; Anson, LW; Pankhurst, L; Sebra, R; Phan, HTT; ... Pitout, JD; + view all (2017) Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli. Scientific Reports , 7 , Article 5917. 10.1038/s41598-017-06256-2. Green open access
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Stoesser, N; Sheppard, AE; Shakya, M; Sthapit, B; Thorson, S; Giess, A; Kelly, D; ... Crook, DW; + view all (2015) Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing. Journal of Antimicrobial Chemotherapy , 70 (4) pp. 1008-1015. 10.1093/jac/dku521. Green open access
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Sy, Aminata; McCabe, Leanne; Hudson, Emma; Ansari, Azim; Pedergnana, Vincent; Lin, Shang-Kuan; Fiorino, Marzia; ... Cooke, Graham; + view all (2023) Utility of a buccal swab point-of-care test for the IFNL4 genotype in the era of direct acting antivirals for hepatitis C virus. PLOS One , 18 (1) , Article e0280551. 10.1371/journal.pone.0280551. Green open access
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Szubert, AJ; Bailey, SL; Cooke, GS; Peto, TEA; Llewelyn, MJ; Edgeworth, JD; Walker, A; (2019) Predictors of recurrence, early treatment failure and death from Staphylococcus aureus bacteraemia: observational analyses within the ARREST trial. Journal of Infection , 79 (4) pp. 332-340. 10.1016/j.jinf.2019.08.001. Green open access
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Szubert, AJ; Musiime, V; Bwakura-Dangarembizi, M; Nahirya-Ntege, P; Kekitiinwa, A; Gibb, DM; Nathoo, K; ... ARROW Trial Team, ; + view all (2015) Pubertal development in HIV-infected African children on first-line antiretroviral therapy. AIDS , 29 (5) 609 - 618. 10.1097/QAD.0000000000000590. Green open access
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Tenforde, MW; Walker, AS; Gibb, DM; Manabe, YC; (2019) Rapid antiretroviral therapy initiation in low and middle-income countries: A resource-based approach. PLoS Medicine , 16 (1) , Article e1002723. 10.1371/journal.pmed.1002723. Green open access
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The Cryptic, Consortium; (2024) Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. Nature Communications , 15 , Article 488. 10.1038/s41467-023-44325-5. Green open access
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The CRYpTIC Consortium, .; (2022) A data compendium of Mycobacterium tuberculosis antibiotic resistance. PLOS Biology , 20 (8) , Article e3001721. 10.1371/journal.pbio.3001721. Green open access
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Thomas, R; Velaphi, S; Ellis, S; Walker, AS; Standing, JF; Heath, P; Sharland, M; (2019) The use of polymyxins to treat carbapenem resistant infections in neonates and children. Expert Opinion on Pharmacotherapy , 20 (4) pp. 415-422. 10.1080/14656566.2018.1559817. Green open access
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Thompson, JA; Kityo, C; Dunn, D; Hoppe, A; Ndashimye, E; Hakim, J; Kambugu, A; ... Paton, NI; + view all (2019) Evolution of protease inhibitor resistance in HIV-1-infected patients failing protease inhibitor monotherapy as second-line therapy in low-income countries: an observational analysis within the EARNEST randomised trial. Clinical Infectious Diseases , 68 (7) pp. 1184-1192. 10.1093/cid/ciy589. Green open access
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Thwaites, G; Auckland, C; Barlow, G; Cunningham, R; Davies, G; Edgeworth, J; Greig, J; ... United Kingdom Clinical Infection Research Group, The; + view all (2012) Adjunctive rifampicin to reduce early mortality from Staphylococcus aureus bacteraemia (ARREST): study protocol for a randomised controlled trial. Trials , 13 , Article 241. 10.1186/1745-6215-13-241. Green open access
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Thwaites, GE; Scarborough, M; Szubert, AJ; Nsutebu, N; Tilley, R; Greig, J; Wyllie, SA; ... Walker, AS; + view all (2017) Adjunctive rifampicin to reduce early mortality from Staphylococcus aureus bacteraemia (ARREST): a multi-centre, randomised, blinded, placebo controlled trial. The Lancet 10.1016/S0140-6736(17)32456-X. (In press). Green open access
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Thwaites, GE; Scarborough, M; Szubert, AJ; Saramango Concalves, P; Soares, M; Bostock, J; Nsutebu, E; ... Walker, AS; + view all (2018) Adjunctive rifampicin to reduce early mortality from Staphylococcus aureus bacteraemia: the ARREST RCT. Health Technology Assessment , 22 (59) 10.3310/hta22590. Green open access
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Thwaites, GE; Szubert, A; Walker, AS; (2018) Rifampicin in treating S aureus bacteraemia - Authors' reply. The Lancet , 392 (10147) pp. 555-556. 10.1016/S0140-6736(18)31545-9. Green open access
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Thwaites, GE; UKCIRG; (2010) The Management of Staphylococcus aureus Bacteremia in the United Kingdom and Vietnam: A Multi-Centre Evaluation. PLOS ONE , 5 (12) , Article e14170. 10.1371/journal.pone.0014170. Green open access
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Tonkin-Crine, Sarah; McLeod, Monsey; Borek, Aleksandra J; Campbell, Anne; Anyanwu, Philip; Costelloe, Céire; Moore, Michael; ... Walker, Ann Sarah; + view all (2023) Implementing antibiotic stewardship in high-prescribing English general practices: a mixed-methods study. British Journal of General Practice , 73 (728) e164-e175. 10.3399/BJGP.2022.0298. Green open access
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Turner, Rebecca M; Clements, Michelle N; Quartagno, Matteo; Cornelius, Victoria; Cro, Suzie; Ford, Deborah; Tweed, Conor D; ... White, Ian R; + view all (2023) Practical approaches to Bayesian sample size determination in non-inferiority trials with binary outcomes. Statistics in Medicine 10.1002/sim.9661. Green open access
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Tyrer, F; Walker, AS; Gillett, J; Porter, K; UK Register of HIV Seroconverters, UK; (2003) The relationship between HIV seroconversion illness, HIV test interval and time to AIDS in a seroconverter cohort. Epidemiol Infect , 131 (3) 1117 - 1123. 10.1017/S0950268803001377. Green open access
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Uyoga, Sophie; Olupot-Olupot, Peter; Connon, Roisin; Kiguli, Sarah; Opoka, Robert O; Alaroker, Florence; Muhindo, Rita; ... Williams, Thomas N; + view all (2022) Sickle cell anaemia and severe P. falciparum malaria: a secondary analysis of the Transfusion and Treatment of African Children Trial (TRACT). The Lancet Child and Adolescent Health , 6 (9) pp. 606-613. 10.1016/S2352-4642(22)00153-5. Green open access
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Uyoga, S; Mpoya, A; Olupot-Olupot, P; Kiguli, S; Opoka, RO; Engoru, C; Mallewa, M; ... Maitland, K; + view all (2019) Haematological quality and age of donor blood issued for paediatric transfusion to four hospitals in sub-Saharan Africa. Vox Sanguinis , 114 (4) pp. 340-348. 10.1111/vox.12764. Green open access
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Van Aartsen, JJ; Moore, CE; Parry, CM; Turner, P; Phot, N; Mao, S; Suy, K; ... Stoesser, N; + view all (2019) Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia. BMC Microbiology , 19 , Article 59. 10.1186/s12866-019-1431-9. Green open access
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van der Westhuizen, Helene-Mari; Soundararajan, Srinidhi; Berry, Tamsin; Agus, David; Carmona, Sergio; Ma, Philip; Davis, Jessica; ... Bell, John; + view all (2024) A consensus statement on dual purpose pathogen surveillance systems: the Always On approach. PLOS Global Public Health , 4 (11) , Article e0003762. 10.1371/journal.pgph.0003762. Green open access
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Vazquez-Montes, Maria DLA; Fanshawe, Thomas R; Smith, Margaret C; Ahmed, Haroon; Stoesser, Nicole; Walker, A Sarah; Butler, Christopher; (2025) Defining recurrent urinary tract infection and reinfection risk: electronic health record study. BJGP Open (In press).

Vazquez-Montes, Maria DLA; Fanshawe, Thomas R; Stoesser, Nicole; Walker, A Sarah; Butler, Christopher; Hayward, Gail; (2024) Epidemiology and microbiology of recurrent UTI in women in the community in Oxfordshire, UK. JAC-Antimicrobial Resistance , 6 (1) , Article dlad156. 10.1093/jacamr/dlad156. Green open access
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Vermund, SH; Walker, AS; (2015) Use of Pharmacokinetic Data in Novel Analyses to Determine the Effect of Topical Microbicides as Preexposure Prophylaxis Against HIV Infection. The Journal of Infectious Diseases , 213 (3) pp. 329-331. 10.1093/infdis/jiv336. Green open access
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Vihta, K-D; Gordon, NC; Stoesser, N; Quan, TP; Tyrrell, CSB; Vongsouvath, M; Ashley, EA; ... Walker, A; + view all (2021) Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections. Scientific Reports , 11 , Article 23359. 10.1038/s41598-021-02755-5. Green open access
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Vihta, K-D; Pouwels, KB; Peto, TEA; Pritchard, E; Eyre, DW; House, T; Gethings, O; ... Walker, A; + view all (2021) Symptoms and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity in the General Population in the United Kingdom. Clinical Infectious Diseases 10.1093/cid/ciab945. (In press). Green open access
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Vihta, Karina-Doris; Pouwels, Koen; Peto, Tim; Pritchard, Emma; House, Thomas; Studley, Ruth; Rourke, Emma; ... Walker, Ann; + view all (2023) Omicron-Associated Changes in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Symptoms in the United Kingdom. Clinical Infectious Diseases , 76 (3) e133-e141. 10.1093/cid/ciac613. Green open access
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Vihta, Karina-Doris; Pritchard, Emma; Pouwels, Koen; Hopkins, Susan; Guy, Rebecca; Henderson, Katherine; Chudasama, Dimple; ... Clifton, David; + view all (2024) Predicting future hospital antimicrobial resistance prevalence using machine learning. Communications Medicine , 4 , Article 197. 10.1038/s43856-024-00606-8. Green open access
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Vihta, K-D; Stoesser, N; Llewelyn, MJ; Quan, TP; Davies, T; Fawcett, NJ; Dunn, L; ... Walker, AS; + view all (2018) Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998–2016: a study of electronic health records. The Lancet Infectious Diseases , 18 (10) pp. 1138-1149. 10.1016/S1473-3099(18)30353-0. Green open access
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Vilde, Elisabeth; Pritchard, Emma; Pouwels, Koen; Ehsaan, Muhammed; Blake, Joshua; Gaughan, Charlotte; Haduli, Eric; ... Walker, Ann; + view all (2024) SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and 1 association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort. BMC Medicine , 22 , Article 143. 10.1186/s12916-024-03351-w. Green open access
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Votintseva, A; Bradley, P; Pankhurst, L; Del Ojo Elias, C; Loose, M; Nilgiriwala, K; Chatterjee, A; ... Iqbal, Z; + view all (2017) Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples. Journal of Clinical Microbiology , 55 (5) pp. 1285-1298. 10.1128/JCM.02483-16. Green open access
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Walker, A; Vihta, K-D; Gethings, O; Pritchard, E; Jones, J; House, T; Bell, I; ... Pouwels, K; + view all (2021) Tracking the Emergence of SARS-CoV-2 Alpha Variant in the United Kingdom. New England Journal of Medicine , 385 (27) pp. 2582-2585. 10.1056/NEJMc2103227. Green open access
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Walker, Ann; Luk, Augustine; Wei, Jia; Eyre, David W; (2025) Community-acquired pneumonia identification from electronic health records in the absence of a gold standard: a Bayesian latent class analysis. PLoS Digital Health (In press).

Walker, AS; White, IR; Turner, RM; Yang, HL; Wen, YT; White, NJ; Sharland, M; (2020) Personalised randomised controlled trial designs—a new paradigm to define optimal treatments for carbapenem-resistant infections. The Lancet Infectious Diseases 10.1016/S1473-3099(20)30791-X. (In press). Green open access
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Walker, Timothy M; Choisy, Marc; Dedicoat, Martin; Drennan, Philip G; Wyllie, David; Yang-Turner, Fan; Crook, Derrick; ... Peto, Timothy EA; + view all (2022) Mycobacterium tuberculosis transmission in Birmingham, UK, 2009-19: an observational study. Lancet Regional Health Europe , 17 , Article 100361. 10.1016/j.lanepe.2022.100361. Green open access
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Walker, TM; Miotto, P; Koser, CU; Fowler, P; Knaggs, J; Iqbal, Z; Hunt, M; ... Rodwell, T; + view all (2021) The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis. The Lancet Microbe (In press). Green open access
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Walker, A; Budgell, E; Laskawiec-Szkonter, M; Sivyer, K; Wordsworth, S; Quaddy, J; Santillo, M; ... Llewelyn, MJ; + view all (2019) Antibiotic Review Kit for Hospitals (ARK-Hospital): study protocol for a stepped wedge cluster randomized controlled trial. Trials , 20 , Article 421. 10.1186/s13063-019-3497-y. Green open access
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Walker, AS; Eyre, DW; Wyllie, DH; Dingle, KE; Harding, RM; O'Connor, L; Griffiths, D; ... Peto, TE; + view all (2012) Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing. PLoS Med , 9 (2) , Article e1001172. 10.1371/journal.pmed.1001172. Green open access
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Walker, AS; Mason, A; Quan, TP; Fawcett, N; Watkinson, P; Llewelyn, M; Stoesser, N; ... Peto, TE; + view all (2017) Mortality risks associated with emergency admissions during weekends and public holidays: electronic health records study. The Lancet , 390 (10089) pp. 62-72. 10.1016/S0140-6736(17)30782-1. Green open access
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Walker, AS; Pritchard, E; House, T; Robotham, JV; Birrell, PJ; Bell, I; Bell, JI; ... COVID-19 Infection Survey team; + view all (2021) Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time. eLife , 10 , Article e64683. 10.7554/eLife.64683. Green open access
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Walker, S; Cox, E; Revill, P; Musiime, V; Bwakura-Dangarembizi, M; Mallewa, J; Cheruiyot, P; ... Soares, M; + view all (2020) The cost-effectiveness of prophylaxis strategies for individuals with advanced HIV starting treatment in Africa. Journal of the International AIDS Society , 23 (3) , Article e25469. 10.1002/jia2.25469. Green open access
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Walker, S; Peto, TE; O'Connor, L; Crook, DW; Wyllie, D; (2008) Are there better methods of monitoring MRSA control than bacteraemia surveillance? An observational database study. PLoS One , 3 (6) , Article e2378. 10.1371/journal.pone.0002378. Green open access
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Walker, TM; Lalor, MK; Broda, A; Saldana Ortega, L; Morgan, M; Parker, L; Churchill, S; ... Conlon, CP; + view all (2014) Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study. Lancet Respir Med , 2 (4) 285 - 292. 10.1016/S2213-2600(14)70027-X. Green open access
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Ward, Isobel L; Bermingham, Charlotte; Ayoubkhani, Daniel; Gethings, Owen J; Pouwels, Koen B; Yates, Tomas; Khunti, Kamlesh; ... Nafilyan, Vahe; + view all (2022) Risk of COVID-19 related deaths for SARS-CoV-2 Omicron (B.1.1.529) compared with Delta (B.1.617.2). BMJ: British Medical Journal (In press). Green open access
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Wasmann, RE; Svensson, EM; Walker, AS; Clements, MN; Denti, P; (2021) Constructing a representative in-silico population for paediatric simulations: Application to HIV-positive African children. British Journal of Clinical Pharmacology 10.1111/bcp.14694. (In press). Green open access
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Wei, J; Matthews, PC; Stoesser, N; Maddox, T; Lorenzi, L; Studley, R; Bell, JI; ... the COVID-19 Infection Survey team, .; + view all (2021) Anti-spike antibody response to natural SARS-CoV-2 infection in the general population. Nature Communications , 12 , Article 6250. 10.1038/s41467-021-26479-2. Green open access
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Wei, J; Pouwels, K; Stoesser, N; Matthews, P; Diamond, I; Studley, R; Rourke, E; ... Eyre, DW; + view all (2022) SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 and correlates of protection in the UK general population. Nature Medicine , 28 pp. 1072-1082. 10.1038/s41591-022-01721-6. Green open access
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Wei, J; Stoesser, N; Matthews, P; Ayoubkhani, D; Studley, R; Bell, I; Bell, JI; ... Walker, A; + view all (2021) Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom. Nature Microbiology , 6 pp. 1140-1149. 10.1038/s41564-021-00947-3. Green open access
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Wei, Jia; Gay, Jo; Brent, Andrew J; Clifton, David A; Walker, A Sarah; Eyre, David W; (2025) Concurrent prediction of in-hospital mortality and length of stay using single-task, multi-class, and multi-task machine learning. BMJ Digital Health & AI (In press).

Wei, Jia; Matthews, Philippa; Stoesser, Nicole; Diamond, Ian; Studley, Ruth; Rourke, Emma; Cook, Duncan; ... Pouwels, Koen B; + view all (2022) SARS-CoV-2 antibody trajectories after a single COVID-19 vaccination with and without prior infection. Nature Communications , 13 , Article 3748. 10.1038/s41467-022-31495-x. Green open access
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Wei, Jia; Matthews, Philippa; Stoesser, Nicole; Newton, John; Diamond, Ian; Studley, Ruth; Taylor, Nick; ... Eyre, David; + view all (2023) Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK. Nature Communications , 14 , Article 2799. 10.1038/s41467-023-38275-1. Green open access
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Wei, Jia; Stoesser, Nicole; Matthews, Philippa C; Khera, Tarnjit; Gethings, Owen; Diamond, Ian; Studley, Ruth; ... The COVID-19 Infection Survey team; + view all (2024) Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population. Nature Communications , 15 , Article 1008. 10.1038/s41467-024-44973-1. Green open access
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Wei, Jia; Uppal, Aashna; Nganjimi, Christy; Warr, Hermione; Ibrahim, Yasin; Gu, Qingze; Yuan, Hang; ... Eyre, David W; + view all (2024) No evidence of difference in mortality with amoxicillin versus co-amoxiclav for hospital treatment of community-acquired pneumonia. Journal of Infection , 88 (6) , Article 106161. 10.1016/j.jinf.2024.106161. Green open access
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Wei, Jia; Walker, A Sarah; Eyre, David W; (2024) Addition of macrolide antibiotics for hospital treatment of community-acquired pneumonia. The Journal of Infectious Diseases , Article jiae639. 10.1093/infdis/jiae639. (In press). Green open access
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Wei, Jia; Zhou, Jiandong; Zhang, Zizheng; Yuan, Kevin; Gu, Qingze; Luk, Augustine; Brent, Andrew J; ... Eyre, David W; + view all (2024) Predicting individual patient and hospital-level discharge using machine learning. Communications Medicine , 4 , Article 236. 10.1038/s43856-024-00673-x. Green open access
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White, Ian R; Quartagno, Matteo; Babiker, Abdel; Turner, Rebecca; Parmar, Mahesh; Walker, Ann; (2025) Tackling control risk problems in non-inferiority trials. BMJ Medicine , 4 (1) , Article e000845. 10.1136/bmjmed-2023-000845. Green open access
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White, Ian R; Szubert, Alexander J; Choodari-Oskooei, Babak; Walker, A Sarah; Parmar, Mahesh KB; (2023) When should factorial designs be used for late-phase randomised controlled trials? Clinical Trials 10.1177/17407745231206261. Green open access
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Wyllie, David H; Do, Trien; Myers, Richard; Nikolayevsky, Vlad; Crook, Derrick; Peto, Tim; Alexander, Eliza; ... Smith, E Grace; + view all (2022) M. tuberculosis microvariation is common and is associated with transmission: analysis of three years prospective universal sequencing in England. Journal of Infection , 85 (1) pp. 31-39. 10.1016/j.jinf.2022.05.011. Green open access
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Wyllie, DH; Robinson, E; Peto, TEA; Crook, DW; Ajileye, A; Rathod, P; Allen, R; ... Walker, AS; + view all (2018) Identifying mixed Mycobacterium tuberculosis infection and laboratory cross-contamination during Mycobacterial sequencing programs. Journal of Clinical Microbiology , 56 (11) , Article e00923-18. 10.1128/JCM.00923-18. Green open access
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Wyllie, DH; Sanderson, N; Myers, R; Peto, TEA; Robinson, E; Crook, DW; Smith, EG; (2018) Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline. Journal of Clinical Microbiology , 56 (8) , Article e00104-18. 10.1128/JCM.00104-18. Green open access
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Xu, Y; Lewandowski, K; Downs, LO; Kavanagh, J; Hender, T; Lumley, S; Jeffery, K; ... Pullan, S; + view all (2020) Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission. Eurosurveillance , 26 (7) , Article 2000004. 10.2807/1560-7917.ES.2021.26.27.2000004. Green open access
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Xu, Y; Lewandowski, K; Jeffery, K; Downs, LO; Foster, D; Sanderson, N; Kavanagh, J; ... Pullan, ST; + view all (2020) Nanopore metagenomic sequencing to investigate nosocomial transmission of human metapneumovirus from a unique genetic group among haematology patients in the United Kingdom. Journal of Infection , 80 (5) pp. 571-577. 10.1016/j.jinf.2020.02.003. Green open access
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Yang, M; Roope, LSJ; Buchanan, J; Attema, AE; Clarke, P; Walker, A; Wordsworth, S; (2022) Eliciting risk preferences that predict risky health behaviour: A comparison of two approaches. Health Economics , 31 (5) pp. 836-858. 10.1002/hec.4486. Green open access
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Yang, Y; Niehaus, KE; Walker, TM; Iqbal, Z; Walker, AS; Wilson, DJ; Peto, TEA; ... Clifton, DA; + view all (2018) Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data. Bioinformatics , 34 (10) pp. 1666-1671. 10.1093/bioinformatics/btx801. Green open access
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Yang, Y; Walker, TM; Walker, AS; Wilson, DJ; Peto, TEA; Crook, DW; Shamout, F; ... Clifton, DA; + view all (2019) DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis. Bioinformatics 10.1093/bioinformatics/btz067. (In press). Green open access
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Yokoyama, Maho; Peto, Leon; Budgell, Eric P; Jones, Nicola; Sheridan, Elizabeth; Liu, Jane; Walker, A Sarah; ... Llewelyn, Martin J; + view all (2023) Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing. PLoS ONE , 18 (3) , Article e0282584. 10.1371/journal.pone.0282584. Green open access
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Yoon, Chang H; Bartlett, Sean; Stoesser, Nicole; Pouwels, Koen; Jones, Nicola; Crook, Derrick; Peto, Tim EA; ... Eyre, David W; + view all (2022) Mortality risks associated with empirical antibiotic activity in E. coli bacteraemia: an analysis of electronic health records. Journal of Antimicrobial Chemotherapy , 77 (9) pp. 2536-2545. 10.1093/jac/dkac189. Green open access
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Young, B; Wu, C-H; Charlesworth, J; Earle, S; Price, JR; Gordon, NC; Cole, K; ... Wilson, DJ; + view all (2021) Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study. Microbial Genomics , 7 (11) , Article 000700. 10.1099/mgen.0.000700. Green open access
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Young, B; Votintseva, VV; Foster, D; Godwin, H; Miller, RR; Anson, LW; Walker, AS; ... Knox, K; + view all (2017) Multisite and nasal swabbing for carriage of Staphylococcus aureus: what does a single nose swab predict? Journal of Hospital Infection , 96 (3) pp. 232-237. 10.1016/j.jhin.2017.01.015. Green open access
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Young, BC; Wu, CH; Gordon, NC; Cole, K; Price, JR; Liu, E; Sheppard, AE; ... Wilson, DJ; + view all (2017) Severe infections emerge from commensal bacteria by adaptive evolution. eLife , 2017 (6) , Article e30637. 10.7554/eLife.30637. Green open access
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Yuan, Kevin; Luk, Augustine; Walker, Ann; Zhu, Tingting; Eyre, David W; (2025) Machine learning and clinician predictions of antibiotic resistance in Enterobacterales bloodstream infections. Journal of Infection , 90 (2) , Article 106388. 10.1016/j.jinf.2024.106388. Green open access
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Yuan, Kevin; Yoon, Chang Ho; Gu, Qingze; Munby, Henry; Walker, Ann; Zhu, Tingting; Eyre, David W; (2025) Transformers and large language models are efficient feature extractors for electronic health record studies. Communications Medicine , 5 , Article 83. 10.1038/s43856-025-00790-1. Green open access
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Zhong, LL; Phan, HTT; Shen, C; Vihta, KD; Sheppard, AE; Huang, X; Zeng, KJ; ... Tian, GB; + view all (2018) High Rates of Human Fecal Carriage of mcr-1–Positive Multidrug-Resistant Enterobacteriaceae Emerge in China in Association With Successful Plasmid Families. Clinical Infectious Diseases , 66 (5) pp. 676-685. 10.1093/cid/cix885. Green open access
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Zwerwer, Leslie R; Peto, Tim EA; Pouwels, Koen B; Walker, Ann Sarah; COVID-19 Infection Survey Team; (2025) Identification of undetected SARS-CoV-2 infections by clustering of Nucleocapsid antibody trajectories. Nature Communications , 16 , Article 4466. 10.1038/s41467-025-57370-z. Green open access
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Working / discussion paper

Constantinedes, B; Chau, K; Quan, TP; Rodger, G; Andersson, M; Jeffery, K; Lipworth, S; ... Stoesser, N; + view all (2020) Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. BioRxiv: Cold Spring Harbor, NY, USA. Green open access
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This list was generated on Sun Jan 11 00:45:59 2026 GMT.