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The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

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Genomic and epidemiological monitoring of yellow fever virus transmission potential

Author(s): N. R. Faria, M. U. G. Kraemer, S. C. Hill, J. Goes de Jesus, R. S. Aguiar, F. C. M. Iani, J. Xavier, J. Quick, L. du Plessis, S. Dellicour, J. Thézé, R. D. O. Carvalho, G. Baele, C.-H. Wu, P. P. Silveira, M. B. Arruda, M. A. Pereira, G. C. Pereira, J. Lourenço, U. Obolski, L. Abade, T. I. Vasylyeva, M. Giovanetti, D. Yi, D. J. Weiss, G. R. W. Wint, F. M. Shearer, S. Funk, B. Nikolay, V. Fonseca
Published in: Science, Issue 361/6405, 2018, Page(s) 894-899, ISSN 0036-8075
DOI: 10.1126/science.aat7115

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Author(s): Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut
Published in: Virus Evolution, Issue 4/1, 2018, ISSN 2057-1577
DOI: 10.1093/ve/vey016

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

Author(s): Simon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-03763-2

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

Author(s): L. E. Kafetzopoulou, S. T. Pullan, P. Lemey, M. A. Suchard, D. U. Ehichioya, M. Pahlmann, A. Thielebein, J. Hinzmann, L. Oestereich, D. M. Wozniak, K. Efthymiadis, D. Schachten, F. Koenig, J. Matjeschk, S. Lorenzen, S. Lumley, Y. Ighodalo, D. I. Adomeh, T. Olokor, E. Omomoh, R. Omiunu, J. Agbukor, B. Ebo, J. Aiyepada, P. Ebhodaghe, B. Osiemi, S. Ehikhametalor, P. Akhilomen, M. Airende, R. Esumeh,
Published in: Science, Issue 363/6422, 2019, Page(s) 74-77, ISSN 0036-8075
DOI: 10.1126/science.aau9343

Transmission dynamics of re-emerging rabies in domestic dogs of rural China

Author(s): Huaiyu Tian, Yun Feng, Bram Vrancken, Bernard Cazelles, Hua Tan, Mandev S. Gill, Qiqi Yang, Yidan Li, Weihong Yang, Yuzhen Zhang, Yunzhi Zhang, Philippe Lemey, Oliver G. Pybus, Nils Chr. Stenseth, Hailin Zhang, Simon Dellicour
Published in: PLOS Pathogens, Issue 14/12, 2018, Page(s) e1007392, ISSN 1553-7374
DOI: 10.1371/journal.ppat.1007392

On the importance of negative controls in viral landscape phylogeography

Author(s): Simon Dellicour, Bram Vrancken, Nídia S Trovão, Denis Fargette, Philippe Lemey
Published in: Virus Evolution, Issue 4/2, 2018, ISSN 2057-1577
DOI: 10.1093/ve/vey023

Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins

Author(s): Bert Vanmechelen, Magda Bletsa, Lies Laenen, Ana Rita Lopes, Valentijn Vergote, Leen Beller, Ward Deboutte, Miša Korva, Tatjana Avšič Županc, Joëlle Goüy de Bellocq, Sophie Gryseels, Herwig Leirs, Philippe Lemey, Bram Vrancken, Piet Maes
Published in: BMC Genomics, Issue 19/1, 2018, ISSN 1471-2164
DOI: 10.1186/s12864-018-4995-0

Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling

Author(s): Bram Vrancken, Marc A Suchard, Philippe Lemey
Published in: Virus Evolution, Issue 3/2, 2017, ISSN 2057-1577
DOI: 10.1093/ve/vex028

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Author(s): Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard
Published in: Systematic Biology, Issue 67/5, 2018, Page(s) 901-904, ISSN 1063-5157
DOI: 10.1093/sysbio/syy032

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates

Author(s): Jade Vincent Membrebe, Marc A Suchard, Andrew Rambaut, Guy Baele, Philippe Lemey
Published in: Molecular Biology and Evolution, Issue 36/8, 2019, Page(s) 1793-1803, ISSN 0737-4038
DOI: 10.1093/molbev/msz094

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

Author(s): Daniel L Ayres, Michael P Cummings, Guy Baele, Aaron E Darling, Paul O Lewis, David L Swofford, John P Huelsenbeck, Philippe Lemey, Andrew Rambaut, Marc A Suchard
Published in: Systematic Biology, Issue 68/6, 2019, Page(s) 1052-1061, ISSN 1063-5157
DOI: 10.1093/sysbio/syz020

HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs

Author(s): Marie-Angélique De Scheerder, Bram Vrancken, Simon Dellicour, Timothy Schlub, Eunok Lee, Wei Shao, Sofie Rutsaert, Chris Verhofstede, Tessa Kerre, Thomas Malfait, Dimitri Hemelsoet, Marc Coppens, Annemieke Dhondt, Danny De Looze, Frank Vermassen, Philippe Lemey, Sarah Palmer, Linos Vandekerckhove
Published in: Cell Host & Microbe, Issue 26/3, 2019, Page(s) 347-358.e7, ISSN 1931-3128
DOI: 10.1016/j.chom.2019.08.003

Divergence dating using mixed effects clock modelling: An application to HIV-1

Author(s): Magda Bletsa, Marc A Suchard, Xiang Ji, Sophie Gryseels, Bram Vrancken, Guy Baele, Michael Worobey, Philippe Lemey
Published in: Virus Evolution, Issue 5/2, 2019, ISSN 2057-1577
DOI: 10.1093/ve/vez036

Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction

Author(s): Mandev S Gill, Philippe Lemey, Marc A Suchard, Andrew Rambaut, Guy Baele
Published in: Molecular Biology and Evolution, 2020, ISSN 0737-4038
DOI: 10.1093/molbev/msaa047

In Search of Covariates of HIV-1 Subtype B Spread in the United States—A Cautionary Tale of Large-Scale Bayesian Phylogeography

Author(s): Samuel L. Hong, Simon Dellicour, Bram Vrancken, Marc A. Suchard, Michael T. Pyne, David R. Hillyard, Philippe Lemey, Guy Baele
Published in: Viruses, Issue 12/2, 2020, Page(s) 182, ISSN 1999-4915
DOI: 10.3390/v12020182

Assessing the role of live poultry trade in community-structured transmission of avian influenza in China

Author(s): Qiqi Yang, Xiang Zhao, Philippe Lemey, Marc A. Suchard, Yuhai Bi, Weifeng Shi, Di Liu, Wenbao Qi, Guogang Zhang, Nils Chr. Stenseth, Oliver G. Pybus, Huaiyu Tian
Published in: Proceedings of the National Academy of Sciences, 2020, Page(s) 201906954, ISSN 0027-8424
DOI: 10.1073/pnas.1906954117

Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa

Author(s): Nuno R. Faria, Nicole Vidal, José Lourenco, Jayna Raghwani, Kim C. E. Sigaloff, Andy J. Tatem, David A. M. van de Vijver, Andrea-Clemencia Pineda-Peña, Rebecca Rose, Carole L. Wallis, Steve Ahuka-Mundeke, Jean-Jacques Muyembe-Tamfum, Jérémie Muwonga, Marc A. Suchard, Tobias F. Rinke de Wit, Raph L. Hamers, Nicaise Ndembi, Guy Baele, Martine Peeters, Oliver G. Pybus, Philippe Lemey, Simon Delli
Published in: PLOS Pathogens, Issue 15/12, 2019, Page(s) e1007976, ISSN 1553-7374
DOI: 10.1371/journal.ppat.1007976

Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

Author(s): Alice Fusaro, Bianca Zecchin, Bram Vrancken, Celia Abolnik, Rose Ademun, Abdou Alassane, Abdelsatar Arafa, Joseph Adongo Awuni, Emmanuel Couacy-Hymann, M.’ Bétiégué Coulibaly, Nicolas Gaidet, Emilie Go-Maro, Tony Joannis, Simon Dickmu Jumbo, Germaine Minoungou, Clement Meseko, Maman Moutari Souley, Deo Birungi Ndumu, Ismaila Shittu, Augustin Twabela, Abel Wade, Lidewij Wiersma, Yao P. Akpeli,
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-13287-y