Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data
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DOI: 10.1371/journal.pcbi.1006930
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- Gavin J. D. Smith & Dhanasekaran Vijaykrishna & Justin Bahl & Samantha J. Lycett & Michael Worobey & Oliver G. Pybus & Siu Kit Ma & Chung Lam Cheung & Jayna Raghwani & Samir Bhatt & J. S. Malik Peiris, 2009. "Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic," Nature, Nature, vol. 459(7250), pages 1122-1125, June.
- Neil M. Ferguson & Christl A. Donnelly & Roy M. Anderson, 2001. "Transmission intensity and impact of control policies on the foot and mouth epidemic in Great Britain," Nature, Nature, vol. 413(6855), pages 542-548, October.
- J. O. Lloyd-Smith & S. J. Schreiber & P. E. Kopp & W. M. Getz, 2005. "Superspreading and the effect of individual variation on disease emergence," Nature, Nature, vol. 438(7066), pages 355-359, November.
- Matthew Hall & Mark Woolhouse & Andrew Rambaut, 2015. "Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set," PLOS Computational Biology, Public Library of Science, vol. 11(12), pages 1-36, December.
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Cited by:
- Joshua L. Warren & Melanie H. Chitwood & Benjamin Sobkowiak & Caroline Colijn & Ted Cohen, 2023. "Spatial modeling of Mycobacterium tuberculosis transmission with dyadic genetic relatedness data," Biometrics, The International Biometric Society, vol. 79(4), pages 3650-3663, December.
- Benjamin B. Lindsey & Ch. Julián Villabona-Arenas & Finlay Campbell & Alexander J. Keeley & Matthew D. Parker & Dhruv R. Shah & Helena Parsons & Peijun Zhang & Nishchay Kakkar & Marta Gallis & Benjami, 2022. "Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
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