Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences by Arnaud Di Franco, Raphaël Poujol, Denis Baurain, Hervé Philippe

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Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis by Sana Naderi, Peter E Chen, Carmen Lia Murall, Raphael Poujol, Susanne Kraemer, Bradley S Pickering, Selena M Sagan, B Jesse Shapiro

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Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission by Mehdi Benlarbi, Shilei Ding, Étienne Bélanger, Alexandra Tauzin, Raphaël Poujol, Halima Medjahed, Omar El Ferri, Yuxia Bo, Catherine Bourassa, Julie Hussin, Judith Fafard, Marzena Pazgier, Inès Levade, Cameron Abrams, Marceline Côté, Andrés Finzi

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Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes. by Bastien Paré, Marieke Rozendaal, Sacha Morin, Léa Kaufmann, Shawn M Simpson, Raphaël Poujol, Fatima Mostefai, Jean-Christophe Grenier, Henry Xing, Miguelle Sanchez, Ariane Yechouron, Ronald Racette, Julie G Hussin, Guy Wolf, Ivan Pavlov, Martin A Smith

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Selection for immune evasion in SARS-CoV-2 revealed by high-resolution epitope mapping and sequence analysis by Arnaud N’Guessan, Senthilkumar Kailasam, Fatima Mostefai, Raphaël Poujol, Jean-Christophe Grenier, Nailya Ismailova, Paola Contini, Raffaele De Palma, Carsten Haber, Volker Stadler, Guillaume Bourque, Julie G. Hussin, B. Jesse Shapiro, Jörg H. Fritz, Ciriaco A. Piccirillo

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Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results by Cantin Baron, Sarah Cherkaoui, Sandra Therrien-Laperriere, Yann Ilboudo, Raphaël Poujol, Pamela Mehanna, Melanie E. Garrett, Marilyn J. Telen, Allison E. Ashley-Koch, Pablo Bartolucci, John D. Rioux, Guillaume Lettre, Christine Des Rosiers, Matthieu Ruiz, Julie G. Hussin

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Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis by Dominique Fournelle, Fatima Mostefai, Elsa Brunet-Ratnasingham, Raphaël Poujol, Jean-Christophe Grenier, José Héctor Gálvez, Amélie Pagliuzza, Inès Levade, Sandrine Moreira, Mehdi Benlarbi, Guillaume Beaudoin-Bussières, Gabrielle Gendron-Lepage, Catherine Bourassa, Alexandra Tauzin, Simon Grandjean Lapierre, Nicolas Chomont, Andrés Finzi, Daniel E. Kaufmann, Morgan Craig, Julie G. Hussin

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Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines by Kevin A. Kovalchik, David J. Hamelin, Peter Kubiniok, Benoîte Bourdin, Fatima Mostefai, Raphaël Poujol, Bastien Paré, Shawn M. Simpson, John Sidney, Éric Bonneil, Mathieu Courcelles, Sunil Kumar Saini, Mohammad Shahbazy, Saketh Kapoor, Vigneshwar Rajesh, Maya Weitzen, Jean-Christophe Grenier, Bayrem Gharsallaoui, Loïze Maréchal, Zhaoguan Wu, Christopher Savoie, Alessandro Sette, Pierre Thibault, Isabelle Sirois, Martin A. Smith, Hélène Decaluwe, Julie G. Hussin, Mathieu Lavallée-Adam, Etienne Caron

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