Practical considerations for measuring the effective reproductive number, Rt von Gostic, Katelyn M, McGough, Lauren, Baskerville, Edward B, Abbott, Sam, Joshi, Keya, Tedijanto, Christine, Kahn, Rebecca, Niehus, Rene, Hay, James A, De Salazar, Pablo M, Hellewell, Joel, Meakin, Sophie, Munday, James D, Bosse, Nikos I, Sherrat, Katharine, Thompson, Robin N, White, Laura F, Huisman, Jana S, Scire, Jérémie, Bonhoeffer, Sebastian, Stadler, Tanja, Wallinga, Jacco, Funk, Sebastian, Lipsitch, Marc, Cobey, Sarah

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Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut von Bakkeren, Erik, Huisman, Jana S., Fattinger, Stefan A., Hausmann, Annika, Furter, Markus, Egli, Adrian, Slack, Emma, Sellin, Mikael E., Bonhoeffer, Sebastian, Regoes, Roland R., Diard, Médéric, Hardt, Wolf-Dietrich

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Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2 von Huisman, Jana S, Scire, Jérémie, Caduff, Lea, Fernandez-Cassi, Xavier, Ganesanandamoorthy, Pravin, Kull, Anina, Scheidegger, Andreas, Stachler, Elyse, Boehm, Alexandria B, Hughes, Bridgette, Knudson, Alisha, Topol, Aaron, Wigginton, Krista R, Wolfe, Marlene K, Kohn, Tamar, Ort, Christoph, Stadler, Tanja, Julian, Timothy R

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

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estimateR: an R package to estimate and monitor the effective reproductive number von Scire, Jérémie, Huisman, Jana S, Grosu, Ana, Angst, Daniel C, Lison, Adrian, Li, Jinzhou, Maathuis, Marloes H, Bonhoeffer, Sebastian, Stadler, Tanja

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The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies von Huisman, Jana S, Vaughan, Timothy G, Egli, Adrian, Tschudin-Sutter, Sarah, Stadler, Tanja, Bonhoeffer, Sebastian

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COVID-19 infectivity profile correction von Ashcroft, Peter, Huisman, Jana S, Lehtinen, Sonja, Bouman, Judith A, Althaus, Christian L, Regoes, Roland R, Bonhoeffer, Sebastian

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Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium von Bakkeren, Erik, Gül, Ersin, Huisman, Jana S., Steiger, Yves, Rocker, Andrea, Hardt, Wolf-Dietrich, Diard, Médéric

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Evolutionary mechanisms that determine which bacterial genes are carried on plasmids von Lehtinen, Sonja, Huisman, Jana S., Bonhoeffer, Sebastian

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Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany von Brockhaus, Elisabeth K, Wolffram, Daniel, Stadler, Tanja, Osthege, Michael, Mitra, Tanmay, Littek, Jonas M, Krymova, Ekaterina, Klesen, Anna J, Huisman, Jana S, Heyder, Stefan, Helleckes, Laura M, An der Heiden, Matthias, Funk, Sebastian, Abbott, Sam, Bracher, Johannes

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Influenza transmission dynamics quantified from RNA in wastewater in Switzerland von Nadeau, Sarah, Devaux, Alexander J, Bagutti, Claudia, Alt, Monica, Ilg Hampe, Evelyn, Kraus, Melanie, Würfel, Eva, Koch, Katrin N, Fuchs, Simon, Tschudin-Sutter, Sarah, Holschneider, Aurélie, Ort, Christoph, Chen, Chaoran, Huisman, Jana S, Julian, Timothy R, Stadler, Tanja

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Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases von Pires, João, Huisman, Jana S, Bonhoeffer, Sebastian, Van Boeckel, Thomas P

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Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications von Pasin, Chloé, Consiglio, Camila R, Huisman, Jana S, de Lange, Ann-Marie G, Peckham, Hannah, Vallejo-Yagüe, Enriqueta, Abela, Irene A, Islander, Ulrika, Neuner-Jehle, Nadia, Pujantell, Maria, Roth, Olivia, Schirmer, Melanie, Tepekule, Burcu, Zeeb, Marius, Hachfeld, Anna, Aebi-Popp, Karoline, Kouyos, Roger D, Bonhoeffer, Sebastian

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Digest: The importance of genetic background in bacterial evolution von Dionisi, Sara, Huisman, Jana S

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Correction: Practical considerations for measuring the effective reproductive number, Rt von Gostic, Katelyn M, McGough, Lauren, Baskerville, Edward B, Abbott, Sam, Joshi, Keya, Tedijanto, Christine, Kahn, Rebecca, Niehus, Rene, Hay, James A, De Salazar, Pablo M, Hellewell, Joel, Meakin, Sophie, Munday, James D, Bosse, Nikos I, Sherrat, Katharine, Thompson, Robin N, White, Laura F, Huisman, Jana S, Scire, Jérémie, Bonhoeffer, Sebastian, Stadler, Tanja, Wallinga, Jacco, Funk, Sebastian, Lipsitch, Marc, Cobey, Sarah

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The origin and early spread of SARS-CoV-2 in Europe von Nadeau, Sarah A., Vaughan, Timothy G., Scire, Jérémie, Huisman, Jana S., Stadler, Tanja

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Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics von Igler, Claudia, Huisman, Jana S, Siedentop, Berit, Bonhoeffer, Sebastian, Lehtinen, Sonja

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Guidelines for the estimation and reporting of plasmid conjugation rates von Kosterlitz, Olivia, Huisman, Jana S.

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Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases von Pires, João, Huisman, Jana S, Bonhoeffer, Sebastian, Van Boeckel, Thomas P

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Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State von Carroll, Laura M., Huisman, Jana S., Wiedmann, Martin

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