Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic von Paredes, Miguel I., Ahmed, Nashwa, Figgins, Marlin, Colizza, Vittoria, Lemey, Philippe, McCrone, John T., Müller, Nicola, Tran-Kiem, Cécile, Bedford, Trevor

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Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli von Zampieri, Mattia, Hörl, Manuel, Hotz, Florian, Müller, Nicola F., Sauer, Uwe

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MASCOT: parameter and state inference under the marginal structured coalescent approximation von Müller, Nicola F, Rasmussen, David, Stadler, Tanja

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A Bayesian approach to infer recombination patterns in coronaviruses von Müller, Nicola F., Kistler, Kathryn E., Bedford, Trevor

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Joint Inference of Migration and Reassortment Patterns for Viruses with Segmented Genomes von Stolz, Ugnė, Stadler, Tanja, Müller, Nicola F, Vaughan, Timothy G

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The Structured Coalescent and Its Approximations von Müller, Nicola F, Rasmussen, David A, Stadler, Tanja

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Adaptive Metropolis-coupled MCMC for BEAST 2 von Müller, Nicola F., Bouckaert, Remco R.

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Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations von Layan, Maylis, Müller, Nicola F, Dellicour, Simon, De Maio, Nicola, Bourhy, Hervé, Cauchemez, Simon, Baele, Guy

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Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses von Müller, Nicola F., Stolz, Ugné, Dudas, Gytis, Stadler, Tanja, Vaughan, Timothy G.

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Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics von Müller, Nicola F, Wüthrich, Daniel, Goldman, Nina, Sailer, Nadine, Saalfrank, Claudia, Brunner, Myrta, Augustin, Noémi, Seth-Smith, Helena Mb, Hollenstein, Yvonne, Syedbasha, Mohammedyaseen, Lang, Daniela, Neher, Richard A, Dubuis, Olivier, Naegele, Michael, Buser, Andreas, Nickel, Christian H, Ritz, Nicole, Zeller, Andreas, Lang, Brian M, Hadfield, James, Bedford, Trevor, Battegay, Manuel, Schneider-Sliwa, Rita, Egli, Adrian, Stadler, Tanja

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Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment von Walas, Nikolina, Müller, Nicola F., Parker, Emily, Henderson, Abigail, Capone, Drew, Brown, Joe, Barker, Troy, Graham, Jay P.

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Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration von Yang, Jing, Müller, Nicola F, Bouckaert, Remco, Xu, Bing, Drummond, Alexei J

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis von Bouckaert, Remco, Vaughan, Timothy G, Barido-Sottani, Joëlle, Duchêne, Sebastián, Fourment, Mathieu, Gavryushkina, Alexandra, Heled, Joseph, Jones, Graham, Kühnert, Denise, De Maio, Nicola, Matschiner, Michael, Mendes, Fábio K, Müller, Nicola F, Ogilvie, Huw A, du Plessis, Louis, Popinga, Alex, Rambaut, Andrew, Rasmussen, David, Siveroni, Igor, Suchard, Marc A, Wu, Chieh-Hsi, Xie, Dong, Zhang, Chi, Stadler, Tanja, Drummond, Alexei J

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Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State von Moncla, Louise H, Black, Allison, DeBolt, Chas, Lang, Misty, Graff, Nicholas R, Pérez-Osorio, Ailyn C, Müller, Nicola F, Haselow, Dirk, Lindquist, Scott, Bedford, Trevor

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Taming the BEAST—A Community Teaching Material Resource for BEAST 2 von Barido-Sottani, Joëlle, Bošková, Veronika, du Plessis, Louis, Kühnert, Denise, Magnus, Carsten, Mitov, Venelin, Müller, Nicola F., Pečerska, Jūlija, Rasmussen, David A., Zhang, Chi, Drummond, Alexei J., Heath, Tracy A., Pybus, Oliver G., Vaughan, Timothy G., Stadler, Tanja

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Neuro-explicit semantic segmentation of the diffusion cloud chamber von Müller, Nicola J., Porawski, Daniel, Wilde, Lukas, Fink, Dennis, Trap, Guillaume, Engel, Annika, Schmartz, Georges P.

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Phylodynamic analysis of the highly pathogenic avian influenza H5N8 epidemic in France, 2016–2017 von Chakraborty, Debapriyo, Guinat, Claire, Müller, Nicola F., Briand, Francois‐Xavier, Andraud, Mathieu, Scoizec, Axelle, Lebouquin, Sophie, Niqueux, Eric, Schmitz, Audrey, Grasland, Beatrice, Guerin, Jean‐Luc, Paul, Mathilde C., Vergne, Timothée

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Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county von Paredes, Miguel I, Perofsky, Amanda C, Frisbie, Lauren, Moncla, Louise H, Roychoudhury, Pavitra, Xie, Hong, Bakhash, Shah A Mohamed, Kong, Kevin, Arnould, Isabel, Nguyen, Tien V, Wendm, Seffir T, Hajian, Pooneh, Ellis, Sean, Mathias, Patrick C, Greninger, Alexander L, Starita, Lea M, Frazar, Chris D, Ryke, Erica, Zhong, Weizhi, Gamboa, Luis, Threlkeld, Machiko, Lee, Jover, Stone, Jeremy, McDermot, Evan, Truong, Melissa, Shendure, Jay, Oltean, Hanna N, Viboud, Cécile, Chu, Helen, Müller, Nicola F, Bedford, Trevor

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Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations von Müller, Nicola F, Dudas, Gytis, Stadler, Tanja

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Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018 von Owuor, D Collins, de Laurent, Zaydah R, Kikwai, Gilbert K, Mayieka, Lillian M, Ochieng, Melvin, Müller, Nicola F, Otieno, Nancy A, Emukule, Gideon O, Hunsperger, Elizabeth A, Garten, Rebecca, Barnes, John R, Chaves, Sandra S, Nokes, D James, Agoti, Charles N

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