Didelot, Xavier; Franceschi, Vinicius; Frost, Simon DW; Dennis, Ann; Volz, Erik M; (2023) Model design for nonparametric phylodynamic inference and applications to pathogen surveillance. Virus evolution, 9 (1). vead028-. ISSN 2057-1577 DOI: https://doi.org/10.1093/ve/vead028

Nabakooza, Grace; Pastusiak, Andrzej; Kateete, David Patrick; Lutwama, Julius Julian; Kitayimbwa, John Mulindwa; Frost, Simon David William; (2022) Whole-genome analysis to determine the rate and patterns of intra-subtype reassortment among influenza type-A viruses in Africa. Virus Evolution, 8 (1). veac005-. DOI: https://doi.org/10.1093/ve/veac005

Stubbs, Samuel CB; Blacklaws, Barbara A; Yohan, Benediktus; Yudhaputri, Frilasita A; Hayati, Rahma F; Schwem, Brian; Salvaña, Edsel M; Destura, Raul V; Lester, James S; Myint, Khin S; +2 more... Sasmono, R Tedjo; Frost, Simon DW; (2020) Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia. VIROLOGY JOURNAL, 17 (1). 24-. ISSN 1743-422X DOI: https://doi.org/10.1186/s12985-020-1294-6

Stubbs, Samuel CB; Johar, Edison; Yudhaputri, Frilasita A; Yohan, Benediktus; Santoso, Marsha S; Hayati, Rahma F; Denis, Dionisius; Blacklaws, Barbara A; Powers, Ann M; Sasmono, R Tedjo; +2 more... Myint, Khin Saw Aye; Frost, Simon DW; (2020) An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia. PLOS NEGLECTED TROPICAL DISEASES, 14 (12). e0008934-. ISSN 1935-2735 DOI: https://doi.org/10.1371/journal.pntd.0008934

Tonkin-Hill, Gerry; MacAlasdair, Neil; Ruis, Christopher; Weimann, Aaron; Horesh, Gal; Lees, John A; Gladstone, Rebecca A; Lo, Stephanie; Beaudoin, Christopher; Floto, R Andres; +4 more... Frost, Simon DW; Corander, Jukka; Bentley, Stephen D; Parkhill, Julian; (2020) Producing polished prokaryotic pangenomes with the Panaroo pipeline. GENOME BIOLOGY, 21 (1). 180-. ISSN 1474-760X DOI: https://doi.org/10.1186/s13059-020-02090-4

Wells, Konstans; Lurgi, Miguel; Collins, Brendan; Lucini, Biagio; Kao, Rowland R; Lloyd, Alun L; Frost, Simon DW; Gravenor, Mike B; (2020) Disease control across urban-rural gradients. JOURNAL OF THE ROYAL SOCIETY INTERFACE, 17 (173). 20200775-. ISSN 1742-5689 DOI: https://doi.org/10.1098/rsif.2020.0775

Xiang, Fei; Dearlove, Bethany; Frost, Simon; (2019) genieR: An R package for inference of demographic history of phylogenies. The Journal of Open Source Software, 4 (33). p. 634. DOI: https://doi.org/10.21105/joss.00634

Ntale, Roman Saba; Rutayisire, Gad; Mujyarugamba, Pierre; Shema, Eliah; Greatorex, Jane; Frost, Simon David William; Kaleebu, Pontiano; (2018) HIV seroprevalence, self-reported STIs and associated risk factors among men who have sex with men: a cross-sectional study in Rwanda, 2015. Sexually transmitted infections, 95 (1). pp. 71-74. ISSN 1368-4973 DOI: https://doi.org/10.1136/sextrans-2017-053311

Heesterbeek, Hans; Anderson, Roy M; Andreasen, Viggo; Bansal, Shweta; De Angelis, Daniela; Dye, Chris; Eames, Ken TD; Edmunds, W John; Frost, Simon DW; Funk, Sebastian; +13 more... Hollingsworth, T Deirdre; House, Thomas; Isham, Valerie; Klepac, Petra; Lessler, Justin; Lloyd-Smith, James O; Metcalf, C Jessica E; Mollison, Denis; Pellis, Lorenzo; Pulliam, Juliet RC; Roberts, Mick G; Viboud, Cecile; Isaac Newton Institute IDD Collaboration; (2015) Modeling infectious disease dynamics in the complex landscape of global health. Science (New York, NY), 347 (6227). aaa4339-. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aaa4339 Full text not available from this repository.

Eames, K; Bansal, S; Frost, S; Riley, S; (2014) Six challenges in measuring contact networks for use in modelling. Epidemics, 10. pp. 72-77. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.08.006

Jombart, Thibaut; Aanensen, David M; Baguelin, Marc; Birrell, Paul; Cauchemez, Simon; Camacho, Anton; Colijn, Caroline; Collins, Caitlin; Cori, Anne; Didelot, Xavier; +13 more... Fraser, Christophe; Frost, Simon; Hens, Niel; Hugues, Joseph; Höhle, Michael; Opatowski, Lulla; Rambaut, Andrew; Ratmann, Oliver; Soubeyrand, Samuel; Suchard, Marc A; Wallinga, Jacco; Ypma, Rolf; Ferguson, Neil; (2014) OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, 7 (100). pp. 28-34. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2014.04.003

McCreesh, Nicky; Copas, Andrew; Seeley, Janet; Johnston, Lisa G; Sonnenberg, Pam; Hayes, Richard J; Frost, Simon DW; White, Richard G; (2013) Respondent driven sampling: determinants of recruitment and a method to improve point estimation. PloS one, 8 (10). e78402-. ISSN 1932-6203 DOI: https://doi.org/10.1371/journal.pone.0078402

McCreesh, Nicky; Frost, Simon DW; Seeley, Janet; Katongole, Joseph; Tarsh, Matilda N; Ndunguse, Richard; Jichi, Fatima; Lunel, Natasha L; Maher, Dermot; Johnston, Lisa G; +4 more... Sonnenberg, Pam; Copas, Andrew J; Hayes, Richard J; White, Richard G; (2012) Evaluation of respondent-driven sampling. Epidemiology (Cambridge, Mass), 23 (1). pp. 138-147. ISSN 1044-3983 DOI: https://doi.org/10.1097/EDE.0b013e31823ac17c

White, Richard G; Lansky, Amy; Goel, Sharad; Wilson, David; Hladik, Wolfgang; Hakim, Avi; Frost, Simon DW; (2012) Respondent driven sampling--where we are and where should we be going? Sexually transmitted infections, 88 (6). pp. 397-399. ISSN 1368-4973 DOI: https://doi.org/10.1136/sextrans-2012-050703

McCreesh, Nicky; Johnston, Lisa G; Copas, Andrew; Sonnenberg, Pam; Seeley, Janet; Hayes, Richard J; Frost, Simon DW; White, Richard G; (2011) Evaluation of the role of location and distance in recruitment in respondent-driven sampling. International journal of health geographics, 10 (1). 56-. ISSN 1476-072X DOI: https://doi.org/10.1186/1476-072X-10-56