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RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

Wellcome open research

Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J.
PMID: 30345380
Wellcome Open Res. 2018 Jul 30;3:93. doi: 10.12688/wellcomeopenres.14694.1. eCollection 2018.

Identifying structure in collections of sequence data sets remains a common problem in genomics. hierBAPS, a popular algorithm for identifying population structure in haploid genomes, has previously only been available as a MATLAB binary. We provide an R implementation...

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Tonkin-Hill G, Lees JA, Bentley SD, et al. RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome Open Res. 2018;3:93doi: 10.12688/wellcomeopenres.14694.1.
Tonkin-Hill, G., Lees, J. A., Bentley, S. D., Frost, S. D. W., & Corander, J. (2018). RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome open research, 393. https://doi.org/10.12688/wellcomeopenres.14694.1
Tonkin-Hill, Gerry, et al. "RhierBAPS: An R implementation of the population clustering algorithm hierBAPS." Wellcome open research vol. 3 (2018): 93. doi: https://doi.org/10.12688/wellcomeopenres.14694.1
Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J. RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome Open Res. 2018 Jul 30;3:93. doi: 10.12688/wellcomeopenres.14694.1. eCollection 2018. PMID: 30345380; PMCID: PMC6178908.
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Epidemiological metrics and benchmarks for a transition in the HIV epidemic.

PLoS medicine

Ghys PD, Williams BG, Over M, Hallett TB, Godfrey-Faussett P.
PMID: 30359372
PLoS Med. 2018 Oct 25;15(10):e1002678. doi: 10.1371/journal.pmed.1002678. eCollection 2018 Oct.

Peter Godfrey-Faussett and colleagues present six epidemiological metrics for tracking progress in reducing the public health threat of HIV.

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Ghys PD, Williams BG, Over M, et al. Epidemiological metrics and benchmarks for a transition in the HIV epidemic. PLoS Med. 2018;15(10):e1002678doi: 10.1371/journal.pmed.1002678.
Ghys, P. D., Williams, B. G., Over, M., Hallett, T. B., & Godfrey-Faussett, P. (2018). Epidemiological metrics and benchmarks for a transition in the HIV epidemic. PLoS medicine, 15(10), e1002678. https://doi.org/10.1371/journal.pmed.1002678
Ghys, Peter D, et al. "Epidemiological metrics and benchmarks for a transition in the HIV epidemic." PLoS medicine vol. 15,10 (2018): e1002678. doi: https://doi.org/10.1371/journal.pmed.1002678
Ghys PD, Williams BG, Over M, Hallett TB, Godfrey-Faussett P. Epidemiological metrics and benchmarks for a transition in the HIV epidemic. PLoS Med. 2018 Oct 25;15(10):e1002678. doi: 10.1371/journal.pmed.1002678. eCollection 2018 Oct. PMID: 30359372; PMCID: PMC6201869.
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Emerging implications of policies on malaria treatment: genetic changes in the .

BMJ global health

Okell LC, Reiter LM, Ebbe LS, Baraka V, Bisanzio D, Watson OJ, Bennett A, Verity R, Gething P, Roper C, Alifrangis M.
PMID: 30397515
BMJ Glob Health. 2018 Oct 19;3(5):e000999. doi: 10.1136/bmjgh-2018-000999. eCollection 2018.

Artemether-lumefantrine (AL) and artesunate-amodiaquine (AS-AQ) are the most commonly used artemisinin-based combination therapies (ACT) for treatment of

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Okell LC, Reiter LM, Ebbe LS, et al. Emerging implications of policies on malaria treatment: genetic changes in the . BMJ Glob Health. 2018;3(5):e000999doi: 10.1136/bmjgh-2018-000999.
Okell, L. C., Reiter, L. M., Ebbe, L. S., Baraka, V., Bisanzio, D., Watson, O. J., Bennett, A., Verity, R., Gething, P., Roper, C., & Alifrangis, M. (2018). Emerging implications of policies on malaria treatment: genetic changes in the . BMJ global health, 3(5), e000999. https://doi.org/10.1136/bmjgh-2018-000999
Okell, Lucy C, et al. "Emerging implications of policies on malaria treatment: genetic changes in the ." BMJ global health vol. 3,5 (2018): e000999. doi: https://doi.org/10.1136/bmjgh-2018-000999
Okell LC, Reiter LM, Ebbe LS, Baraka V, Bisanzio D, Watson OJ, Bennett A, Verity R, Gething P, Roper C, Alifrangis M. Emerging implications of policies on malaria treatment: genetic changes in the . BMJ Glob Health. 2018 Oct 19;3(5):e000999. doi: 10.1136/bmjgh-2018-000999. eCollection 2018. PMID: 30397515; PMCID: PMC6202998.
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Erratum to: Robust Design for Coalescent Model Inference.

Systematic biology

[No authors listed]
PMID: 31028695
Syst Biol. 2019 Nov 01;68(6):1062. doi: 10.1093/sysbio/syz018.

No abstract available.

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Erratum to: Robust Design for Coalescent Model Inference. Syst Biol. 2019;68(6):1062doi: 10.1093/sysbio/syz018.
(2019). Erratum to: Robust Design for Coalescent Model Inference. Systematic biology, 68(6), 1062. https://doi.org/10.1093/sysbio/syz018
"Erratum to: Robust Design for Coalescent Model Inference." Systematic biology vol. 68,6 (2019): 1062. doi: https://doi.org/10.1093/sysbio/syz018
Erratum to: Robust Design for Coalescent Model Inference. Syst Biol. 2019 Nov 01;68(6):1062. doi: 10.1093/sysbio/syz018. PMID: 31028695.
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Strengthening primary HIV prevention: better use of data to improve programmes, develop strategies and evaluate progress.

Journal of the International AIDS Society

Hargreaves JR, Auerbach JD, Hensen B, Johnson S, Gregson S.
PMID: 32602656
J Int AIDS Soc. 2020 Jun;23:e25538. doi: 10.1002/jia2.25538.

No abstract available.

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Hargreaves JR, Auerbach JD, Hensen B, et al. Strengthening primary HIV prevention: better use of data to improve programmes, develop strategies and evaluate progress. J Int AIDS Soc. 2020;23:e25538doi: 10.1002/jia2.25538.
Hargreaves, J. R., Auerbach, J. D., Hensen, B., Johnson, S., & Gregson, S. (2020). Strengthening primary HIV prevention: better use of data to improve programmes, develop strategies and evaluate progress. Journal of the International AIDS Society, 23e25538. https://doi.org/10.1002/jia2.25538
Hargreaves, James R, et al. "Strengthening primary HIV prevention: better use of data to improve programmes, develop strategies and evaluate progress." Journal of the International AIDS Society vol. 23 (2020): e25538. doi: https://doi.org/10.1002/jia2.25538
Hargreaves JR, Auerbach JD, Hensen B, Johnson S, Gregson S. Strengthening primary HIV prevention: better use of data to improve programmes, develop strategies and evaluate progress. J Int AIDS Soc. 2020 Jun;23:e25538. doi: 10.1002/jia2.25538. PMID: 32602656; PMCID: PMC7325501.
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Corrigendum: Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages.

Microbial genomics

Yahara K, Nakayama SI, Shimuta K, Lee KI, Morita M, Kawahata T, Kuroki T, Watanabe Y, Ohya H, Yasuda M, Deguchi T, Didelot X, Ohnishi M.
PMID: 30265235
Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000215.

No abstract available.

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Yahara K, Nakayama SI, Shimuta K, et al. Corrigendum: Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages. Microb Genom. 2018;4(9)doi: 10.1099/mgen.0.000215.
Yahara, K., Nakayama, S. I., Shimuta, K., Lee, K. I., Morita, M., Kawahata, T., Kuroki, T., Watanabe, Y., Ohya, H., Yasuda, M., Deguchi, T., Didelot, X., & Ohnishi, M. (2018). Corrigendum: Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages. Microbial genomics, 4(9), . https://doi.org/10.1099/mgen.0.000215
Yahara, Koji, et al. "Corrigendum: Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages." Microbial genomics vol. 4,9 (2018). doi: https://doi.org/10.1099/mgen.0.000215
Yahara K, Nakayama SI, Shimuta K, Lee KI, Morita M, Kawahata T, Kuroki T, Watanabe Y, Ohya H, Yasuda M, Deguchi T, Didelot X, Ohnishi M. Corrigendum: Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages. Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000215. PMID: 30265235; PMCID: PMC6202446.
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Epidemic Models of Contact Tracing: Systematic Review of Transmission Studies of Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome.

Computational and structural biotechnology journal

Kwok KO, Tang A, Wei VWI, Park WH, Yeoh EK, Riley S.
PMID: 30809323
Comput Struct Biotechnol J. 2019 Jan 26;17:186-194. doi: 10.1016/j.csbj.2019.01.003. eCollection 2019.

The emergence and reemergence of coronavirus epidemics sparked renewed concerns from global epidemiology researchers and public health administrators. Mathematical models that represented how contact tracing and follow-up may control Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome...

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Kwok KO, Tang A, Wei VWI, et al. Epidemic Models of Contact Tracing: Systematic Review of Transmission Studies of Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome. Comput Struct Biotechnol J. 2019;17:186-194doi: 10.1016/j.csbj.2019.01.003.
Kwok, K. O., Tang, A., Wei, V. W. I., Park, W. H., Yeoh, E. K., & Riley, S. (2019). Epidemic Models of Contact Tracing: Systematic Review of Transmission Studies of Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome. Computational and structural biotechnology journal, 17186-194. https://doi.org/10.1016/j.csbj.2019.01.003
Kwok, Kin On, et al. "Epidemic Models of Contact Tracing: Systematic Review of Transmission Studies of Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome." Computational and structural biotechnology journal vol. 17 (2019): 186-194. doi: https://doi.org/10.1016/j.csbj.2019.01.003
Kwok KO, Tang A, Wei VWI, Park WH, Yeoh EK, Riley S. Epidemic Models of Contact Tracing: Systematic Review of Transmission Studies of Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome. Comput Struct Biotechnol J. 2019 Jan 26;17:186-194. doi: 10.1016/j.csbj.2019.01.003. eCollection 2019. PMID: 30809323; PMCID: PMC6376160.
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The role of genetic sequencing and analysis in the polio eradication programme.

Virus evolution

Jorgensen D, Pons-Salort M, Shaw AG, Grassly NC.
PMID: 32782825
Virus Evol. 2020 May 20;6(2):veaa040. doi: 10.1093/ve/veaa040. eCollection 2020 Jul.

Genetic sequencing of polioviruses detected through clinical and environmental surveillance is used to confirm detection, identify their likely origin, track geographic patterns of spread, and determine the appropriate vaccination response. The critical importance of genetic sequencing and analysis to...

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Jorgensen D, Pons-Salort M, Shaw AG, et al. The role of genetic sequencing and analysis in the polio eradication programme. Virus Evol. 2020;6(2):veaa040doi: 10.1093/ve/veaa040.
Jorgensen, D., Pons-Salort, M., Shaw, A. G., & Grassly, N. C. (2020). The role of genetic sequencing and analysis in the polio eradication programme. Virus evolution, 6(2), veaa040. https://doi.org/10.1093/ve/veaa040
Jorgensen, David, et al. "The role of genetic sequencing and analysis in the polio eradication programme." Virus evolution vol. 6,2 (2020): veaa040. doi: https://doi.org/10.1093/ve/veaa040
Jorgensen D, Pons-Salort M, Shaw AG, Grassly NC. The role of genetic sequencing and analysis in the polio eradication programme. Virus Evol. 2020 May 20;6(2):veaa040. doi: 10.1093/ve/veaa040. eCollection 2020 Jul. PMID: 32782825; PMCID: PMC7409915.
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Systematic selection between age and household structure for models aimed at emerging epidemic predictions.

Nature communications

Pellis L, Cauchemez S, Ferguson NM, Fraser C.
PMID: 32060265
Nat Commun. 2020 Feb 14;11(1):906. doi: 10.1038/s41467-019-14229-4.

Numerous epidemic models have been developed to capture aspects of human contact patterns, making model selection challenging when they fit (often-scarce) early epidemic data equally well but differ in predictions. Here we consider the invasion of a novel directly...

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Pellis L, Cauchemez S, Ferguson NM, et al. Systematic selection between age and household structure for models aimed at emerging epidemic predictions. Nat Commun. 2020;11(1):906doi: 10.1038/s41467-019-14229-4.
Pellis, L., Cauchemez, S., Ferguson, N. M., & Fraser, C. (2020). Systematic selection between age and household structure for models aimed at emerging epidemic predictions. Nature communications, 11(1), 906. https://doi.org/10.1038/s41467-019-14229-4
Pellis, Lorenzo, et al. "Systematic selection between age and household structure for models aimed at emerging epidemic predictions." Nature communications vol. 11,1 (2020): 906. doi: https://doi.org/10.1038/s41467-019-14229-4
Pellis L, Cauchemez S, Ferguson NM, Fraser C. Systematic selection between age and household structure for models aimed at emerging epidemic predictions. Nat Commun. 2020 Feb 14;11(1):906. doi: 10.1038/s41467-019-14229-4. PMID: 32060265; PMCID: PMC7021781.
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Improving the quality of economic evaluation in health in low- and middle-income countries: where are we now?.

Journal of comparative effectiveness research

Wilkinson T, Chalkidou K.
PMID: 31558038
J Comp Eff Res. 2019 Oct;8(13):1041-1043. doi: 10.2217/cer-2019-0119. Epub 2019 Sep 27.

No abstract available.

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Wilkinson T, Chalkidou K. Improving the quality of economic evaluation in health in low- and middle-income countries: where are we now?. J Comp Eff Res. 2019;8(13):1041-1043doi: 10.2217/cer-2019-0119.
Wilkinson, T., & Chalkidou, K. (2019). Improving the quality of economic evaluation in health in low- and middle-income countries: where are we now?. Journal of comparative effectiveness research, 8(13), 1041-1043. https://doi.org/10.2217/cer-2019-0119
Wilkinson, Thomas, and Chalkidou, Kalipso. "Improving the quality of economic evaluation in health in low- and middle-income countries: where are we now?." Journal of comparative effectiveness research vol. 8,13 (2019): 1041-1043. doi: https://doi.org/10.2217/cer-2019-0119
Wilkinson T, Chalkidou K. Improving the quality of economic evaluation in health in low- and middle-income countries: where are we now?. J Comp Eff Res. 2019 Oct;8(13):1041-1043. doi: 10.2217/cer-2019-0119. Epub 2019 Sep 27. PMID: 31558038.
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Adoption and impact of non-pharmaceutical interventions for COVID-19.

Wellcome open research

Imai N, Gaythorpe KAM, Abbott S, Bhatia S, van Elsland S, Prem K, Liu Y, Ferguson NM.
PMID: 32529040
Wellcome Open Res. 2020 Apr 02;5:59. doi: 10.12688/wellcomeopenres.15808.1. eCollection 2020.

No abstract available.

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Imai N, Gaythorpe KAM, Abbott S, et al. Adoption and impact of non-pharmaceutical interventions for COVID-19. Wellcome Open Res. 2020;5:59doi: 10.12688/wellcomeopenres.15808.1.
Imai, N., Gaythorpe, K. A. M., Abbott, S., Bhatia, S., van Elsland, S., Prem, K., Liu, Y., & Ferguson, N. M. (2020). Adoption and impact of non-pharmaceutical interventions for COVID-19. Wellcome open research, 559. https://doi.org/10.12688/wellcomeopenres.15808.1
Imai, Natsuko, et al. "Adoption and impact of non-pharmaceutical interventions for COVID-19." Wellcome open research vol. 5 (2020): 59. doi: https://doi.org/10.12688/wellcomeopenres.15808.1
Imai N, Gaythorpe KAM, Abbott S, Bhatia S, van Elsland S, Prem K, Liu Y, Ferguson NM. Adoption and impact of non-pharmaceutical interventions for COVID-19. Wellcome Open Res. 2020 Apr 02;5:59. doi: 10.12688/wellcomeopenres.15808.1. eCollection 2020. PMID: 32529040; PMCID: PMC7255913.
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epicontacts: Handling, visualisation and analysis of epidemiological contacts.

F1000Research

Nagraj VP, Randhawa N, Campbell F, Crellen T, Sudre B, Jombart T.
PMID: 31240097
F1000Res. 2018 May 10;7:566. doi: 10.12688/f1000research.14492.2. eCollection 2018.

Epidemiological outbreak data is often captured in line list and contact format to facilitate contact tracing for outbreak control.

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Nagraj VP, Randhawa N, Campbell F, et al. epicontacts: Handling, visualisation and analysis of epidemiological contacts. F1000Res. 2018;7:566doi: 10.12688/f1000research.14492.2.
Nagraj, V. P., Randhawa, N., Campbell, F., Crellen, T., Sudre, B., & Jombart, T. (2018). epicontacts: Handling, visualisation and analysis of epidemiological contacts. F1000Research, 7566. https://doi.org/10.12688/f1000research.14492.2
Nagraj, V P, et al. "epicontacts: Handling, visualisation and analysis of epidemiological contacts." F1000Research vol. 7 (2018): 566. doi: https://doi.org/10.12688/f1000research.14492.2
Nagraj VP, Randhawa N, Campbell F, Crellen T, Sudre B, Jombart T. epicontacts: Handling, visualisation and analysis of epidemiological contacts. F1000Res. 2018 May 10;7:566. doi: 10.12688/f1000research.14492.2. eCollection 2018. PMID: 31240097; PMCID: PMC6572866.
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Showing 1 to 12 of 114 entries