HIV PANGEA II: Renewal of phyogenetics and networks for the generalized HIV epidemics in Africa

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  • 2023

    Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

    Tsui, J. L-H., McCrone, J. T., Lambert, B., Bajaj, S., Inward, R. P. D., Bosetti, P., Pena, R. E., Tegally, H., Hill, V., Zarebski, A. E., Peacock, T. P., Liu, L., Wu, N., Davis, M., Bogoch, I. I., Khan, K., Kall, M., Abdul Aziz, N. I. B., Colquhoun, R., O'Toole, Á., & 20 othersJackson, B., Dasgupta, A., Wilkinson, E., de Oliveira, T., Connor, T. R., Loman, N. J., Colizza, V., Fraser, C., Volz, E., Ji, X., Gutierrez, B., Chand, M., Dellicour, S., Cauchemez, S., Raghwani, J., Suchard, M. A., Lemey, P., Rambaut, A., Pybus, O. G. & Kraemer, M. U. G., 21 Jul 2023, In: Science (New York, N.Y.). 381, 6655, p. 336-343 8 p.

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  • 2022

    Genomics-informed outbreak investigations of SARS-CoV-2 using civet

    O'Toole, Á., Hill, V., Jackson, B., Dewar, R., Sahadeo, N., Colquhoun, R., Rooke, S., McCrone, J. T., Duggan, K., McHugh, M. P., Nicholls, S. M., Poplawski, R., Aanensen, D., Holden, M., Connor, T., Loman, N., Goodfellow, I., Carrington, C. V. F., Templeton, K. & Rambaut, A., 9 Dec 2022, In: PLOS Global Public Health . 2, 12, 15 p., e0000704.

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  • Context-specific emergence and growth of the SARS-CoV-2 Delta variant

    McCrone, J. T., Hill, V., Bajaj, S., Pena, R. E., Lambert, B. C., Inward, R., Bhatt, S., Volz, E., Ruis, C., Dellicour, S., Baele, G., Zarebski, A. E., Sadilek, A., Wu, N., Schneider, A., Ji, X., Raghwani, J., Jackson, B., Colquhoun, R., O'Toole, Á., & 20 othersPeacock, T. P., Twohig, K., Thelwall, S., Dabrera, G., Myers, R., Faria, N. R., Huber, C., Bogoch, I. I., Khan, K., du Plessis, L., Barrett, J. C., Aanensen, D. M., Barclay, W. S., Chand, M., Connor, T., Loman, N. J., Suchard, M. A., Pybus, O. G., Rambaut, A. & Kraemer, M. U. G., 6 Oct 2022, In: Nature. 610, 7930, p. 154-160 6 p.

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  • The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

    Hill, V., Du Plessis, L., Peacock, T. P., Aggarwal, D., Colquhoun, R., Carabelli, A. M., Ellaby, N., Gallagher, E., Groves, N., Jackson, B., McCrone, J. T., O’Toole, Á., Price, A., Sanderson, T., Scher, E., Southgate, J., Volz, E., Barclay, W. S., Barrett, J. C., Chand, M., & 9 othersConnor, T., Goodfellow, I., Gupta, R. K., Harrison, E. M., Loman, N., Myers, R., Robertson, D. L., Pybus, O. G. & Rambaut, A., 21 Sept 2022, In: Virus Evolution. 8, 2, 13 p., veac080.

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  • 2021

    Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

    Volz, E. M., Mishra, S., Chand, M., Barrett, J., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O'Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S., Jorgensen, D., & 14 othersMyers, R., Hill, V., Jackson, D. K., Gaythorpe, K., Groves, N., Sillitoe, J., Kwiatkowski, D. P., Flaxman, S., Ratmann, O., Bhatt, S., Hopkins, S., Gandy, A., Rambaut, A. & Ferguson, N. M., 25 Mar 2021, In: Nature. 593, p. 266-269 4 p.

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  • 2020

    Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction

    Gill, M. S., Lemey, P., Suchard, M. A., Rambaut, A. & Baele, G., 26 Feb 2020, In: Molecular Biology and Evolution. msaa047.

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  • 2019

    Bayesian inference of evolutionary histories under time-dependent substitution rates

    Membrebe, J. V., Suchard, M. A., Rambaut, A., Baele, G. & Lemey, P., 19 Apr 2019, (E-pub ahead of print) In: Molecular Biology and Evolution. 11 p.

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