Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set. av Matthew Hall, Mark Woolhouse, Andrew Rambaut

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Correction: MERS-CoV spillover at the camel-human interface av Gytis Dudas, Luiz Max Carvalho, Andrew Rambaut, Trevor Bedford

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MERS-CoV spillover at the camel-human interface av Gytis Dudas, Luiz Max Carvalho, Andrew Rambaut, Trevor Bedford

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Relaxed phylogenetics and dating with confidence. av Alexei J Drummond, Simon Y W Ho, Matthew J Phillips, Andrew Rambaut

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Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences av Áine O’Toole, Oliver G. Pybus, Michael E. Abram, Elizabeth J. Kelly, Andrew Rambaut

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Reconstructing Geographical Movements and Host Species Transitions of Foot-and-Mouth Disease Virus Serotype SAT 2 av Matthew D. Hall, Nick J. Knowles, Jemma Wadsworth, Andrew Rambaut, Mark E. J. Woolhouse

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Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. av J Joukje Siebenga, Philippe Lemey, Sergei L Kosakovsky Pond, Andrew Rambaut, Harry Vennema, Marion Koopmans

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The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. av John Archer, Andrew Rambaut, Bruce E Taillon, P Richard Harrigan, Marilyn Lewis, David L Robertson

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Phylogenetic Analysis of a Human Isolate from the 2000 Israel West Nile virus Epidemic av Thomas Briese, Andrew Rambaut, Melissa Pathmajeyan, Jihad Bishara, Miriam Weinberger, Silvio Pitlik, W. Ian Lipkin

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Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination. av Kathryn Campbell, Robert J Gifford, Joshua Singer, Verity Hill, Aine O'Toole, Andrew Rambaut, Katie Hampson, Kirstyn Brunker

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Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak av Simon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey

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Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. av Philippe Lemey, Sergei L Kosakovsky Pond, Alexei J Drummond, Oliver G Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut

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Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. av Gareth J Hughes, Esther Fearnhill, David Dunn, Samantha J Lycett, Andrew Rambaut, Andrew J Leigh Brown, UK HIV Drug Resistance Collaboration

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BEAST 2: a software platform for Bayesian evolutionary analysis. av Remco Bouckaert, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A Suchard, Andrew Rambaut, Alexei J Drummond

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The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. av Bram Vrancken, Andrew Rambaut, Marc A Suchard, Alexei Drummond, Guy Baele, Inge Derdelinckx, Eric Van Wijngaerden, Anne-Mieke Vandamme, Kristel Van Laethem, Philippe Lemey

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Integrating influenza antigenic dynamics with molecular evolution av Trevor Bedford, Marc A Suchard, Philippe Lemey, Gytis Dudas, Victoria Gregory, Alan J Hay, John W McCauley, Colin A Russell, Derek J Smith, Andrew Rambaut

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

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Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building av Martha I. Nelson, James O. Lloyd-Smith, Lone Simonsen, Andrew Rambaut, Edward C. Holmes, Gerardo Chowell, Mark A. Miller, David J. Spiro, Bryan Grenfell, Cécile Viboud

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Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting. av Hervé Bourhy, Emmanuel Nakouné, Matthew Hall, Pierre Nouvellet, Anthony Lepelletier, Chiraz Talbi, Laurence Watier, Edward C Holmes, Simon Cauchemez, Philippe Lemey, Christl A Donnelly, Andrew Rambaut

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Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus av Matthew Cotten, Tommy T. Lam, Simon J. Watson, Anne L. Palser, Velislava Petrova, Paul Grant, Oliver G. Pybus, Andrew Rambaut, Yi Guan, Deenan Pillay, Paul Kellam, Eleni Nastouli

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