Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2.

Autor: Philippe Lemey, Andrew Rambaut, Trevor Bedford, Nuno Faria, Filip Bielejec, Guy Baele, Colin A Russell, Derek J Smith, Oliver G Pybus, Dirk Brockmann, Marc A Suchard

Publikováno v: PLoS Pathogens, Vol 10, Iss 2, p e1003932 (2014)

Information on global human movement patterns is central to spatial epidemiological models used to predict the behavior of influenza and other infectious diseases. Yet it remains difficult to test which modes of dispersal drive pathogen spread at var

Externí odkaz: https://doaj.org/article/b1ff4becd42c480cb05214b14b6d3fcf

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Autor: Kilian Stoecker, Chantal B.E.M. Reusken, Stephen F. Schaffner, Marion Koopmans, Sarah M. Winnicki, Augustine Goba, My V. T. Phan, Lucy Thorne, Michael R. Wiley, Simon Dellicour, Andrew Rambaut, James Qu, Fatorma K. Bolay, Christian T. Happi, Stephen K. Gire, Oliver G. Pybus, Jeffrey R. Kugelman, Bernice Dahn, Pardis C. Sabeti, Marc A. Suchard, Gytis Dudas, Kristian G. Andersen, Gustavo Palacios, Mohamed A. Vandi, Simon J. Watson, Saskia L. Smits, Amadou A. Sall, Isatta Wurie, Miles W. Carroll, Andrew J. Tatem, David A. Matthews, Georgios Pollakis, Sahr M. Gevao, George F. Gao, Philippe Lemey, Filip Bielejec, Shannon L.M. Whitmer, Roman Wölfel, Nuno R. Faria, Jonathan D'ambrozio, Jason T. Ladner, Christine M. Malboeuf, Danny Asogun, Christian B. Matranga, Christophe Fraser, N’Faly Magassouba, Guy Baele, Luke W. Meredith, Robert F. Garry, Ekaete Alice Tobin, Etienne Simon-Loriere, Pierre Formenty, Sophie Duraffour, Jens H. Kuhn, Edward C. Holmes, Paul Kellam, Ousmane Faye, Brima Kargbo, Kendra West, Sarah L Caddy, Dhamari Naidoo, Stuart T. Nichol, Rachel Sealfon, Joshua Quick, Shirlee Wohl, Andreas Gnirke, Matthew Cotten, Mariano Sanchez-Lockhart, Donald S. Grant, Nicholas J. Loman, Trevor Bedford, Antonino Di Caro, Daniel J. Park, Julian A. Hiscox, Sylvia O. Blyden, Stephan Günther, Lawrence Fakoli, Susan D. Pas, Suzanne Mate, Armando Arias, Ian Goodfellow, Bart L. Haagmans, Adrianne Gladden-Young, Joseph W. Diclaro, Nathan L. Yozwiak, Merle L. Gilbert, Umaru Jah, Sakoba Keita, Michael J. Elmore, Jia Lu, John S. Schieffelin, Ute Ströher, Tolbert Nyenswah, Luiz Max Carvalho, Boubacar Diallo, Di Liu

Publikováno v: Dudas, G & et al. 2017, ' Virus genomes reveal factors that spread and sustained the Ebola epidemic ', Nature, vol. 544, no. 7650, pp. 309-315 . https://doi.org/10.1038/nature22040
NATURE
Nature: international weekly journal of science, 544(7650), 309-315
Dudas, G & et al. 2017, ' Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic ' Nature, vol 544, no. 7650, pp. 309-315 . DOI: 10.1038/nature22040
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Nature, 544(7650), 309-315. Nature Publishing Group
Nature
Dudas, G, Carvalho, L M, Bedford, T, Tatem, A J, Baele, G, Faria, N R, Park, D J, Ladner, JT, Arias, A, Asogun, D, Bielejec, F, Caddy, S L, Cotten, M, D'Ambrozio, J, Dellicour, S, Di Caro, A, Diclaro II, J W, Duraffour, S, Elmore, M J, Fakoli, L S, Faye, O, Gilbert, M L, Gevao, S M, Gire, S K, Gladden-Young, A, Gnirke, A, Goba, A, Grant, D S, Haagmans, B L, Hiscox, J A, Jah, U, Kugelman, JR, Liu, D, Lu, J, Malboeuf, C M, Mate, S, Matthews, D A, Matranga, C B, Meredith, L W, Qu, J, Quick, J, Pas, S D, Phan, M V T, Pollakis, G, Reusken, C B, Sanchez-Lockhart, M, Schaffner, S F, Schieffelin, JS, Sealfon, R S, Simon-Loriere, E, Smits, S L, Stoecker, K, Thorne, L, Tobin, E A, Vandi, MA, Watson, S J, West, K, Whitmer, SL M, Wiley, M R, Winnicki, SM, Wohl, S, Wölfel, R, Yozwiak, N L, Andersen, K G, Blyden, S O, Bolay, F K, Carroll, M W, Dahn, B, Diallo, B, Formenty, P, Fraser, C, Gao, G F, Garry, R F, Goodfellow, I, Günther, S, Happi, C, Holmes, E C, Kargbo, B, Keïta, S, Kellam, P, Koopmans, M P G, Kuhn, JH, Loman, N, Magassouba, NF, Naidoo, D, Nichol, ST, Nyenswah, T, Palacios, GF, Pybus, O G, Sabeti, P C, Sall, A A, Ströher, U, Wurie, I, Suchard, M A, Lemey, P & Rambaut, A 2017, ' Virus genomes reveal factors that spread and sustained the Ebola epidemic ', Nature, vol. 544, pp. 309–315 . https://doi.org/10.1038/nature22040
Nature, vol 544, iss 7650

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genome

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ac064faa30fb3fbc4403ce6eff2437ff
https://research-information.bris.ac.uk/en/publications/974de1b8-66ef-4dfa-a852-4a9e498cc43d

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

Autor: Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno Faria, Daniel J. Park, Jason Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah Caddy, Matt Cotten, Jonathan Dambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Mike Elmore, Lawrence Fakoli, Merle Gilbert, Sahr M. Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart Haagmans, Julian A. Hiscox, Umaru Jah, Brima Kargbo, Jeffrey Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke Meredith, James Qu, Joshua Quick, Susan D. Pas, My VT Phan, Georgios Poliakis, Chantal Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete A. Tobin, Mohamed A. Vandi, Simon J. Watson, Kendra West, Shannon Whitmer, Michael R. Wiley, Sarah M. Winnicki, Shirlee Wohl, Roman Wölfel, Nathan L. Yozwiak, Kristian G. Andersen, Sylvia Blyden, Fatorma Bolay, Miles Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian Happi, Edward C Holmes, Paul Kellam, Marion P.G. Koopmans, Nicholas J. Loman, N’Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo Palacios, Oliver G Pybus, Pardis Sabeti, Amadou Sall, Keïta Sakoba, Ute Ströeher, Isatta Wurie, Marc A Suchard, Philippe Lemey, Andrew Rambaut

SummaryThe 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude, duration and impact. Extensive collaborative sequencing projects have produced a large collection of over 1600 Ebola virus genomes, representing over

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2f8b2666eb382e8f03bd34a03a77f82e

Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation

Autor: Filip Bielejec, Philippe Lemey, Marc A. Suchard, Guy Baele

Publikováno v: Microbial genomics, vol 2, iss 6
Microbial Genomics

Phylodynamic reconstructions rely on a measurable molecular footprint of epidemic processes in pathogen genomes. Identifying the factors that govern the tempo and mode by which these processes leave a footprint in pathogen genomes represents an impor

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1ebfdd85ea244ed0bb9e60515071d98a
https://escholarship.org/uc/item/8gf3085r

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

Autor: Filip Bielejec, Vladimir N. Minin, Philippe Lemey, Sergei L. Kosakovsky Pond, Marc A. Suchard

Publikováno v: Bioinformatics; Vol 28

Motivation: Statistical methods for comparing relative rates of synonymous and non-synonymous substitutions maintain a central role in detecting positive selection. To identify selection, researchers often estimate the ratio of these relative rates (

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::96e5b6d6875ebfe1bfaea7cc0cc79cdd
https://doi.org/10.1093/bioinformatics/bts580