Search Results - "Lemey, Philippe"

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic by Boni, Maciej F., Lemey, Philippe, Jiang, Xiaowei, Lam, Tommy Tsan-Yuk, Perry, Blair W., Castoe, Todd A., Rambaut, Andrew, Robertson, David L.

“…There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of…”
Get full text

The emergence of SARS-CoV-2 in Europe and North America by Worobey, Michael, Pekar, Jonathan, Larsen, Brendan B, Nelson, Martha I, Hill, Verity, Joy, Jeffrey B, Rambaut, Andrew, Suchard, Marc A, Wertheim, Joel O, Lemey, Philippe

“…Accurate understanding of the global spread of emerging viruses is critical for public health responses and for anticipating and preventing future outbreaks…”
Get full text

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes by Bielejec, Filip, Baele, Guy, Vrancken, Bram, Suchard, Marc A, Rambaut, Andrew, Lemey, Philippe

“…Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes…”
Get full text

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 by Suchard, Marc A, Lemey, Philippe, Baele, Guy, Ayres, Daniel L, Drummond, Alexei J, Rambaut, Andrew

“…The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference…”
Get full text

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty by Baele, Guy, Lemey, Philippe, Bedford, Trevor, Rambaut, Andrew, Suchard, Marc A, Alekseyenko, Alexander V

“…Recent developments in marginal likelihood estimation for model selection in the field of Bayesian phylogenetics and molecular evolution have emphasized the…”
Get full text

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics by Bielejec, Filip, Rambaut, Andrew, Suchard, Marc A., Lemey, Philippe

“…SPREAD is a user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial-temporal…”
Get full text

RDP3: a flexible and fast computer program for analyzing recombination by Martin, Darren P., Lemey, Philippe, Lott, Martin, Moulton, Vincent, Posada, David, Lefeuvre, Pierre

“…RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments. Among other novelties, this version includes four…”
Get full text

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen by MacLean, Oscar A, Lytras, Spyros, Weaver, Steven, Singer, Joshua B, Boni, Maciej F, Lemey, Philippe, Kosakovsky Pond, Sergei L, Robertson, David L

“…Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute…”
Get full text

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

“…Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype…”
Get full text

Virome characterization of game animals in China reveals a spectrum of emerging pathogens by He, Wan-Ting, Hou, Xin, Zhao, Jin, Sun, Jiumeng, He, Haijian, Si, Wei, Wang, Jing, Jiang, Zhiwen, Yan, Ziqing, Xing, Gang, Lu, Meng, Suchard, Marc A., Ji, Xiang, Gong, Wenjie, He, Biao, Li, Jun, Lemey, Philippe, Guo, Deyin, Tu, Changchun, Holmes, Edward C., Shi, Mang, Su, Shuo

“…Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic…”
Get full text

Bayesian phylogeography finds its roots by Lemey, Philippe, Rambaut, Andrew, Drummond, Alexei J, Suchard, Marc A

“…As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic…”
Get full text

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2 by Lemey, Philippe, Hong, Samuel L., Hill, Verity, Baele, Guy, Poletto, Chiara, Colizza, Vittoria, O’Toole, Áine, McCrone, John T., Andersen, Kristian G., Worobey, Michael, Nelson, Martha I., Rambaut, Andrew, Suchard, Marc A.

“…Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the…”
Get full text

Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution by Baele, Guy, Lemey, Philippe, Vansteelandt, Stijn

“…Accurate model comparison requires extensive computation times, especially for parameter-rich models of sequence evolution. In the Bayesian framework, model…”
Get full text

The early spread and epidemic ignition of HIV-1 in human populations by Faria, Nuno R., Rambaut, Andrew, Suchard, Marc A., Baele, Guy, Bedford, Trevor, J. Ward, Melissa, Tatem, Andrew J., Sousa, João D., Arinaminpathy, Nimalan, Pépin, Jacques, Posada, David, Peeters, Martine, Pybus, Oliver G., Lemey, Philippe

“…Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using…”
Get full text

SERAPHIM: studying environmental rasters and phylogenetically informed movements by Dellicour, Simon, Rose, Rebecca, Faria, Nuno R, Lemey, Philippe, Pybus, Oliver G

“…SERAPHIM ("Studying Environmental Rasters and PHylogenetically Informed Movements") is a suite of computational methods developed to study phylogenetic…”
Get full text

Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks by Keita, Alpha Kabinet, Koundouno, Fara R., Faye, Martin, Düx, Ariane, Hinzmann, Julia, Diallo, Haby, Ayouba, Ahidjo, Le Marcis, Frederic, Soropogui, Barré, Ifono, Kékoura, Diagne, Moussa M., Sow, Mamadou S., Bore, Joseph A., Calvignac-Spencer, Sebastien, Vidal, Nicole, Camara, Jacob, Keita, Mamadou B., Renevey, Annick, Diallo, Amadou, Soumah, Abdoul K., Millimono, Saa L., Mari-Saez, Almudena, Diop, Mamadou, Doré, Ahmadou, Soumah, Fodé Y., Kourouma, Kaka, Vielle, Nathalie J., Loucoubar, Cheikh, Camara, Ibrahima, Kourouma, Karifa, Annibaldis, Giuditta, Bah, Assaïtou, Thielebein, Anke, Pahlmann, Meike, Pullan, Steven T., Carroll, Miles W., Quick, Joshua, Formenty, Pierre, Legand, Anais, Pietro, Karla, Wiley, Michael R., Tordo, Noel, Peyrefitte, Christophe, McCrone, John T., Rambaut, Andrew, Sidibé, Youssouf, Barry, Mamadou D., Kourouma, Madeleine, Saouromou, Cé D., Condé, Mamadou, Baldé, Moussa, Povogui, Moriba, Keita, Sakoba, Diakite, Mandiou, Bah, Mamadou S., Sidibe, Amadou, Diakite, Dembo, Sako, Fodé B., Traore, Fodé A., Ki-Zerbo, Georges A., Lemey, Philippe, Günther, Stephan, Kafetzopoulou, Liana E., Sall, Amadou A., Delaporte, Eric, Duraffour, Sophie, Faye, Ousmane, Leendertz, Fabian H., Peeters, Martine, Toure, Abdoulaye, Magassouba, N’. Faly

“…Seven years after the declaration of the first epidemic of Ebola virus disease in Guinea, the country faced a new outbreak—between 14 February and 19 June…”
Get full text

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages by Martin, Darren P., Weaver, Steven, Tegally, Houriiyah, San, James Emmanuel, Shank, Stephen D., Wilkinson, Eduan, Lucaci, Alexander G., Giandhari, Jennifer, Naidoo, Sureshnee, Pillay, Yeshnee, Singh, Lavanya, Lessells, Richard J., Gupta, Ravindra K., Wertheim, Joel O., Nekturenko, Anton, Murrell, Ben, Harkins, Gordon W., Lemey, Philippe, MacLean, Oscar A., Robertson, David L., de Oliveira, Tulio, Kosakovsky Pond, Sergei L.

“…The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of…”
Get full text

Mapping the Origins and Expansion of the Indo-European Language Family by Bouckaert, Remco, Lemey, Philippe, Dunn, Michael, Greenhill, Simon J., Alekseyenko, Alexander V., Drummond, Alexei J., Gray, Russell D., Suchard, Marc A., Atkinson, Quentin D.

“…There are two competing hypotheses for the origin of the Indo-European language family. The conventional view places the homeland in the Pontic steppes about…”
Get full text

Untangling introductions and persistence in COVID-19 resurgence in Europe by Lemey, Philippe, Ruktanonchai, Nick, Hong, Samuel L., Colizza, Vittoria, Poletto, Chiara, Van den Broeck, Frederik, Gill, Mandev S., Ji, Xiang, Levasseur, Anthony, Oude Munnink, Bas B., Koopmans, Marion, Sadilek, Adam, Lai, Shengjie, Tatem, Andrew J., Baele, Guy, Suchard, Marc A., Dellicour, Simon

“…After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and…”
Get full text

HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs by De Scheerder, Marie-Angélique, Vrancken, Bram, Dellicour, Simon, Schlub, Timothy, Lee, Eunok, Shao, Wei, Rutsaert, Sofie, Verhofstede, Chris, Kerre, Tessa, Malfait, Thomas, Hemelsoet, Dimitri, Coppens, Marc, Dhondt, Annemieke, De Looze, Danny, Vermassen, Frank, Lemey, Philippe, Palmer, Sarah, Vandekerckhove, Linos

“…Viral rebound upon stopping combined antiretroviral therapy poses a major barrier toward an HIV cure. Cellular and anatomical sources responsible for…”
Get full text