pyseer: a comprehensive tool for microbial pangenome-wide association studies von Lees, John A, Galardini, Marco, Bentley, Stephen D, Weiser, Jeffrey N, Corander, Jukka

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Producing polished prokaryotic pangenomes with the Panaroo pipeline von Tonkin-Hill, Gerry, MacAlasdair, Neil, Ruis, Christopher, Weimann, Aaron, Horesh, Gal, Lees, John A., Gladstone, Rebecca A., Lo, Stephanie, Beaudoin, Christopher, Floto, R. Andres, Frost, Simon D.W., Corander, Jukka, Bentley, Stephen D., Parkhill, Julian

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Fast hierarchical Bayesian analysis of population structure von Tonkin-Hill, Gerry, Lees, John A, Bentley, Stephen D, Frost, Simon D W, Corander, Jukka

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Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes von Lees, John A., Vehkala, Minna, Välimäki, Niko, Harris, Simon R., Chewapreecha, Claire, Croucher, Nicholas J., Marttinen, Pekka, Davies, Mark R., Steer, Andrew C., Tong, Steven Y. C., Honkela, Antti, Parkhill, Julian, Bentley, Stephen D., Corander, Jukka

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Immune exclusion by naturally acquired secretory IgA against pneumococcal pilus-1 von Binsker, Ulrike, Lees, John A, Hammond, Alexandria J, Weiser, Jeffrey N

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Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions von Lees, John A, Mai, T Tien, Galardini, Marco, Wheeler, Nicole E, Horsfield, Samuel T, Parkhill, Julian, Corander, Jukka

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Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era von Pöntinen, Anna K., Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R., Novais, Carla, Gladstone, Rebecca A., Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A., Jamrozy, Dorota, Bentley, Stephen D., Lanza, Val F., Torres, Carmen, Peixe, Luisa, Coque, Teresa M., Parkhill, Julian, Schürch, Anita C., Willems, Rob J. L., Corander, Jukka

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RhierBAPS: An R implementation of the population clustering algorithm hierBAPS von Tonkin-Hill, Gerry, Lees, John A, Bentley, Stephen D, Frost, Simon D W, Corander, Jukka

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Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration von Lees, John A, Croucher, Nicholas J, Goldblatt, David, Nosten, François, Parkhill, Julian, Turner, Claudia, Turner, Paul, Bentley, Stephen D

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Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria von Watson, Oliver J., Alhaffar, Mervat, Mehchy, Zaki, Whittaker, Charles, Akil, Zack, Brazeau, Nicholas F., Cuomo-Dannenburg, Gina, Hamlet, Arran, Thompson, Hayley A., Baguelin, Marc, FitzJohn, Richard G., Knock, Edward, Lees, John A., Whittles, Lilith K., Mellan, Thomas, Winskill, Peter, Howard, Natasha, Clapham, Hannah, Checchi, Francesco, Ferguson, Neil, Ghani, Azra, Beals, Emma, Walker, Patrick

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Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia von Chapman, Lloyd A. C., Aubry, Maite, Maset, Noémie, Russell, Timothy W., Knock, Edward S., Lees, John A., Mallet, Henri-Pierre, Cao-Lormeau, Van-Mai, Kucharski, Adam J.

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Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis von Xie, Ouli, Morris, Jacqueline M., Hayes, Andrew J., Towers, Rebecca J., Jespersen, Magnus G., Lees, John A., Ben Zakour, Nouri L., Berking, Olga, Baines, Sarah L., Carter, Glen P., Tonkin-Hill, Gerry, Schrieber, Layla, McIntyre, Liam, Lacey, Jake A., James, Taylah B., Sriprakash, Kadaba S., Beatson, Scott A., Hasegawa, Tadao, Giffard, Phil, Steer, Andrew C., Batzloff, Michael R., Beall, Bernard W., Pinho, Marcos D., Ramirez, Mario, Bessen, Debra E., Dougan, Gordon, Bentley, Stephen D., Walker, Mark J., Currie, Bart J., Tong, Steven Y. C., McMillan, David J., Davies, Mark R.

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Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population ge... von Gladstone, Rebecca A, McNally, Alan, Pöntinen, Anna K, Tonkin-Hill, Gerry, Lees, John A, Skytén, Kusti, Cléon, François, Christensen, Martin O K, Haldorsen, Bjørg C, Bye, Kristina K, Gammelsrud, Karianne W, Hjetland, Reidar, Kümmel, Angela, Larsen, Hege E, Lindemann, Paul Christoffer, Löhr, Iren H, Marvik, Åshild, Nilsen, Einar, Noer, Marie T, Simonsen, Gunnar S, Steinbakk, Martin, Tofteland, Ståle, Vattøy, Marit, Bentley, Stephen D, Croucher, Nicholas J, Parkhill, Julian, Johnsen, Pål J, Samuelsen, Ørjan, Corander, Jukka

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Pneumococcal genetic variability in age-dependent bacterial carriage von Kremer, Philip H C, Ferwerda, Bart, Bootsma, Hester J, Rots, Nienke Y, Wijmenga-Monsuur, Alienke J, Sanders, Elisabeth A M, Trzciński, Krzysztof, Wyllie, Anne L, Turner, Paul, van der Ende, Arie, Brouwer, Matthijs C, Bentley, Stephen D, van de Beek, Diederik, Lees, John A

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Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study von Lees, John A, Kendall, Michelle, Parkhill, Julian, Colijn, Caroline, Bentley, Stephen D, Harris, Simon R

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Pneumococcal capsule blocks protection by immunization with conserved surface proteins von Zangari, Tonia, Zafar, M. Ammar, Lees, John A., Abruzzo, Annie R., Bee, Gavyn Chern Wei, Weiser, Jeffrey N.

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Fast and flexible bacterial genomic epidemiology with PopPUNK von Lees, John A, Harris, Simon R, Tonkin-Hill, Gerry, Gladstone, Rebecca A, Lo, Stephanie W, Weiser, Jeffrey N, Corander, Jukka, Bentley, Stephen D, Croucher, Nicholas J

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Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation von Lees, John A., Tonkin-Hill, Gerry, Yang, Zhirong, Corander, Jukka

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Genealogical inference and more flexible sequence clustering using iterative-PopPUNK von Zhao, Bin, Lees, John A, Wu, Hongjin, Yang, Chao, Falush, Daniel

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Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study von Sonabend, Raphael, Whittles, Lilith K, Imai, Natsuko, Perez-Guzman, Pablo N, Knock, Edward S, Rawson, Thomas, Gaythorpe, Katy A M, Djaafara, Bimandra A, Hinsley, Wes, FitzJohn, Richard G, Lees, John A, Kanapram, Divya Thekke, Volz, Erik M, Ghani, Azra C, Ferguson, Neil M, Baguelin, Marc, Cori, Anne

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