Recombination rate and selection strength in HIV intra-patient evolution. Autor Richard A Neher, Thomas Leitner

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Eco-evolutionary dynamics of adapting pathogens and host immunity Autor Pierre Barrat-Charlaix, Richard A Neher

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Inferring HIV escape rates from multi-locus genotype data Autor Taylor A Kessinger, Alan S Perelson, Richard A Neher

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Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens Autor Le Yan, Richard A Neher, Boris I Shraiman

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Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition Autor Jover Lee, James Hadfield, Allison Black, Thomas R. Sibley, Richard A. Neher, Richard A. Neher, Trevor Bedford, Trevor Bedford, John Huddleston

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TreeKnit: Inferring ancestral reassortment graphs of influenza viruses. Autor Pierre Barrat-Charlaix, Timothy G Vaughan, Richard A Neher

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Predicting evolution from the shape of genealogical trees Autor Richard A Neher, Colin A Russell, Boris I Shraiman

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Potential impact of seasonal forcing on a SARS-CoV-2 pandemic Autor Richard A. Neher, Robert Dyrdak, Valentin Druelle, Emma B. Hodcroft, Jan Albert

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Correlated evolution of nearby residues in Drosophilid proteins. Autor Benjamin Callahan, Richard A Neher, Doris Bachtrog, Peter Andolfatto, Boris I Shraiman

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Population genomics of intrapatient HIV-1 evolution Autor Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Göran Bratt, Jan Albert, Richard A Neher

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Challenges with using primer IDs to improve accuracy of next generation sequencing. Autor Johanna Brodin, Charlotte Hedskog, Alexander Heddini, Emmanuel Benard, Richard A Neher, Mattias Mild, Jan Albert

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Establishment and stability of the latent HIV-1 DNA reservoir Autor Johanna Brodin, Fabio Zanini, Lina Thebo, Christa Lanz, Göran Bratt, Richard A Neher, Jan Albert

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2019-Novel Coronavirus (2019-nCoV): estimating the case fatality rate – a word of caution Autor Manuel Battegay, Richard Kuehl, Sarah Tschudin-Sutter, Hans H. Hirsch, Andreas F. Widmer, Richard A. Neher

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Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021 Autor Martina L. Reichmuth, Emma B. Hodcroft, Julien Riou, Richard A. Neher, Niel Hens, Christian L. Althaus

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Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2 Autor Jana S Huisman, Jérémie Scire, Daniel C Angst, Jinzhou Li, Richard A Neher, Marloes H Maathuis, Sebastian Bonhoeffer, Tanja Stadler

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Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering Autor Yuan You, Aneta Sawikowska, Manuela Neumann, David Posé, Giovanna Capovilla, Tobias Langenecker, Richard A. Neher, Paweł Krajewski, Markus Schmid

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HIV Cell-to-Cell Spread Results in Earlier Onset of Viral Gene Expression by Multiple Infections per Cell. Autor Mikaël Boullé, Thorsten G Müller, Sabrina Dähling, Yashica Ganga, Laurelle Jackson, Deeqa Mahamed, Lance Oom, Gila Lustig, Richard A Neher, Alex Sigal

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Asynchrony between virus diversity and antibody selection limits influenza virus evolution Autor Dylan H Morris, Velislava N Petrova, Fernando W Rossine, Edyth Parker, Bryan T Grenfell, Richard A Neher, Simon A Levin, Colin A Russell

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Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform Autor Adrian Egli, Dominique S. Blanc, Gilbert Greub, Peter M. Keller, Vladimir Lazarevic, Aitana Lebrand, Stephen Leib, Richard A. Neher, Vincent Perreten, Alban Ramette, Jacques Schrenzel, Roger Stephan, Karoline Wagner, Daniel Wüthrich, Ioannis Xenarios

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Evolution, geographic spreading, and demographic distribution of Enterovirus D68. Autor Emma B Hodcroft, Robert Dyrdak, Cristina Andrés, Adrian Egli, Josiane Reist, Diego García Martínez de Artola, Julia Alcoba-Flórez, Hubert G M Niesters, Andrés Antón, Randy Poelman, Marijke Reynders, Elke Wollants, Richard A Neher, Jan Albert

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