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

Publikacje

SPREAD 4: online visualisation of pathogen phylogeographic reconstructions

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

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

Autorzy: 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
Opublikowane w: Science, Numer 11, 2020, ISSN 0036-8075
Wydawca: 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

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

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

Autorzy: 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
Opublikowane w: Science Translational Medicine, Numer 14, 2022, ISSN 1946-6234
Wydawca: American Association for the Advancement of Science
DOI: 10.17863/cam.82478

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

Autorzy: Samuel L. Hong; Philippe Lemey; Marc A. Suchard; Guy Baele
Opublikowane w: Curr Protoc, Numer 7, 2021, ISSN 1934-3396
Wydawca: 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

Autorzy: 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
Opublikowane w: Nature Communications, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1101/2021.09.22.461380

Untangling introductions and persistence in COVID-19 resurgence in Europe

Autorzy: 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
Opublikowane w: Nature, Numer 595, 2021, Strona(/y) 713–717, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s41586-021-03754-2

Scalable Bayesian Divergence Time Estimation With Ratio Transformations

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

Symptom evolution following the emergence of maize streak virus

Autorzy: 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
Opublikowane w: eLife, Numer 9, 2020, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/elife.51984

Tracking virus outbreaks in the twenty-first century

Autorzy: Nathan D. Grubaugh, Jason T. Ladner, Philippe Lemey, Oliver G. Pybus, Andrew Rambaut, Edward C. Holmes, Kristian G. Andersen
Opublikowane w: Nature Microbiology, Numer 4/1, 2019, Strona(/y) 10-19, ISSN 2058-5276
Wydawca: Nature Publishing Group
DOI: 10.1038/s41564-018-0296-2

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

Autorzy: Sebastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele
Opublikowane w: Methods in Ecology and Evolution, Numer 11/8, 2020, Strona(/y) 1002-1007, ISSN 2041-210X
Wydawca: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.13422

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

Autorzy: 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
Opublikowane w: Nature Communications, Numer 18, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1101/788059

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

Autorzy: Abbas Jariani; Christopher Warth; Koen Deforche; Pieter Libin; Pieter Libin; Alexei J. Drummond; Alexei J. Drummond; Andrew Rambaut; Frederick A. Matsen; Kristof Theys
Opublikowane w: Virus Evolution, Numer 19, 2019, ISSN 2057-1577
Wydawca: Oxford Academic
DOI: 10.1093/ve/vez003

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

Autorzy: Kristof Theys; Philippe Lemey; Anne-Mieke Vandamme; Guy Baele
Opublikowane w: Frontiers in Public Health, Vol 7 (2019), Numer 17, 2019, ISSN 2296-2565
Wydawca: Frontiers Media S.A.
DOI: 10.3389/fpubh.2019.00208

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

Autorzy: 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
Opublikowane w: Science, 2023, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.adg660

Efficient Bayesian inference of general Gaussian models on large phylogenetic trees

Autorzy: Paul Bastide; Lam Si Tung Ho; Guy Baele; Philippe Lemey; Marc A. Suchard
Opublikowane w: Annals of Applied Statistics, Numer 15(2), 2021, ISSN 1932-6157
Wydawca: Institute of Mathematical Statistics
DOI: 10.1214/20-aoas1419

Recent advances in computational phylodynamics

Autorzy: Guy Baele, Simon Dellicour, Marc A Suchard, Philippe Lemey, Bram Vrancken
Opublikowane w: Current Opinion in Virology, Numer 31, 2018, Strona(/y) 24-32, ISSN 1879-6257
Wydawca: 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.

Autorzy: 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
Opublikowane w: Epidemics, 2023, ISSN 1755-4365
Wydawca: Elsevier BV
DOI: 10.1016/j.epidem.2023.100701

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

Autorzy: Maciej F. Boni, Philippe Lemey, Xiaowei Jiang, Tommy Tsan-Yuk Lam, Blair W. Perry, Todd A. Castoe, Andrew Rambaut, David L. Robertson
Opublikowane w: Nature Microbiology, 2020, ISSN 2058-5276
Wydawca: 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

Autorzy: 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
Opublikowane w: Eurosurveillance, Numer 2, 2019, ISSN 1560-7917
Wydawca: ECDC
DOI: 10.2807/1560-7917.es.2019.24.9.1800227

Data Integration in Bayesian Phylogenetics

Autorzy: Hassler, G.W., Magee, A.F., Zhang, Z., Baele, G., Lemey P., Ji, X., Fourment, M. and Suchard, M.A.
Opublikowane w: Annual Review of Statistics and Its Application, Numer 10(1), 2023, Strona(/y) 353-377, ISSN 2326-8298
Wydawca: Annual Reviews
DOI: 10.1146/annurev-statistics-033021-112532

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

Autorzy: Sebastián Duchêne; Leo Featherstone; Melina Haritopoulou-Sinanidou; Andrew Rambaut; Philippe Lemey; Guy Baele
Opublikowane w: Virus Evolution, Numer 10, 2020, ISSN 2057-1577
Wydawca: Oxford University Press
DOI: 10.1093/ve/veaa061

Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements

Autorzy: Gabriel W. Hassler; Max R. Tolkoff; William L. Allen; Lam Si Tung Ho; Philippe Lemey; Marc A. Suchard
Opublikowane w: Journal of the American Statistical Association, Numer vol 117, iss 538, 2022, ISSN 0162-1459
Wydawca: 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.

Autorzy: 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
Opublikowane w: Cell, Numer Volume 184, Numer 20, 2021, Strona(/y) 5189-5200.e7, ISSN 0092-8674
Wydawca: Cell Press
DOI: 10.1101/2021.02.23.21252268

Accelerating Bayesian inference of dependency between complex biological traits

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

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

Autorzy: 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
Opublikowane w: Virus Evolution, Numer Volume 7, Numer 1, 2021, Strona(/y) veab036, ISSN 2057-1577
Wydawca: Oxford Academic
DOI: 10.1093/ve/veab036

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

Autorzy: Sophie Gryseels, Thomas D. Watts, Jean-Marie Kabongo Mpolesha, Brendan B. Larsen, Philippe Lemey, Jean-Jacques Muyembe-Tamfum, Dirk E. Teuwen, Michael Worobey
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 117/22, 2020, Strona(/y) 12222-12229, ISSN 0027-8424
Wydawca: 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

Autorzy: 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;
Opublikowane w: ISSN: 1664-302X, Numer 10, 2019, ISSN 1664-302X
Wydawca: Frontiers Media
DOI: 10.3389/fmicb.2019.00613

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

Autorzy: 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
Opublikowane w: Emerging Infectious Diseases, Numer 26/6, 2020, Strona(/y) 1084-1090, ISSN 1080-6040
Wydawca: US National Center for Infectious Diseases
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Genomic and epidemiological monitoring of yellow fever virus transmission potential

Autorzy: 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
Opublikowane w: Science, Numer 361/6405, 2018, Strona(/y) 894-899, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
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Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Autorzy: Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut
Opublikowane w: Virus Evolution, Numer 4/1, 2018, ISSN 2057-1577
Wydawca: Oxford University Press
DOI: 10.1093/ve/vey016

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

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

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

Autorzy: 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,
Opublikowane w: Science, Numer 363/6422, 2019, Strona(/y) 74-77, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.1126/science.aau9343

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

Autorzy: 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
Opublikowane w: PLOS Pathogens, Numer 14/12, 2018, Strona(/y) e1007392, ISSN 1553-7374
Wydawca: PLoS
DOI: 10.1371/journal.ppat.1007392

On the importance of negative controls in viral landscape phylogeography

Autorzy: Simon Dellicour, Bram Vrancken, Nídia S Trovão, Denis Fargette, Philippe Lemey
Opublikowane w: Virus Evolution, Numer 4/2, 2018, ISSN 2057-1577
Wydawca: 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

Autorzy: 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
Opublikowane w: BMC Genomics, Numer 19/1, 2018, ISSN 1471-2164
Wydawca: BioMed Central
DOI: 10.1186/s12864-018-4995-0

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

Autorzy: Bram Vrancken, Marc A Suchard, Philippe Lemey
Opublikowane w: Virus Evolution, Numer 3/2, 2017, ISSN 2057-1577
Wydawca: Oxford University Press
DOI: 10.1093/ve/vex028

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Autorzy: Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard
Opublikowane w: Systematic Biology, Numer 67/5, 2018, Strona(/y) 901-904, ISSN 1063-5157
Wydawca: Taylor & Francis
DOI: 10.1093/sysbio/syy032

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates

Autorzy: Jade Vincent Membrebe, Marc A Suchard, Andrew Rambaut, Guy Baele, Philippe Lemey
Opublikowane w: Molecular Biology and Evolution, Numer 36/8, 2019, Strona(/y) 1793-1803, ISSN 0737-4038
Wydawca: Oxford University Press
DOI: 10.1093/molbev/msz094

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

Autorzy: 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
Opublikowane w: Systematic Biology, Numer 68/6, 2019, Strona(/y) 1052-1061, ISSN 1063-5157
Wydawca: Taylor & Francis
DOI: 10.1093/sysbio/syz020

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

Autorzy: 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
Opublikowane w: Cell Host & Microbe, Numer 26/3, 2019, Strona(/y) 347-358.e7, ISSN 1931-3128
Wydawca: Cell Press
DOI: 10.1016/j.chom.2019.08.003

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

Autorzy: Magda Bletsa, Marc A Suchard, Xiang Ji, Sophie Gryseels, Bram Vrancken, Guy Baele, Michael Worobey, Philippe Lemey
Opublikowane w: Virus Evolution, Numer 5/2, 2019, ISSN 2057-1577
Wydawca: Oxford University Presss
DOI: 10.1093/ve/vez036

Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction

Autorzy: Mandev S Gill, Philippe Lemey, Marc A Suchard, Andrew Rambaut, Guy Baele
Opublikowane w: Molecular Biology and Evolution, 2020, ISSN 0737-4038
Wydawca: 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

Autorzy: Samuel L. Hong, Simon Dellicour, Bram Vrancken, Marc A. Suchard, Michael T. Pyne, David R. Hillyard, Philippe Lemey, Guy Baele
Opublikowane w: Viruses, Numer 12/2, 2020, Strona(/y) 182, ISSN 1999-4915
Wydawca: 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

Autorzy: 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
Opublikowane w: Proceedings of the National Academy of Sciences, 2020, Strona(/y) 201906954, ISSN 0027-8424
Wydawca: 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

Autorzy: 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
Opublikowane w: PLOS Pathogens, Numer 15/12, 2019, Strona(/y) e1007976, ISSN 1553-7374
Wydawca: PLoS
DOI: 10.1371/journal.ppat.1007976

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

Autorzy: 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,
Opublikowane w: Nature Communications, Numer 10/1, 2019, ISSN 2041-1723
Wydawca: 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.

Autorzy: Oscar A. MacLean; Spyros Lytras; Steven Weaver; Joshua B Singer; Maciej F. Boni; Philippe Lemey; Sergei L Kosakovsky Pond; David Robertson
Opublikowane w: PLoS Biology, Numer Vol 19, Iss 3, 2021, Strona(/y) e3001115, ISSN 1544-9173
Wydawca: Public Library of Science
DOI: 10.1371/journal.pbio.3001115

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

Autorzy: Gabriel W. Hassler; Brigida Gallone; Leandro Aristide; William L. Allen; Max R. Tolkoff; Andrew J. Holbrook; Guy Baele; Philippe Lemey; Marc A. Suchard
Opublikowane w: Methods in ecology and evolution, Numer 13, 2023, ISSN 2041-210X
Wydawca: 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

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

Uncovering the endemic circulation of rabies in Cambodia

Autorzy: 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
Opublikowane w: Molecular Ecology, 2022, ISSN 1365-294X
Wydawca: John Wiley & Sons Ltd
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Phylogeography of Lassa Virus in Nigeria

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The International Virus Bioinformatics Meeting 2022

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