Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2
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
Published in Nature communications (09.10.2020)
Published in Nature communications (09.10.2020)
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Untangling introductions and persistence in COVID-19 resurgence in Europe
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
Published in Nature (London) (29.07.2021)
Published in Nature (London) (29.07.2021)
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Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City - from Alpha to Omicron
Dellicour, Simon, Hong, Samuel L, Hill, Verity, Dimartino, Dacia, Marier, Christian, Zappile, Paul, Harkins, Gordon W, Lemey, Philippe, Baele, Guy, Duerr, Ralf, Heguy, Adriana
Published in PLoS pathogens (01.04.2023)
Published in PLoS pathogens (01.04.2023)
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Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City
Dellicour, Simon, Hong, Samuel L, Vrancken, Bram, Chaillon, Antoine, Gill, Mandev S, Maurano, Matthew T, Ramaswami, Sitharam, Zappile, Paul, Marier, Christian, Harkins, Gordon W, Baele, Guy, Duerr, Ralf, Heguy, Adriana
Published in PLoS pathogens (01.05.2021)
Published in PLoS pathogens (01.05.2021)
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Transmission of Multidrug-Resistant Salmonella enterica Subspecies enterica 4,[5],12:i:- Sequence Type 34 between Europe and the United States
Elnekave, Ehud, Hong, Samuel L, Lim, Seunghyun, Boxrud, Dave, Rovira, Albert, Mather, Alison E, Perez, Andres, Alvarez, Julio
Published in Emerging infectious diseases (01.12.2020)
Published in Emerging infectious diseases (01.12.2020)
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Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020
Bollen, Nena, Artesi, Maria, Durkin, Keith, Hong, Samuel L., Potter, Barney, Boujemla, Bouchra, Vanmechelen, Bert, Martí-Carreras, Joan, Wawina-Bokalanga, Tony, Meex, Cécile, Bontems, Sébastien, Hayette, Marie-Pierre, André, Emmanuel, Maes, Piet, Bours, Vincent, Baele, Guy, Dellicour, Simon
Published in Scientific reports (17.09.2021)
Published in Scientific reports (17.09.2021)
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In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography
Hong, Samuel L, Dellicour, Simon, Vrancken, Bram, Suchard, Marc A, Pyne, Michael T, Hillyard, David R, Lemey, Philippe, Baele, Guy
Published in Viruses (05.02.2020)
Published in Viruses (05.02.2020)
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Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants
Cuypers, Lize, Dellicour, Simon, Hong, Samuel L, Potter, Barney I, Verhasselt, Bruno, Vereecke, Nick, Lambrechts, Laurens, Durkin, Keith, Bours, Vincent, Klamer, Sofieke, Bayon-Vicente, Guillaume, Vael, Carl, Ariën, Kevin K, De Mendonca, Ricardo, Soetens, Oriane, Michel, Charlotte, Bearzatto, Bertrand, Naesens, Reinout, Gras, Jeremie, Vankeerberghen, Anne, Matheeussen, Veerle, Martens, Geert, Obbels, Dagmar, Lemmens, Ann, Van den Poel, Bea, Van Even, Ellen, De Rauw, Klara, Waumans, Luc, Reynders, Marijke, Degosserie, Jonathan, Maes, Piet, André, Emmanuel, Baele, Guy
Published in Viruses (01.10.2022)
Published in Viruses (01.10.2022)
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Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium
El Moussaoui, Majdouline, Maes, Nathalie, Hong, Samuel L, Lambert, Nicolas, Gofflot, Stéphanie, Dellot, Patricia, Belhadj, Yasmine, Huynen, Pascale, Hayette, Marie-Pierre, Meex, Cécile, Bontems, Sébastien, Defêche, Justine, Godderis, Lode, Molenberghs, Geert, Meuris, Christelle, Artesi, Maria, Durkin, Keith, Rahmouni, Souad, Grégoire, Céline, Beguin, Yves, Moutschen, Michel, Dellicour, Simon, Darcis, Gilles
Published in Viruses (14.06.2022)
Published in Viruses (14.06.2022)
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Delta-Omicron recombinant escapes therapeutic antibody neutralization
Duerr, Ralf, Zhou, Hao, Tada, Takuya, Dimartino, Dacia, Marier, Christian, Zappile, Paul, Wang, Guiqing, Plitnick, Jonathan, Griesemer, Sara B., Girardin, Roxanne, Machowski, Jessica, Bialosuknia, Sean, Lasek-Nesselquist, Erica, Hong, Samuel L., Baele, Guy, Dittmann, Meike, Ortigoza, Mila B., Prasad, Prithiv J., McDonough, Kathleen, Landau, Nathaniel R., St George, Kirsten, Heguy, Adriana
Published in iScience (17.02.2023)
Published in iScience (17.02.2023)
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Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations
Pirnay, Jean-Paul, Selhorst, Philippe, Hong, Samuel L., Cochez, Christel, Potter, Barney, Maes, Piet, Petrillo, Mauro, Dudas, Gytis, Claes, Vincent, Van der Beken, Yolien, Verbeken, Gilbert, Degueldre, Julie, Dellicour, Simon, Cuypers, Lize, T’Sas, France, Van den Eede, Guy, Verhasselt, Bruno, Weuts, Wouter, Smets, Cedric, Mertens, Jan, Geeraerts, Philippe, Ariën, Kevin K., André, Emmanuel, Neirinckx, Pierre, Soentjens, Patrick, Baele, Guy
Published in Viruses (13.07.2021)
Published in Viruses (13.07.2021)
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The phylodynamics of SARS-CoV-2 during 2020 in Finland
Truong Nguyen, Phuoc, Kant, Ravi, Van den Broeck, Frederik, Suvanto, Maija T, Alburkat, Hussein, Virtanen, Jenni, Ahvenainen, Ella, Castren, Robert, Hong, Samuel L, Baele, Guy, Ahava, Maarit J, Jarva, Hanna, Jokiranta, Suvi Tuulia, Kallio-Kokko, Hannimari, Kekäläinen, Eliisa, Kirjavainen, Vesa, Kortela, Elisa, Kurkela, Satu, Lappalainen, Maija, Liimatainen, Hanna, Suchard, Marc A, Hannula, Sari, Ellonen, Pekka, Sironen, Tarja, Lemey, Philippe, Vapalahti, Olli, Smura, Teemu
Published in Communications medicine (10.06.2022)
Published in Communications medicine (10.06.2022)
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Ecological Changes Exacerbating the Spread of Invasive Ticks has Driven the Dispersal of Severe Fever with Thrombocytopenia Syndrome Virus Throughout Southeast Asia
Pérez, Lester J, Baele, Guy, Hong, Samuel L, Cloherty, Gavin A, Berg, Michael G
Published in Molecular biology and evolution (28.08.2024)
Published in Molecular biology and evolution (28.08.2024)
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A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages
Dellicour, Simon, Durkin, Keith, Hong, Samuel L, Vanmechelen, Bert, Martí-Carreras, Joan, Gill, Mandev S, Meex, Cécile, Bontems, Sébastien, André, Emmanuel, Gilbert, Marius, Walker, Conor, Maio, Nicola De, Faria, Nuno R, Hadfield, James, Hayette, Marie-Pierre, Bours, Vincent, Wawina-Bokalanga, Tony, Artesi, Maria, Baele, Guy, Maes, Piet
Published in Molecular biology and evolution (01.04.2021)
Published in Molecular biology and evolution (01.04.2021)
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Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST
Hong, Samuel L, Lemey, Philippe, Suchard, Marc A, Baele, Guy
Published in Current protocols (01.04.2021)
Published in Current protocols (01.04.2021)
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Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis
Lefrancq, Noémie, Bouchez, Valérie, Fernandes, Nadia, Barkoff, Alex-Mikael, Bosch, Thijs, Dalby, Tine, Åkerlund, Thomas, Darenberg, Jessica, Fabianova, Katerina, Vestrheim, Didrik F, Fry, Norman K, González-López, Juan José, Gullsby, Karolina, Habington, Adele, He, Qiushui, Litt, David, Martini, Helena, Piérard, Denis, Stefanelli, Paola, Stegger, Marc, Zavadilova, Jana, Armatys, Nathalie, Landier, Annie, Guillot, Sophie, Hong, Samuel L, Lemey, Philippe, Parkhill, Julian, Toubiana, Julie, Cauchemez, Simon, Salje, Henrik, Brisse, Sylvain
Published in Science translational medicine (27.04.2022)
Published in Science translational medicine (27.04.2022)
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Investigation of an international water polo tournament in Czechia as a potential source for early introduction of the SARS-CoV-2 Omicron variant into Belgium, Switzerland and Germany, November 2021
Rudin, Christoph, Bollen, Nena, Hong, Samuel L, Wegner, Fanny, Politi, Lida, Mellou, Kassiani, Geenen, Caspar, Gorissen, Sarah, Verhasselt, Bruno, Durkin, Keith, Henin, Coralie, Logist, Anne-Sophie, Dellicour, Simon, Resa, Tobias, Stadler, Tanja, Maes, Piet, Cuypers, Lize, André, Emmanuel, Egli, Adrian, Baele, Guy
Published in Euro surveillance : bulletin européen sur les maladies transmissibles (09.11.2023)
Published in Euro surveillance : bulletin européen sur les maladies transmissibles (09.11.2023)
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Circulation of Plasmids Harboring Resistance Genes to Quinolones and/or Extended-Spectrum Cephalosporins in Multiple Salmonella enterica Serotypes from Swine in the United States
Elnekave, Ehud, Hong, Samuel L, Lim, Seunghyun, Hayer, Shivdeep S, Boxrud, Dave, Taylor, Angela J, Lappi, Victoria, Noyes, Noelle, Johnson, Timothy J, Rovira, Albert, Davies, Peter, Perez, Andres, Alvarez, Julio
Published in Antimicrobial agents and chemotherapy (01.04.2019)
Published in Antimicrobial agents and chemotherapy (01.04.2019)
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Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica : a large-scale analysis of 37 serotypes with a public health impact in the USA
Elnekave, Ehud, Hong, Samuel L, Lim, Seunghyun, Johnson, Timothy J, Perez, Andres, Alvarez, Julio
Published in Microbial genomics (01.09.2020)
Published in Microbial genomics (01.09.2020)
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On the importance of assessing topological convergence in Bayesian phylogenetic inference
Brusselmans, Marius, Carvalho, Luiz Max, Hong, Samuel L, Gao, Jiansi, Matsen, Frederick A, Rambaut, Andrew, Lemey, Philippe, Suchard, Marc A, Dudas, Gytis, Baele, Guy
Published in ArXiv.org (19.08.2024)
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Published in ArXiv.org (19.08.2024)
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