Eight challenges in phylodynamic inference
The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, signif...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2015-03-01
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| Series: | Epidemics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1755436514000437 |
| _version_ | 1831765402840989696 |
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| author | Simon D.W. Frost Oliver G. Pybus Julia R. Gog Cecile Viboud Sebastian Bonhoeffer Trevor Bedford |
| author_facet | Simon D.W. Frost Oliver G. Pybus Julia R. Gog Cecile Viboud Sebastian Bonhoeffer Trevor Bedford |
| author_sort | Simon D.W. Frost |
| collection | DOAJ |
| description | The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data. |
| first_indexed | 2024-12-22T06:01:51Z |
| format | Article |
| id | doaj.art-10fb898006da46ecb29e0a56267b4781 |
| institution | Directory Open Access Journal |
| issn | 1755-4365 1878-0067 |
| language | English |
| last_indexed | 2024-12-22T06:01:51Z |
| publishDate | 2015-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Epidemics |
| spelling | doaj.art-10fb898006da46ecb29e0a56267b47812022-12-21T18:36:31ZengElsevierEpidemics1755-43651878-00672015-03-0110C889210.1016/j.epidem.2014.09.001Eight challenges in phylodynamic inferenceSimon D.W. Frost0Oliver G. Pybus1Julia R. Gog2Cecile Viboud3Sebastian Bonhoeffer4Trevor Bedford5Department of Veterinary Medicine, University of Cambridge, Cambridge, UKDepartment of Zoology, University of Oxford, Oxford, UKDepartment of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UKFogarty International Center, National Institutes of Health, Bethesda, USAInstitute of. Integrative Biology, ETH Zurich, Zurich, SwitzerlandVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USAThe field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data.http://www.sciencedirect.com/science/article/pii/S1755436514000437PhylodynamicsCoalescent modelsSelectionRecombination |
| spellingShingle | Simon D.W. Frost Oliver G. Pybus Julia R. Gog Cecile Viboud Sebastian Bonhoeffer Trevor Bedford Eight challenges in phylodynamic inference Epidemics Phylodynamics Coalescent models Selection Recombination |
| title | Eight challenges in phylodynamic inference |
| title_full | Eight challenges in phylodynamic inference |
| title_fullStr | Eight challenges in phylodynamic inference |
| title_full_unstemmed | Eight challenges in phylodynamic inference |
| title_short | Eight challenges in phylodynamic inference |
| title_sort | eight challenges in phylodynamic inference |
| topic | Phylodynamics Coalescent models Selection Recombination |
| url | http://www.sciencedirect.com/science/article/pii/S1755436514000437 |
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