Arenas-Pinto, Alejandro; Thompson, Jennifer; Musoro, Godfrey; Musana, Hellen; Lugemwa, Abbas; Kambugu, Andrew; Mweemba, Aggrey; Atwongyeire, Dickens; Thomason, Margaret J; Walker, A Sarah; +2 more... Paton, Nicholas I; EARNEST Trial Team; (2015) 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. ISSN 1355-0284 DOI: https://doi.org/10.1007/s13365-015-0374-7 Full text not available from this repository.

Beard, Emma; Lewis, James J; Copas, Andrew; Davey, Calum; Osrin, David; Baio, Gianluca; Thompson, Jennifer A; Fielding, Katherine L; Omar, Rumana Z; Ononge, Sam; +2 more... Hargreaves, James; Prost, Audrey; (2015) Stepped wedge randomised controlled trials: systematic review of studies published between 2010 and 2014. Trials, 16 (1). 353-. ISSN 1745-6215 DOI: https://doi.org/10.1186/s13063-015-0839-2

Copas, Andrew J; Lewis, James J; Thompson, Jennifer A; Davey, Calum; Baio, Gianluca; Hargreaves, James R; (2015) Designing a stepped wedge trial: three main designs, carry-over effects and randomisation approaches. Trials, 16 (1). 352-. ISSN 1745-6215 DOI: https://doi.org/10.1186/s13063-015-0842-7

Davey, Calum; Hargreaves, James; Thompson, Jennifer A; Copas, Andrew J; Beard, Emma; Lewis, James J; Fielding, Katherine L; (2015) Analysis and reporting of stepped wedge randomised controlled trials: synthesis and critical appraisal of published studies, 2010 to 2014. Trials, 16 (1). 358-. ISSN 1745-6215 DOI: https://doi.org/10.1186/s13063-015-0838-3

Dodd, Matthew; Fielding, Katherine; Carpenter, James R; Thompson, Jennifer A; Elbourne, Diana; (2022) Statistical methods for non-adherence in non-inferiority trials: useful and used? A systematic review. BMJ open, 12 (1). e052656-. ISSN 2044-6055 DOI: https://doi.org/10.1136/bmjopen-2021-052656

Easter, Christina; Thompson, Jennifer A; Eldridge, Sandra; Taljaard, Monica; Hemming, Karla; (2021) Cluster randomized trials of individual-level interventions were at high risk of bias. Journal of clinical epidemiology, 138. pp. 49-59. ISSN 0895-4356 DOI: https://doi.org/10.1016/j.jclinepi.2021.06.021

Fearon, Elizabeth; Chabata, Sungai T; Thompson, Jennifer A; Cowan, Frances M; Hargreaves, James R; (2017) Sample Size Calculations for Population Size Estimation Studies Using Multiplier Methods With Respondent-Driven Sampling Surveys. JMIR public health and surveillance, 3 (3). e59-. ISSN 2369-2960 DOI: https://doi.org/10.2196/publichealth.7909

Hakim, James G; Thompson, Jennifer; Kityo, Cissy; Hoppe, Anne; Kambugu, Andrew; van Oosterhout, Joep J; Lugemwa, Abbas; Siika, Abraham; Mwebaze, Raymond; Mweemba, Aggrey; +7 more... Abongomera, George; Thomason, Margaret J; Easterbrook, Philippa; Mugyenyi, Peter; Walker, A Sarah; Paton, Nicholas I; Europe Africa Research Network for Evaluation of Second-line The; (2018) 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. The Lancet. Infectious diseases, 18 (1). pp. 47-57. ISSN 1473-3099 DOI: https://doi.org/10.1016/S1473-3099(17)30630-8

Hargreaves, James R; Copas, Andrew J; Beard, Emma; Osrin, David; Lewis, James J; Davey, Calum; Thompson, Jennifer A; Baio, Gianluca; Fielding, Katherine L; Prost, Audrey; (2015) Five questions to consider before conducting a stepped wedge trial. Trials, 16 (1). 350-. ISSN 1745-6215 DOI: https://doi.org/10.1186/s13063-015-0841-8

Hemming, Karla; Carroll, Kelly; Thompson, Jennifer; Forbes, Andrew; Taljaard, Monica; SW-CRT Review Group; (2019) Quality of stepped-wedge trial reporting can be reliably assessed using an updated CONSORT: crowd-sourcing systematic review. Journal of Clinical Epidemiology, 107. pp. 77-88. ISSN 0895-4356 DOI: https://doi.org/10.1016/j.jclinepi.2018.11.017

Hemming, Karla; Taljaard, Monica; McKenzie, Joanne E; Hooper, Richard; Copas, Andrew; Thompson, Jennifer A; Dixon-Woods, Mary; Aldcroft, Adrian; Doussau, Adelaide; Grayling, Michael; +10 more... Kristunas, Caroline; Goldstein, Cory E; Campbell, Marion K; Girling, Alan; Eldridge, Sandra; Campbell, Mike J; Lilford, Richard J; Weijer, Charles; Forbes, Andrew B; Grimshaw, Jeremy M; (2018) Reporting of stepped wedge cluster randomised trials: extension of the CONSORT 2010 statement with explanation and elaboration. BMJ (Clinical research ed), 363. k1614-. ISSN 0959-8138 DOI: https://doi.org/10.1136/bmj.k1614

Hoppe, Anne; Giuliano, Marina; Lugemwa, Abbas; Thompson, Jennifer A; Floridia, Marco; Walker, Ann S; Senoga, Ismail; Abwola, Mary C; Pirillo, Maria F; Kityo, Cissy M; +3 more... Arenas-Pinto, Alejandro; Paton, Nicholas I; EARNEST Trial Team; (2017) HIV-1 viral load and resistance in genital secretions in patients taking protease-inhibitor-based second-line therapy in Africa. Antiviral therapy, 23 (2). pp. 191-195. ISSN 1359-6535 DOI: https://doi.org/10.3851/IMP3200

Jairath, Vipul; Thompson, J; Kahan, BC; Daniel, R; Hearnshaw, SA; Travis, SPL; Murphy, MF; Palmer, KR; Logan, RFA; (2014) Poor outcomes in hospitalized patients with gastrointestinal bleeding: impact of baseline risk, bleeding severity, and process of care. The American journal of gastroenterology, 109 (10). pp. 1603-1612. ISSN 0002-9270 DOI: https://doi.org/10.1038/ajg.2014.263 Full text not available from this repository.

Jarvis, Christopher I; Gimma, Amy; Finger, Flavio; Morris, Tim P; Thompson, Jennifer A; le Polain de Waroux, Olivier; Edmunds, W John; Funk, Sebastian; Jombart, Thibaut; (2022) Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics. PLoS Computational Biology, 18 (5). e1008800-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1008800

Kambugu, Andrew; Thompson, Jennifer; Hakim, James; Tumukunde, Dinah; van Oosterhout, Joep J; Mwebaze, Raymond; Hoppe, Anne; Abach, James; Kwobah, Charles; Arenas-Pinto, Alejandro; +3 more... Walker, Sarah A; Paton, Nicholas I; EARNEST Trial Team; (2016) Neurocognitive Function at the First-Line Failure and on the Second-Line Antiretroviral Therapy in Africa: Analyses From the EARNEST Trial. Journal of acquired immune deficiency syndromes (1999), 71 (5). pp. 506-513. ISSN 1525-4135 DOI: https://doi.org/10.1097/QAI.0000000000000898

Kityo, Cissy; Thompson, Jennifer; Nankya, Immaculate; Hoppe, Anne; Ndashimye, Emmanuel; Warambwa, Colin; Mambule, Ivan; van Oosterhout, Joep J; Wools-Kaloustian, Kara; Bertagnolio, Silvia; +5 more... Easterbrook, Philippa J; Mugyenyi, Peter; Walker, A Sarah; Paton, Nicholas I; Europe Africa Research Network for Evaluation of Second-line The; (2017) HIV Drug Resistance Mutations in Non-B Subtypes After Prolonged Virological Failure on NNRTI-Based First-Line Regimens in Sub-Saharan Africa. Journal of acquired immune deficiency syndromes (1999), 75 (2). e45-e54. ISSN 1525-4135 DOI: https://doi.org/10.1097/QAI.0000000000001285

Korevaar, Elizabeth; Kasza, Jessica; Taljaard, Monica; Hemming, Karla; Haines, Terry; Turner, Elizabeth L; Thompson, Jennifer A; Hughes, James P; Forbes, Andrew B; (2021) Intra-cluster correlations from the CLustered OUtcome Dataset bank to inform the design of longitudinal cluster trials. Clinical trials (London, England), 18 (5). pp. 529-540. ISSN 1740-7745 DOI: https://doi.org/10.1177/17407745211020852

Olupot-Olupot, Peter; Engoru, Charles; Thompson, Jennifer; Nteziyaremye, Julius; Chebet, Martin; Ssenyondo, Tonny; Dambisya, Cornelius M; Okuuny, Vicent; Wokulira, Ronald; Amorut, Denis; +8 more... Ongodia, Paul; Mpoya, Ayub; Williams, Thomas N; Uyoga, Sophie; Macharia, Alex; Gibb, Diana M; Walker, A Sarah; Maitland, Kathryn; (2014) Phase II trial of standard versus increased transfusion volume in Ugandan children with acute severe anemia. BMC medicine, 12 (1). 67-. ISSN 1741-7015 DOI: https://doi.org/10.1186/1741-7015-12-67

Paton, Nicholas I; Kityo, Cissy; Hoppe, Anne; Reid, Andrew; Kambugu, Andrew; Lugemwa, Abbas; van Oosterhout, Joep J; Kiconco, Mary; Siika, Abraham; Mwebaze, Raymond; +17 more... Abwola, Mary; Abongomera, George; Mweemba, Aggrey; Alima, Hillary; Atwongyeire, Dickens; Nyirenda, Rose; Boles, Justine; Thompson, Jennifer; Tumukunde, Dinah; Chidziva, Ennie; Mambule, Ivan; Arribas, Jose R; Easterbrook, Philippa J; Hakim, James; Walker, A Sarah; Mugyenyi, Peter; EARNEST Trial Team; (2014) Assessment of second-line antiretroviral regimens for HIV therapy in Africa. The New England journal of medicine, 371 (3). pp. 234-247. ISSN 0028-4793 DOI: https://doi.org/10.1056/NEJMoa1311274

Paton, Nicholas I; Kityo, Cissy; Thompson, Jennifer; Nankya, Immaculate; Bagenda, Leonard; Hoppe, Anne; Hakim, James; Kambugu, Andrew; van Oosterhout, Joep J; Kiconco, Mary; +5 more... Bertagnolio, Silvia; Easterbrook, Philippa J; Mugyenyi, Peter; Walker, A Sarah; Europe Africa Research Network for Evaluation of Second-line The; (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. ISSN 2405-4704 DOI: https://doi.org/10.1016/S2352-3018(17)30065-6

Shi, Yuan; Thompson, Jennifer; Walker, A Sarah; Paton, Nicholas I; Cheung, Yin Bun; EARNEST Trial Team; (2019) Mapping the medical outcomes study HIV health survey (MOS-HIV) to the EuroQoL 5 Dimension (EQ-5D-3 L) utility index. HEALTH AND QUALITY OF LIFE OUTCOMES, 17 (1). 83-. ISSN 1477-7525 DOI: https://doi.org/10.1186/s12955-019-1135-8

Stagg, Helen R; Thompson, Jennifer A; Lipman, Marc CI; Sloan, Derek J; Flook, Mary; Fielding, Katherine L; (2022) Forgiveness Is the Attribute of the Strong: Nonadherence and Regimen Shortening in Drug-sensitive Tuberculosis. American journal of respiratory and critical care medicine, 207 (2). pp. 193-205. ISSN 1073-449X DOI: https://doi.org/10.1164/rccm.202201-0144OC

Thompson, JA; Davey, C; Fielding, K; Hargreaves, JR; Hayes, RJ; (2018) Robust analysis of stepped wedge trials using cluster-level summaries within periods. Statistics in medicine, 37 (16). pp. 2487-2500. ISSN 0277-6715 DOI: https://doi.org/10.1002/sim.7668

Thompson, JA; Hemming, K; Forbes, A; Fielding, K; Hayes, R; (2020) Comparison of small-sample standard-error corrections for generalised estimating equations in stepped wedge cluster randomised trials with a binary outcome: A simulation study. Statistical Methods in Medical Research, 30 (2). pp. 425-439. ISSN 0962-2802 DOI: https://doi.org/10.1177/0962280220958735

Thompson, Jennifer A; Fielding, Katherine L; Davey, Calum; Aiken, Alexander M; Hargreaves, James R; Hayes, Richard J; (2017) Bias and inference from misspecified mixed-effect models in stepped wedge trial analysis. Statistics in medicine, 36 (23). pp. 3670-3682. ISSN 0277-6715 DOI: https://doi.org/10.1002/sim.7348

Thompson, Jennifer A; Fielding, Katherine; Hargreaves, James; Copas, Andrew; (2017) The optimal design of stepped wedge trials with equal allocation to sequences and a comparison to other trial designs. Clinical trials (London, England), 14 (6). pp. 639-647. ISSN 1740-7745 DOI: https://doi.org/10.1177/1740774517723921

Thompson, Jennifer A; Francis, Suzanna C; (2021) Better Evidence for Programmatic Approaches to Routine Syphilis Testing Among Men Living With Human Immunodeficiency Virus: Does a Stepped Wedge Trial Provide the Answer? Clinical Infectious Diseases, 74 (5). pp. 854-856. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciab585

Thompson, Jennifer A; Kityo, Cissy; Dunn, David; Hoppe, Anne; Ndashimye, Emmanuel; Hakim, James; Kambugu, Andrew; van Oosterhout, Joep J; Arribas, Jose; Mugyenyi, Peter; +3 more... Walker, A Sarah; Paton, Nicholas I; Europe–Africa Research Network for Evaluation of Second-line The; (2018) Evolution of Protease Inhibitor Resistance in Human Immunodeficiency Virus Type 1 Infected Patients Failing Protease Inhibitor Monotherapy as Second-line Therapy in Low-income Countries: An Observational Analysis Within the EARNEST Randomized Trial. Clinical infectious diseases, 68 (7). pp. 1184-1192. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciy589

Thompson, Jennifer A; Leurent, Baptiste; Nash, Stephen; Moulton, Lawrence H; Hayes, Richard J; (2023) Cluster randomized controlled trial analysis at the cluster level: The clan command. The Stata journal, 23 (3). pp. 754-773. ISSN 1536-867X DOI: https://doi.org/10.1177/1536867X231196294

Thompson, Jennifer A; Leyrat, Clemence; Fielding, Katherine L; Hayes, Richard J; (2022) Cluster randomised trials with a binary outcome and a small number of clusters: comparison of individual and cluster level analysis method. BMC Medical Research Methodology, 22 (1). 222-. ISSN 1471-2288 DOI: https://doi.org/10.1186/s12874-022-01699-2

Thompson, Jennifer; Davey, Calum; Hayes, Richard; Hargreaves, James; Fielding, Katherine; (2019) swpermute: Permutation tests for Stepped-Wedge Cluster-Randomised Trials. The Stata Journal, 19 (4). pp. 803-819. ISSN 1097-8879 DOI: https://doi.org/10.1177/1536867X19893624

Arenas-Pinto, A; Thompson, J; Musoro, G; Musana, H; Lugemwa, A; Kambugu, A; Mweemba, A; Walker, AS; Paton, N; Team., FTET; (2015) Peripheral neuropathy at first-line failure and on second-line in sub-Saharan Africa. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/4646753 Full text not available from this repository.

Davey, C; Thompson, JA; (2015) Assessing sensitivity to assumptions in mixed effects analyses of stepped-wedge trials. [Conference or Workshop Item] https://doi.org/10.1186/1745-6215-16-s2-o46 Full text not available from this repository.

Hakim, J; Thompson, J; Kityo, C; Walker, AS; van Oosterhout, JJ; Hoppe, A; Kambugu, A; Mugyenyi, P; Paton, N; Team., FTET; (2015) Second-line treatment in sub-Saharan Africa: week 144 follow-up of the EARNEST trial. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/4646749 Full text not available from this repository.

Kambugu, A; Thompson, J; Hakim, J; Tumukunde, D; van Oosterhout, JJ; Hoppe, A; Kwobah, C; Walker, AS; Paton, N; Team., FTET; (2015) Neurocognitive function in patients failing first-line ART in Africa and responses to second-line. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/4646732 Full text not available from this repository.

Kityo, C; Walker, AS; Nankya, I; Hoppe, A; Thompson, J; Bertagnolio, S; Easterbrook, PJ; Mugyenyi, P; Paton, N; Team., FTET; (2015) Differences in Resistance Mutations in Non-B Subtypes at First-line Failure in Africa. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/4646748 Full text not available from this repository.

Paton, N; Thompson, J; Bagenda, L; Hakim, J; van Oosterhout, JJ; Kambugu, A; Hoppe, A; Walker, AS; Team., FTET; (2015) Impact of NRTI Cross-Resistance on Second-line PI + NRTI Therapy Outcomes in Africa. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/4646743 Full text not available from this repository.

Thompson, J; Fielding, K; Hargreaves, J; Copas, A; (2015) Considering the design effect for the stepped wedge trial: what can it tell us? [Conference or Workshop Item] https://doi.org/10.1186/1745-6215-16-s2-o45 Full text not available from this repository.

Thompson, JA; Davey, C; Fielding, K; Hargreaves, J; Hayes, RJ; (2016) A reanalysis of the Brazil XpertMTB/RIF stepped wedge trial using a novel cluster summary analysis method. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/4646727 Full text not available from this repository.

Thompson, JA; Fielding, K; Hargreaves, J; Copas, A; (2017) The optimal design of the stepped wedge trial and a comparison to other trial designs. [Conference or Workshop Item] https://doi.org/10.1186/s13063-017-1902-y Full text not available from this repository.

Thompson, JA; Fielding, KL; Davey, C; Aiken, AM; Hargreaves, JR; Hayes, RJ; (2016) Implications of Misspecifed Mixed Effect Models in Stepped Wedge Trial Analysis: How Wrong Can It Be? [Conference or Workshop Item] https://doi.org/10.1186/s13063-016-1436-8 Full text not available from this repository.

Thompson, JA; Kityo, C; Walker, AS; Hakim, J; van Oosterhout, JJ; Siika, A; Mweemba, A; van Den Eede, P; Dunn, DT; Paton, N; +1 more... , ForTheEarnestTrialTeam; (2016) Effect of PI Resistance Mutations on Viral Load in Patients on PI Monotherapy. [Conference or Workshop Item] https://researchonline.lshtm.ac.uk/id/eprint/4646744 Full text not available from this repository.