Publications by authors named "Timothy Vaughan"

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Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data.
Timothy G Vaughan, Tanja Stadler

Mol Biol Evol· June 2025

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The Fossilized Birth-Death Model Is Identifiable.
Kate Truman, Timothy G Vaughan, Alex Gavryushkin, Alexandra Sasha Gavryushkina

Syst Biol· February 2025

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Estimating pathogen spread using structured coalescent and birth-death models: A quantitative comparison.
Sophie Seidel, Tanja Stadler, Timothy G Vaughan

Epidemics· December 2024

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EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.
Ciara Judge, Timothy Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis

PLoS Comput Biol· November 2024

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Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction.
Bethany J Allen, Maria V Volkova Oliveira, Tanja Stadler, Timothy G Vaughan, Rachel C M Warnock

Camb Prism Extinct· April 2024

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Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data.
Timothy G Vaughan, Jérémie Scire, Sarah A Nadeau, Tanja Stadler

Proc Natl Acad Sci U S A· January 2024

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ReMASTER: improved phylodynamic simulation for BEAST 2.7.
Timothy G Vaughan

Bioinformatics· January 2024

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Correction: Chaby et al. Cross-Platform Evaluation of Commercially Targeted and Untargeted Metabolomics Approaches to Optimize the Investigation of Psychiatric Disease. 2021, , 609.
Lauren E Chaby, Heather C Lasseter, Kévin Contrepois, Reza M Salek, Christoph W Turck, Timothy Vaughan

Metabolites· August 2023

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Decoding the Fundamental Drivers of Phylodynamic Inference.
Leo A Featherstone, Sebastian Duchene, Timothy G Vaughan

Mol Biol Evol· June 2023

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Bayesian phylodynamics reveals the transmission dynamics of avian influenza A(H7N9) virus at the human-live bird market interface in China.
Claire Guinat, Hao Tang, Qiqi Yang, Cecilia Valenzuela Agüí, Timothy G Vaughan

Proc Natl Acad Sci U S A· April 2023

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Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data.
Sarah A Nadeau, Timothy G Vaughan, Christiane Beckmann, Ivan Topolsky, Chaoran Chen

Sci Transl Med· January 2023

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Comparative Epidemiology of Rabbit Haemorrhagic Disease Virus Strains from Viral Sequence Data.
Carlo Pacioni, Robyn N Hall, Tanja Strive, David S L Ramsey, Mandev S Gill, Timothy G Vaughan

Viruses· December 2022

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The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies.
Jana S Huisman, Timothy G Vaughan, Adrian Egli, Sarah Tschudin-Sutter, Tanja Stadler

Philos Trans R Soc Lond B Biol Sci· October 2022

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TreeKnit: Inferring ancestral reassortment graphs of influenza viruses.
Pierre Barrat-Charlaix, Timothy G Vaughan, Richard A Neher

PLoS Comput Biol· August 2022

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Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus in Europe.
Claire Guinat, Cecilia Valenzuela Agüí, Timothy G Vaughan, Jérémie Scire, Anne Pohlmann

Virus Evol· August 2022

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Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations.
Jérémie Scire, Joëlle Barido-Sottani, Denise Kühnert, Timothy G Vaughan, Tanja Stadler

Viruses· July 2022

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Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications.
Leo A Featherstone, Joshua M Zhang, Timothy G Vaughan, Sebastian Duchene

Virus Evol· June 2022

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Field validation of phylodynamic analytical methods for inference on epidemiological processes in wildlife.
Carlo Pacioni, Timothy G Vaughan, Tanja Strive, Susan Campbell, David S L Ramsey

Transbound Emerg Dis· May 2022

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

Mol Biol Evol· January 2022

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Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales.
Huw A Ogilvie, Fábio K Mendes, Timothy G Vaughan, Nicholas J Matzke, Tanja Stadler

Syst Biol· December 2021

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Cross-Platform Evaluation of Commercially Targeted and Untargeted Metabolomics Approaches to Optimize the Investigation of Psychiatric Disease.
Lauren E Chaby, Heather C Lasseter, Kévin Contrepois, Reza M Salek, Christoph W Turck, Timothy Vaughan

Metabolites· September 2021

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Spread of a SARS-CoV-2 variant through Europe in the summer of 2020.
Emma B Hodcroft, Moira Zuber, Sarah Nadeau, Timothy G Vaughan, Katharine H D Crawford

Nature· July 2021

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Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020.
Emma B Hodcroft, Moira Zuber, Sarah Nadeau, Timothy G Vaughan, Katharine H D Crawford

medRxiv· March 2021

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The origin and early spread of SARS-CoV-2 in Europe.
Sarah A Nadeau, Timothy G Vaughan, Jérémie Scire, Jana S Huisman, Tanja Stadler

Proc Natl Acad Sci U S A· March 2021

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The probability distribution of the ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data.
Marc Manceau, Ankit Gupta, Timothy Vaughan, Tanja Stadler

J Theor Biol· January 2021

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