Molecular‐clock methods for estimating evolutionary rates and timescales
… Choosing a clock-partitioning scheme poses an interesting challenge and can have a
considerable influence on the resulting estimates of divergence times (Duchêne & Ho 2014a). …
considerable influence on the resulting estimates of divergence times (Duchêne & Ho 2014a). …
[HTML][HTML] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
…, J Barido-Sottani, S Duchêne… - PLoS computational …, 2019 - journals.plos.org
… The calculation time of Felsenstein’s likelihood, ie, the probability of sequence data given
a tree or network and model parameters, which typically takes up the bulk of computing time, …
a tree or network and model parameters, which typically takes up the bulk of computing time, …
[PDF][PDF] The recovery, interpretation and use of ancient pathogen genomes
… catastrophe because a quarter of Ireland’s people subsisted on potatoes and a great
many … demographic decline near 30% of Ireland’s population (worse than what Ireland suffered …
many … demographic decline near 30% of Ireland’s population (worse than what Ireland suffered …
Temporal signal and the phylodynamic threshold of SARS-CoV-2
S Duchene, L Featherstone… - Virus …, 2020 - academic.oup.com
… For example, before the phylodynamic threshold is reached, genomic variation is so low
that even large amounts of genome sequences may be insufficient to estimate the virus’s …
that even large amounts of genome sequences may be insufficient to estimate the virus’s …
[HTML][HTML] Understanding dengue virus evolution to support epidemic surveillance and counter-measure development
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global
burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological …
burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological …
Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus
Recent genomic data have revealed multiple interactions between Neanderthals and modern
humans 1 , but there is currently little genetic evidence regarding Neanderthal behaviour, …
humans 1 , but there is currently little genetic evidence regarding Neanderthal behaviour, …
Depth synthesis and local warps for plausible image-based navigation
… We denote the set of all superpixels in an image by S = {Si }i∈{0...n−1}. We project the … We
concatenate the histograms to give a 60D descriptor HLab[Si ] for each superpixel Si ∈ S. We …
concatenate the histograms to give a 60D descriptor HLab[Si ] for each superpixel Si ∈ S. We …
[HTML][HTML] Tracking the COVID-19 pandemic in Australia using genomics
… credit to the original author(s) and the source, provide a … ’s Creative Commons license,
unless indicated otherwise in a credit line to the material. If material is not included in the article’s …
unless indicated otherwise in a credit line to the material. If material is not included in the article’s …
Genome-scale rates of evolutionary change in bacteria
Estimating the rates at which bacterial genomes evolve is critical to understanding major
evolutionary and ecological processes such as disease emergence, long-term host–pathogen …
evolutionary and ecological processes such as disease emergence, long-term host–pathogen …
[PDF][PDF] 17th century variola virus reveals the recent history of smallpox
…, D Poinar, MV Emery, JP Buchmann, S Duchêne… - Current Biology, 2016 - cell.com
Smallpox holds a unique position in the history of medicine. It was the first disease for which
a vaccine was developed and remains the only human disease eradicated by vaccination. …
a vaccine was developed and remains the only human disease eradicated by vaccination. …