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

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Symptom evolution following the emergence of maize streak virus

Author(s): Adérito L Monjane, Simon Dellicour, Penelope Hartnady, Kehinde A Oyeniran, Betty E Owor, Marion Bezuidenhout, Daphné Linderme, Rizwan A Syed, Lara Donaldson, Shane Murray, Edward P Rybicki, Anders Kvarnheden, Elham Yazdkhasti, Pierre Lefeuvre, Rémy Froissart, Philippe Roumagnac, Dionne N Shepherd, Gordon W Harkins, Marc A Suchard, Philippe Lemey, Arvind Varsani, Darren P Martin
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
DOI: 10.7554/elife.51984

Tracking virus outbreaks in the twenty-first century

Author(s): Nathan D. Grubaugh, Jason T. Ladner, Philippe Lemey, Oliver G. Pybus, Andrew Rambaut, Edward C. Holmes, Kristian G. Andersen
Published in: Nature Microbiology, Issue 4/1, 2019, Page(s) 10-19, ISSN 2058-5276
DOI: 10.1038/s41564-018-0296-2

nosoi: A stochastic agent‐based transmission chain simulation framework in r

Author(s): Sebastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele
Published in: Methods in Ecology and Evolution, Issue 11/8, 2020, Page(s) 1002-1007, ISSN 2041-210X
DOI: 10.1111/2041-210x.13422

Recent advances in computational phylodynamics

Author(s): Guy Baele, Simon Dellicour, Marc A Suchard, Philippe Lemey, Bram Vrancken
Published in: Current Opinion in Virology, Issue 31, 2018, Page(s) 24-32, ISSN 1879-6257
DOI: 10.1016/j.coviro.2018.08.009

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Author(s): Maciej F. Boni, Philippe Lemey, Xiaowei Jiang, Tommy Tsan-Yuk Lam, Blair W. Perry, Todd A. Castoe, Andrew Rambaut, David L. Robertson
Published in: Nature Microbiology, 2020, ISSN 2058-5276
DOI: 10.1038/s41564-020-0771-4

A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue

Author(s): Sophie Gryseels, Thomas D. Watts, Jean-Marie Kabongo Mpolesha, Brendan B. Larsen, Philippe Lemey, Jean-Jacques Muyembe-Tamfum, Dirk E. Teuwen, Michael Worobey
Published in: Proceedings of the National Academy of Sciences, Issue 117/22, 2020, Page(s) 12222-12229, ISSN 0027-8424
DOI: 10.1073/pnas.1913682117

Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde

Author(s): Oumar Faye, Maria de Lourdes Monteiro, Bram Vrancken, Matthieu Prot, Sebastian Lequime, Maryam Diarra, Oumar Ndiaye, Tomas Valdez, Sandra Tavarez, Jessica Ramos, Silvânia da Veiga Leal, Cecilio Pires, Antonio Moreira, Maria Filomena Tavares, Linete Fernandes, Jorge Noel Barreto, Maria do Céu Teixeira, Maria da Luz de Lima Mendonça, Carolina Cardoso da Silva Leite Gomes, Mariano Salazar Castello
Published in: Emerging Infectious Diseases, Issue 26/6, 2020, Page(s) 1084-1090, ISSN 1080-6040
DOI: 10.3201/eid2606.190928

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

Phylogeography of Lassa Virus in Nigeria

Author(s): Deborah U. Ehichioya, Simon Dellicour, Meike Pahlmann, Toni Rieger, Lisa Oestereich, Beate Becker-Ziaja, Daniel Cadar, Yemisi Ighodalo, Thomas Olokor, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Jacqueline Agbukor, Benevolence Ebo, John Aiyepada, Paulson Ebhodaghe, Blessing Osiemi, Solomon Ehikhametalor, Patience Akhilomen, Michael Airende, Rita Esumeh, Ekene Muoebonam, Rosemary Giwa, An
Published in: Journal of Virology, Issue 93/21, 2019, ISSN 0022-538X
DOI: 10.1128/JVI.00929-19

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

Author(s): Sebastian Duchene, Philippe Lemey, Tanja Stadler, Simon Y W Ho, David A Duchene, Vijaykrishna Dhanasekaran, Guy Baele
Published in: Molecular Biology and Evolution, Issue 06 July 2020, 2020, ISSN 0737-4038
DOI: 10.1093/molbev/msaa163

Measles virus and rinderpest virus divergence dated to the sixth century BCE

Author(s): Ariane Düx, Sebastian Lequime, Livia Victoria Patrono, Bram Vrancken, Sengül Boral, Jan F. Gogarten, Antonia Hilbig, David Horst, Kevin Merkel, Baptiste Prepoint, Sabine Santibanez, Jasmin Schlotterbeck, Marc A. Suchard, Markus Ulrich, Navena Widulin, Annette Mankertz, Fabian H. Leendertz, Kyle Harper, Thomas Schnalke, Philippe Lemey, Sébastien Calvignac-Spencer
Published in: Science, Issue 368/6497, 2020, Page(s) 1367-1370, ISSN 0036-8075
DOI: 10.1126/science.aba9411

Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa

Author(s): Mbolarinosy Rakotomalala, Bram Vrancken, Agnès Pinel-Galzi, Perle Ramavovololona, Eugénie Hébrard, Jean Stéphan Randrianangaly, Simon Dellicour, Philippe Lemey, Denis Fargette
Published in: Virus Evolution, Issue 5/2, 2019, ISSN 2057-1577
DOI: 10.1093/ve/vez023

Massive Parallelization Boosts Big Bayesian Multidimensional Scaling

Author(s): Andrew J. Holbrook, Philippe Lemey, Guy Baele, Simon Dellicour, Dirk Brockmann, Andrew Rambaut, Marc A. Suchard
Published in: Journal of Computational and Graphical Statistics, Issue 08 Jun 2020, 2020, Page(s) 1-14, ISSN 1061-8600
DOI: 10.1080/10618600.2020.1754226