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

Publicaciones

SPREAD 4: online visualisation of pathogen phylogeographic reconstructions

Autores: Kanika D Nahata, Filip Bielejec, Juan Monetta, Simon Dellicour, Andrew Rambaut, Marc A Suchard, Guy Baele, Philippe Lemey
Publicado en: Virus Evolution, 2022, ISSN 2057-1577
Editor: Oxford Academic
DOI: 10.1093/ve/veac088

The emergence of SARS-CoV-2 in Europe and North America.

Autores: Michael Worobey; Jonathan Pekar; Brendan B. Larsen; Martha I. Nelson; Verity Hill; Jeffrey B. Joy; Andrew Rambaut; Marc A. Suchard; Joel O. Wertheim; Philippe Lemey
Publicado en: Science, Edición 11, 2020, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.abc8169

Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models

Autores: Zhenyu Zhang; Akihiko Nishimura; Paul Bastide; Xiang Ji; Rebecca Payne; Philip J. R. Goulder; Philippe Lemey; Marc A. Suchard
Publicado en: https://hal.archives-ouvertes.fr/hal-03254483, Edición 18, 2021, ISSN 1932-6157
Editor: Institute of Mathematical Statistics
DOI: 10.1214/20-aoas1394

Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis.

Autores: Noémie Lefrancq; Valérie Bouchez; Nadia Fernandes; Alex-Mikael Barkoff; Thijs Bosch; Tine Dalby; Thomas Åkerlund; Jessica Darenberg; Katerina Fabianova; Didrik F. Vestrheim; Norman K. Fry; Juan José González-López; Karolina Gullsby; Adele Habington; Qiushui He; David Litt; Helena Martini; Denis Piérard; Paola Stefanelli; Marc Stegger; Jana Zavadilova; Nathalie Armatys; Annie Landier; Sophie
Publicado en: Science Translational Medicine, Edición 14, 2022, ISSN 1946-6234
Editor: American Association for the Advancement of Science
DOI: 10.17863/cam.82478

Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST.

Autores: Samuel L. Hong; Philippe Lemey; Marc A. Suchard; Guy Baele
Publicado en: Curr Protoc, Edición 7, 2021, ISSN 1934-3396
Editor: John Wiley & Sons Inc.
DOI: 10.1002/cpz1.98

Predicting the evolution of Lassa Virus endemic area and population at risk over the next decades

Autores: Raphaëlle Klitting; Liana E. Kafetzopoulou; Liana E. Kafetzopoulou; W. Thiery; G. Dudas; Sophie Gryseels; A. Kotamarthi; Bram Vrancken; Karthik Gangavarapu; Mambu Momoh; J. Demby Sandy; Augustine Goba; F. Alhasan; Don Grant; Robert F. Garry; Allison R. Smither; Mark Zeller; Matthias Pauthner; Michelle McGraw; Laura D. Hughes; Sophie Duraffour; Stephan Günther; Marc A. Suchard; Marc A. Suchard; P
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2021.09.22.461380

Untangling introductions and persistence in COVID-19 resurgence in Europe

Autores: Philippe Lemey, Nick Ruktanonchai, Samuel L. Hong, Vittoria Colizza, Chiara Poletto, Frederik Van den Broeck, Mandev S. Gill, Xiang Ji, Anthony Levasseur, Bas B. Oude Munnink, Marion Koopmans, Adam Sadilek, Shengjie Lai, Andrew J. Tatem, Guy Baele, Marc A. Suchard, Simon Dellicour
Publicado en: Nature, Edición 595, 2021, Página(s) 713–717, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-021-03754-2

Scalable Bayesian Divergence Time Estimation With Ratio Transformations

Autores: X., Fisher A.A., Su S., Thorne J.L., Potter B., Lemey P., Baele G., Suchard M.A
Publicado en: Systematic Biology, 2023, ISSN 1063-5157
Editor: Taylor & Francis
DOI: 10.1093/sysbio/syad039

Symptom evolution following the emergence of maize streak virus

Autores: 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
Publicado en: eLife, Edición 9, 2020, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.51984

Tracking virus outbreaks in the twenty-first century

Autores: Nathan D. Grubaugh, Jason T. Ladner, Philippe Lemey, Oliver G. Pybus, Andrew Rambaut, Edward C. Holmes, Kristian G. Andersen
Publicado en: Nature Microbiology, Edición 4/1, 2019, Página(s) 10-19, ISSN 2058-5276
Editor: Nature Publishing Group
DOI: 10.1038/s41564-018-0296-2

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

Autores: Sebastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele
Publicado en: Methods in Ecology and Evolution, Edición 11/8, 2020, Página(s) 1002-1007, ISSN 2041-210X
Editor: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.13422

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

Autores: Dellicour, Simon; Lequime, Sebastian; Vrancken, Bram; Gill, Mandev S.; Bastide, Paul; Gangavarapu, Karthik; Matteson, Nate; Tan, Yi; Plessis, Louis du; Fisher, Alexander A.; Nelson, Martha I.; Gilbert, Marius; Suchard, Marc A.; Grubaugh, Nathan D.; Andersen, Kristian G.; Pybus, Oliver G.; Lemey, Philippe
Publicado en: Nature Communications, Edición 18, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/788059

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.

Autores: Abbas Jariani; Christopher Warth; Koen Deforche; Pieter Libin; Pieter Libin; Alexei J. Drummond; Alexei J. Drummond; Andrew Rambaut; Frederick A. Matsen; Kristof Theys
Publicado en: Virus Evolution, Edición 19, 2019, ISSN 2057-1577
Editor: Oxford Academic
DOI: 10.1093/ve/vez003

Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases

Autores: Kristof Theys; Philippe Lemey; Anne-Mieke Vandamme; Guy Baele
Publicado en: Frontiers in Public Health, Vol 7 (2019), Edición 17, 2019, ISSN 2296-2565
Editor: Frontiers Media S.A.
DOI: 10.3389/fpubh.2019.00208

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

Autores: Tsui, Joseph L-H; McCrone, John T; Lambert, Ben; Bajaj, Sumali; Inward, Rhys PD; Bosetti, Paolo; Pena, Rosario Evans; Tegally, Houriiyah; Hill, Verity; Zarebski, Alexander E; Peacock, Thomas P; Liu, Luyang; Wu, Neo; Davis, Megan; Bogoch, Isaac I; Khan, Kamran; Kall, Meaghan; Aziz, Nurin Iwani Binti Abdul; Colquhoun, Rachel; O'Toole, Aine; Jackson, Ben; Dasgupta, Abhishek; Wilkinson, Eduan; de Oliv
Publicado en: Science, 2023, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.adg660

Efficient Bayesian inference of general Gaussian models on large phylogenetic trees

Autores: Paul Bastide; Lam Si Tung Ho; Guy Baele; Philippe Lemey; Marc A. Suchard
Publicado en: Annals of Applied Statistics, Edición 15(2), 2021, ISSN 1932-6157
Editor: Institute of Mathematical Statistics
DOI: 10.1214/20-aoas1419

Recent advances in computational phylodynamics

Autores: Guy Baele, Simon Dellicour, Marc A Suchard, Philippe Lemey, Bram Vrancken
Publicado en: Current Opinion in Virology, Edición 31, 2018, Página(s) 24-32, ISSN 1879-6257
Editor: Elsevier BV
DOI: 10.1016/j.coviro.2018.08.009

Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data.

Autores: Kremer C., Torneri A., Libin P.J.K., Meex C., Hayette M.P., Bontems S., Durkin K., Artesi M., Bours V., Lemey P., Darcis G., Hens N., Meuris C
Publicado en: Epidemics, 2023, ISSN 1755-4365
Editor: Elsevier BV
DOI: 10.1016/j.epidem.2023.100701

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

Autores: Maciej F. Boni, Philippe Lemey, Xiaowei Jiang, Tommy Tsan-Yuk Lam, Blair W. Perry, Todd A. Castoe, Andrew Rambaut, David L. Robertson
Publicado en: Nature Microbiology, 2020, ISSN 2058-5276
Editor: Nature Publishing Group
DOI: 10.1038/s41564-020-0771-4

Increasing importance of European lineages in seeding the hepatitis C virus subtype 1a epidemic in Spain

Autores: Ana Belén Pérez; Bram Vrancken; Natalia Chueca; Antonio Aguilera; Gabriel Reina; Miguel Garcia del Toro; Francisco Vera; Miguel Angel Von Wichman; Juan Arenas; Francisco Téllez; Juan A. Pineda; Mohamed Omar; Enrique Bernal; Antonio Rivero-Juárez; Elisa Fernández-Fuertes; Alberto de la Iglesia; Juan Manuel Pascasio; Philippe Lemey; Federico García; Lize Cuypers
Publicado en: Eurosurveillance, Edición 2, 2019, ISSN 1560-7917
Editor: ECDC
DOI: 10.2807/1560-7917.es.2019.24.9.1800227

Data Integration in Bayesian Phylogenetics

Autores: Hassler, G.W., Magee, A.F., Zhang, Z., Baele, G., Lemey P., Ji, X., Fourment, M. and Suchard, M.A.
Publicado en: Annual Review of Statistics and Its Application, Edición 10(1), 2023, Página(s) 353-377, ISSN 2326-8298
Editor: Annual Reviews
DOI: 10.1146/annurev-statistics-033021-112532

Temporal signal and the phylodynamic threshold of SARS-CoV-2

Autores: Sebastián Duchêne; Leo Featherstone; Melina Haritopoulou-Sinanidou; Andrew Rambaut; Philippe Lemey; Guy Baele
Publicado en: Virus Evolution, Edición 10, 2020, ISSN 2057-1577
Editor: Oxford University Press
DOI: 10.1093/ve/veaa061

Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements

Autores: Gabriel W. Hassler; Max R. Tolkoff; William L. Allen; Lam Si Tung Ho; Philippe Lemey; Marc A. Suchard
Publicado en: Journal of the American Statistical Association, Edición vol 117, iss 538, 2022, ISSN 0162-1459
Editor: American Statistical Association
DOI: 10.1080/01621459.2020.1799812

The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.

Autores: Darren P, Martin; Steven, Weaver; Houryiah, Tegally; Emmanuel James, San; Stephen D, Shank; Eduan, Wilkinson; Alexander G, Lucaci; Jennifer, Giandhari; Sureshnee, Naidoo; Yeshnee, Pillay; Lavanya, Singh; Richard J, Lessells; Ravindra K, Gupta; Joel O, Wertheim; Anton, Nekturenko; Ben, Murrell; Gordon W, Harkins; Philippe, Lemey; Oscar A, MacLean; David L, Robertson; Tulio, de Oliveira; Sergei L, K
Publicado en: Cell, Edición Volume 184, Edición 20, 2021, Página(s) 5189-5200.e7, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1101/2021.02.23.21252268

Accelerating Bayesian inference of dependency between complex biological traits

Autores: Zhang, Zhenyu; Nishimura, Akihiko; Trovão, Nídia S.; Cherry, Joshua L.; Holbrook, Andrew J.; Ji, Xiang; Lemey, Philippe; Suchard, Marc A.
Publicado en: Plos Computational Biology, Edición 3, 2023, ISSN 1553-734X
Editor: Public Library of Science
DOI: 10.1371/journal.pcbi.1011419

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

Autores: Magda Bletsa, Bram Vrancken, Sophie Gryseels, Ine Boonen, Antonios Fikatas, Yiqiao Li, Anne Laudisoit, Sebastian Lequime, Josef Bryja, Rhodes Makundi, Yonas Meheretu, Benjamin Dudu Akaibe, Sylvestre Gambalemoke Mbalitini, Frederik Van de Perre, Natalie Van Houtte, Jana Těšíková, Elke Wollants, Marc Van Ranst, Oliver G Pybus, Jan Felix Drexler, Erik Verheyen, H
Publicado en: Virus Evolution, Edición Volume 7, Edición 1, 2021, Página(s) veab036, ISSN 2057-1577
Editor: Oxford Academic
DOI: 10.1093/ve/veab036

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

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

Earlier initiation of antiretroviral treatment coincides with an initial control of the HIV-1 sub-subtype F1 outbreak among men-having-sex-with-men in Flanders, Belgium

Autores: Lore Vinken; Katrien Fransen; Lize Cuypers; Ivailo Alexiev; Claudia Balotta; Laurent Debaisieux; Carole Seguin-Devaux; Sergio García Ribas; Perpétua Gomes; Perpétua Gomes; Francesca Incardona; Rolf Kaiser; Jean Ruelle; Murat Sayan; Murat Sayan; Simona Paraschiv; Roger Paredes; Martine Peeters; Anders Sönnerborg; Ellen Vancutsem; Anne-Mieke Vandamme; Anne-Mieke Vandamme; Sigi Van den Wijngaert;
Publicado en: ISSN: 1664-302X, Edición 10, 2019, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2019.00613

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

Autores: 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
Publicado en: Emerging Infectious Diseases, Edición 26/6, 2020, Página(s) 1084-1090, ISSN 1080-6040
Editor: US National Center for Infectious Diseases
DOI: 10.3201/eid2606.190928

Genomic and epidemiological monitoring of yellow fever virus transmission potential

Autores: 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
Publicado en: Science, Edición 361/6405, 2018, Página(s) 894-899, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.aat7115

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Autores: Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut
Publicado en: Virus Evolution, Edición 4/1, 2018, ISSN 2057-1577
Editor: Oxford University Press
DOI: 10.1093/ve/vey016

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

Autores: Simon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
Publicado en: Nature Communications, Edición 9/1, 2018, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-018-03763-2

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

Autores: 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,
Publicado en: Science, Edición 363/6422, 2019, Página(s) 74-77, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.aau9343

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

Autores: 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
Publicado en: PLOS Pathogens, Edición 14/12, 2018, Página(s) e1007392, ISSN 1553-7374
Editor: PLoS
DOI: 10.1371/journal.ppat.1007392

On the importance of negative controls in viral landscape phylogeography

Autores: Simon Dellicour, Bram Vrancken, Nídia S Trovão, Denis Fargette, Philippe Lemey
Publicado en: Virus Evolution, Edición 4/2, 2018, ISSN 2057-1577
Editor: Oxford University Press
DOI: 10.1093/ve/vey023

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

Autores: 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
Publicado en: BMC Genomics, Edición 19/1, 2018, ISSN 1471-2164
Editor: BioMed Central
DOI: 10.1186/s12864-018-4995-0

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

Autores: Bram Vrancken, Marc A Suchard, Philippe Lemey
Publicado en: Virus Evolution, Edición 3/2, 2017, ISSN 2057-1577
Editor: Oxford University Press
DOI: 10.1093/ve/vex028

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Autores: Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard
Publicado en: Systematic Biology, Edición 67/5, 2018, Página(s) 901-904, ISSN 1063-5157
Editor: Taylor & Francis
DOI: 10.1093/sysbio/syy032

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates

Autores: Jade Vincent Membrebe, Marc A Suchard, Andrew Rambaut, Guy Baele, Philippe Lemey
Publicado en: Molecular Biology and Evolution, Edición 36/8, 2019, Página(s) 1793-1803, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msz094

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

Autores: 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
Publicado en: Systematic Biology, Edición 68/6, 2019, Página(s) 1052-1061, ISSN 1063-5157
Editor: Taylor & Francis
DOI: 10.1093/sysbio/syz020

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

Autores: 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
Publicado en: Cell Host & Microbe, Edición 26/3, 2019, Página(s) 347-358.e7, ISSN 1931-3128
Editor: Cell Press
DOI: 10.1016/j.chom.2019.08.003

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

Autores: Magda Bletsa, Marc A Suchard, Xiang Ji, Sophie Gryseels, Bram Vrancken, Guy Baele, Michael Worobey, Philippe Lemey
Publicado en: Virus Evolution, Edición 5/2, 2019, ISSN 2057-1577
Editor: Oxford University Presss
DOI: 10.1093/ve/vez036

Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction

Autores: Mandev S Gill, Philippe Lemey, Marc A Suchard, Andrew Rambaut, Guy Baele
Publicado en: Molecular Biology and Evolution, 2020, ISSN 0737-4038
Editor: Oxford University Press
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

Autores: Samuel L. Hong, Simon Dellicour, Bram Vrancken, Marc A. Suchard, Michael T. Pyne, David R. Hillyard, Philippe Lemey, Guy Baele
Publicado en: Viruses, Edición 12/2, 2020, Página(s) 182, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12020182

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

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, 2020, Página(s) 201906954, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1906954117

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

Autores: 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
Publicado en: PLOS Pathogens, Edición 15/12, 2019, Página(s) e1007976, ISSN 1553-7374
Editor: PLoS
DOI: 10.1371/journal.ppat.1007976

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

Autores: 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,
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-13287-y

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.

Autores: Oscar A. MacLean; Spyros Lytras; Steven Weaver; Joshua B Singer; Maciej F. Boni; Philippe Lemey; Sergei L Kosakovsky Pond; David Robertson
Publicado en: PLoS Biology, Edición Vol 19, Iss 3, 2021, Página(s) e3001115, ISSN 1544-9173
Editor: Public Library of Science
DOI: 10.1371/journal.pbio.3001115

Principled, practical, flexible, fast: A new approach to phylogenetic factor analysis

Autores: Gabriel W. Hassler; Brigida Gallone; Leandro Aristide; William L. Allen; Max R. Tolkoff; Andrew J. Holbrook; Guy Baele; Philippe Lemey; Marc A. Suchard
Publicado en: Methods in ecology and evolution, Edición 13, 2023, ISSN 2041-210X
Editor: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.13920

Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics

Autores: Ji, Xiang; Zhang, Zhenyu; Holbrook, Andrew; Nishimura, Akihiko; Baele, Guy; Rambaut, Andrew; Lemey, Philippe; Suchard, Marc A.
Publicado en: Molecular Biology and Evolution, 2020, ISSN 1537-1719
Editor: Oxford University Press
DOI: 10.1093/molbev/msaa130

Uncovering the endemic circulation of rabies in Cambodia

Autores: Layan M., Dacheux L, Lemey P., Brunker K., Ma L., Troupin C., Dussart P., Chevalier V., Wood J.L.N., Ly S., Duong V., Bourhy H., Dellicour S
Publicado en: Molecular Ecology, 2022, ISSN 1365-294X
Editor: John Wiley & Sons Ltd
DOI: 10.1111/mec.17087

Phylogeography of Lassa Virus in Nigeria

Autores: 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
Publicado en: Journal of Virology, Edición 93/21, 2019, ISSN 0022-538X
Editor: American Society for Microbiology
DOI: 10.1128/JVI.00929-19

Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas

Autores: de Moraes L., Portilho M.M., Vrancken B., Van den Broeck F., Santos L.A., Cucco M., Tauro L.B., Kikuti M., Silva M.M.O., Campos G.S., Reis M.G., Barral A., Barral-Netto M., Boaventura V.S., Vandamme A.M., Theys K., Lemey P., Ribeiro G.S. and Khouri R
Publicado en: Viruses, 2023, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15061236

Scalable Bayesian phylogenetics

Autores: Alexander A. Fisher; Gabriel W. Hassler; Xiang Ji; Guy Baele; Marc A. Suchard; Philippe Lemey
Publicado en: PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B, Edición Volume 377Edición 1861, 2022, ISSN 0962-8436
Editor: Royal Society of London
DOI: 10.1098/rstb.2021.0242

Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework.

Autores: Baele, Guy; Gill, Mandev S.; Lemey, Philippe; Suchard, Marc A.
Publicado en: Wellcome Open Research, Edición 4, 2020, ISSN 2398-502X
Editor: F1000 Research
DOI: 10.12688/wellcomeopenres.15770.1

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

Autores: Sebastian Duchene, Philippe Lemey, Tanja Stadler, Simon Y W Ho, David A Duchene, Vijaykrishna Dhanasekaran, Guy Baele
Publicado en: Molecular Biology and Evolution, Edición 06 July 2020, 2020, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msaa163

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

Autores: 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
Publicado en: Science, Edición 368/6497, 2020, Página(s) 1367-1370, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.aba9411

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

Autores: Mbolarinosy Rakotomalala, Bram Vrancken, Agnès Pinel-Galzi, Perle Ramavovololona, Eugénie Hébrard, Jean Stéphan Randrianangaly, Simon Dellicour, Philippe Lemey, Denis Fargette
Publicado en: Virus Evolution, Edición 5/2, 2019, ISSN 2057-1577
Editor: Oxford Academic
DOI: 10.1093/ve/vez023

Relaxed random walks at scale

Autores: Fisher, Alexander A.; Ji, Xiang; Lemey, Philippe; Suchard, Marc A.
Publicado en: Systematic Biology, 2021, ISSN 1063-5157
Editor: Taylor & Francis
DOI: 10.1093/sysbio/syaa056

Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses.

Autores: Bert Vanmechelen; Zafeiro Zisi; Sophie Gryseels; Joëlle Goüy de Bellocq; Bram Vrancken; Philippe Lemey; Piet Maes; Magda Bletsa
Publicado en: Volume 13, Edición 1, 2021, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13091842

In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression.

Autores: Silvie Van den Hoecke; Marlies Ballegeer; Bram Vrancken; Lei Deng; Emma R. Job; Kenny Roose; Bert Schepens; Lien Van Hoecke; Philippe Lemey; Xavier Saelens
Publicado en: MBIO, Edición 15, 2021, ISSN 2150-7511
Editor: American Society for Microbiology
DOI: 10.1128/mbio.00745-21

Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study

Autores: George M Nduva; Frederick Otieno; Joshua Kimani; Elizabeth Wahome; Lyle R McKinnon; Francois Cholette; Maxwell Majiwa; Moses Masika; Gaudensia Mutua; Omu Anzala; Susan M Graham; Larry Gelmon; Matt A Price; Adrian D Smith; Robert C Bailey; Guy Baele; Philippe Lemey; Amin S Hassan; Eduard J Sanders; Joakim Esbjörnsson
Publicado en: Virus Evolution, Edición Volume 8, Edición 1, 2022, Página(s) veac016, ISSN 2057-1577
Editor: Oxford University Press
DOI: 10.1093/ve/veac016

Detection of Marburg Virus Disease in Guinea

Autores: Fara R. Koundouno; Liana E. Kafetzopoulou; Martin Faye; Annick Renevey; Barrè Soropogui; Kékoura Ifono; Emily V. Nelson; Aly A. Kamano; Charles Tolno; Giuditta Annibaldis; Saa L. Millimono; Jacob Camara; Karifa Kourouma; Ahmadou Doré; Tamba E. Millimouno; Fernand M.B. Tolno; Julia Hinzmann; Hugo Soubrier; Mette Hinrichs; Anke Thielebein; Glaucia Herzer; Meike Pahlmann; Georges A. Ki-Zerbo; Pier
Publicado en: The New England Journal of Medicine, 2022, ISSN 0028-4793
Editor: Massachusetts Medical Society
DOI: 10.1056/nejmc2120183

Massive Parallelization Boosts Big Bayesian Multidimensional Scaling

Autores: Andrew J. Holbrook, Philippe Lemey, Guy Baele, Simon Dellicour, Dirk Brockmann, Andrew Rambaut, Marc A. Suchard
Publicado en: Journal of Computational and Graphical Statistics, Edición 08 Jun 2020, 2020, Página(s) 1-14, ISSN 1061-8600
Editor: American Statistical Association
DOI: 10.1080/10618600.2020.1754226

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

Autores: Philippe Lemey, Samuel L. Hong, Verity Hill, Guy Baele, Chiara Poletto, Vittoria Colizza, Áine O’Toole, John T. McCrone, Kristian G. Andersen, Michael Worobey, Martha I. Nelson, Andrew Rambaut & Marc A. Suchard
Publicado en: Nature Communications, Edición 11, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-18877-9

The evolutionary history of hepaciviruses

Autores: YQ Li, M Ghafari, AJ Holbrook, I Boonen, N Amor, S Catalano, JP Webster, YY Li, HT Li, V Vergote, P Maes, YL Chong, A Laudisoit, P Baelo, S Ngoy, SG Mbalitini, GC Gembu, P Musaba Akawa, J Goüy de Bellocq, H Leirs, E Verheyen, OG Pybus, A Katzourakis, AN Alagaili, S Gryseels, YC Li, MA Suchard, M Bletsa, P Lemey
Publicado en: bioRxiv, 2023
Editor: Cold Spring Harbour Laboratory
DOI: 10.1101/2023.06.30.547218

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

Autores: Lytras, Spyros ; Ghafari, Mahan ; Magee, Andrew F ; Parker, Edyth ; Havens, Jennifer L ; Katzourakis, Aris ; Vasylyeva, Tetyana I ; Suchard, Marc A ; Hughes, Alice C ; Hughes, Joseph ; Robertson, David L ; Dellicour, Simon ; Worobey, Michael ; Wertheim, Joel O ; Lemey, Philippe
Publicado en: bioArxiv, 2023
Editor: Cold Spring Harbour Laboratory
DOI: 10.1101/2023.07.12.548617

The International Virus Bioinformatics Meeting 2022

Autores: Franziska Hufsky; Denis Beslic; Dimitri Boeckaerts; Sebastian Duchene; Enrique González-Tortuero; Andreas J. Gruber; Jiarong Guo; Daan Jansen; John Juma; Kunaphas Kongkitimanon; Antoni Luque; Muriel Ritsch; Gabriel Lencioni Lovate; Luca Nishimura; Célia Pas; Esteban Domingo; Emma Hodcroft; Philippe Lemey; Matthew B. Sullivan; Friedemann Weber; Fernando González-Candelas; Sarah Krautwurst; Alba
Publicado en: VIRUSES, Edición 14(5), 2022, ISSN 1999-4915
Editor: MDPI
DOI: 10.48350/170316

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