SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent von De Maio, Nicola, Wu, Chieh-Hsi, Wilson, Daniel J

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phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets von De Maio, Nicola, Boulton, William, Weilguny, Lukas, Walker, Conor R, Turakhia, Yatish, Corbett-Detig, Russell, Goldman, Nick

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Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system von Crispell, Joseph, Benton, Clare H, Balaz, Daniel, De Maio, Nicola, Ahkmetova, Assel, Allen, Adrian, Biek, Roman, Presho, Eleanor L, Dale, James, Hewinson, Glyn, Lycett, Samantha J, Nunez-Garcia, Javier, Skuce, Robin A, Trewby, Hannah, Wilson, Daniel J, Zadoks, Ruth N, Delahay, Richard J, Kao, Rowland Raymond

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Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines von Bush, Stephen J, Foster, Dona, Eyre, David W, Clark, Emily L, De Maio, Nicola, Shaw, Liam P, Stoesser, Nicole, Peto, Tim E A, Crook, Derrick W, Walker, A Sarah

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VGsim: Scalable viral genealogy simulator for global pandemic von Shchur, Vladimir, Spirin, Vadim, Sirotkin, Dmitry, Burovski, Evgeni, De Maio, Nicola, Corbett-Detig, Russell

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Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic von Turakhia, Yatish, Thornlow, Bryan, Hinrichs, Angie S., De Maio, Nicola, Gozashti, Landen, Lanfear, Robert, Haussler, David, Corbett-Detig, Russell

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New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation von De Maio, Nicola, Wu, Chieh-Hsi, O'Reilly, Kathleen M, Wilson, Daniel

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PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals von Kofler, Robert, Orozco-terWengel, Pablo, De Maio, Nicola, Pandey, Ram Vinay, Nolte, Viola, Futschik, Andreas, Kosiol, Carolin, Schlötterer, Christian

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Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk von Kalkauskas, Antanas, Perron, Umberto, Sun, Yuxuan, Goldman, Nick, Baele, Guy, Guindon, Stephane, De Maio, Nicola

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Stability of SARS-CoV-2 phylogenies von Turakhia, Yatish, De Maio, Nicola, Thornlow, Bryan, Gozashti, Landen, Lanfear, Robert, Walker, Conor R., Hinrichs, Angie S., Fernandes, Jason D., Borges, Rui, Slodkowicz, Greg, Weilguny, Lukas, Haussler, David, Goldman, Nick, Corbett-Detig, Russell

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A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages von 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

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The Bacterial Sequential Markov Coalescent von De Maio, Nicola, Wilson, Daniel J

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Short-range template switching in great ape genomes explored using pair hidden Markov models von Walker, Conor R., Scally, Aylwyn, De Maio, Nicola, Goldman, Nick

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Bayesian reconstruction of transmission within outbreaks using genomic variants von De Maio, Nicola, Worby, Colin J, Wilson, Daniel J, Stoesser, Nicole

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Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131 von Stoesser, Nicole, Sheppard, Anna E, Pankhurst, Louise, De Maio, Nicola, Moore, Catrin E, Sebra, Robert, Turner, Paul, Anson, Luke W, Kasarskis, Andrew, Batty, Elizabeth M, Kos, Veronica, Wilson, Daniel J, Phetsouvanh, Rattanaphone, Wyllie, David, Sokurenko, Evgeni, Manges, Amee R, Johnson, Timothy J, Price, Lance B, Peto, Timothy E A, Johnson, James R, Didelot, Xavier, Walker, A Sarah, Crook, Derrick W

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Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple... von Martin, Jessica, Phan, Hang T T, Findlay, Jacqueline, Stoesser, Nicole, Pankhurst, Louise, Navickaite, Indre, De Maio, Nicola, Eyre, David W, Toogood, Giles, Orsi, Nicolas M, Kirby, Andrew, Young, Nicola, Turton, Jane F, Hill, Robert L R, Hopkins, Katie L, Woodford, Neil, Peto, Tim E A, Walker, A Sarah, Crook, Derrick W, Wilcox, Mark H

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Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum von Ionescu, Danny, Bizic-Ionescu, Mina, De Maio, Nicola, Cypionka, Heribert, Grossart, Hans-Peter

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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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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes von De Maio, Nicola, Shaw, Liam P, Hubbard, Alasdair, George, Sophie, Sanderson, Nicholas D, Swann, Jeremy, Wick, Ryan, AbuOun, Manal, Stubberfield, Emma, Hoosdally, Sarah J, Crook, Derrick W, Peto, Timothy E A, Sheppard, Anna E, Bailey, Mark J, Read, Daniel S, Anjum, Muna F, Walker, A Sarah, Stoesser, Nicole, On Behalf Of The Rehab Consortium

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Genomic network analysis of environmental and livestock F-type plasmid populations von Matlock, William, Chau, Kevin K., AbuOun, Manal, Stubberfield, Emma, Barker, Leanne, Kavanagh, James, Pickford, Hayleah, Gilson, Daniel, Smith, Richard P., Gweon, H. Soon, Hoosdally, Sarah J., Swann, Jeremy, Sebra, Robert, Bailey, Mark J., Peto, Timothy E. A., Crook, Derrick W., Anjum, Muna F., Read, Daniel S., Walker, A. Sarah, Stoesser, Nicole, Shaw, Liam P.

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