Details

Monday August 26

13.00 - 14.00
Registration
14.00 - 16.00
Lecture: Introduction to phylogenetics, phylodynamics and phylogeography
16.00 - 16.30
Coffee break
16.30 - 18.30
Lecture: Continuous-time Markov chain (CTMC) models on trees

Tuesday August 27

9.00 - 10.30
Lecture: Bayesian phylogenetics
10.30 - 11.00
Coffee break
11.00 - 13.00
Practical: Estimating rates and dates in yellow fever
13.00 - 14.30
Lunch
14.30 - 16.30
Lecture: Coalescent and birth-death-sampling processes
16.30 - 17.00
Coffee break
17.00 - 18.30
Participants' session
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Flexible phylodynamic modelling using general branching processes Frederik Mølkjær Andersen, Samir Bhatt, Carsten Wiuf

Bayesian Birth-Death Skyline Model - A Case Study on Heterochronous Maltese SARS-CoV-2 Genomic Data Gianluca Ursino, Monique Borg Inguanez, David Suda, Joseph Borg, Graziella Zahra

Time depth and the limits of phylogenetic inference in linguistics Emma Kopp, Robin J Ryder, Thomas Pellard, Guillaume Jacques

Bayesian inference of mixed Gaussian phylogenetic models Bayu Brahmantio, Krzysztof Bartoszek, Etka Yapar

Unravelling spatiotemporal heterogeneities of wild and vaccine-derived poliovirus spread: past and present Darlan da Silva Candido, Simon Dellicour, Laura V Cooper, Carlos A Prete Jr, David Jorgensen, Christopher B Uzzell, Arend Voorman, Hil Lyons, Dimitra Klapsa, Manasi Majumdar, Kafayat Arowolo, Corey M Peak, Ananda S Bandyopadhyay, Javier Martin, Nicholas C Grassly, Isobel M Blake

Quantifying the cross-species transmission events of SARS-CoV-2 between farmed mink and humans in Denmark between June and November 2020 Amanda Gammelby Qvesel, Marlies Jilles Francine Goedknegt, Esben Rahbek Thuesen, Thomas Bruun Rasmussen, Anders Gorm Pedersen

Wednesday August 28

9.00 - 11.00
Practical: Phylodynamic inference of respiratory viruses
11.00 - 11.30
Coffee break
11.30 - 13.00
Lecture: Scalable gradients in phylogenetics
13.00
Free afternoon and evening

Thursday August 29

9.00 - 10.30
Lecture: Modern CTMCs and phylogeography
10.30 - 11.00
Coffee break
11.00 - 13.00
Practical: Phylogeography diffusion in discrete space
13.00 - 14.30
Lunch
14.30 - 16.00
Lecture: Approximations and surrogate sampling
16.00 - 16.30
Coffee break
16.30 - 18.00
Students' choice lecture
19.00 - 22.00
Social dinner

Friday August 30

9.00 - 11.00
Lecture: Brownian diffusions on trees
11.00 - 11.30
Coffee break
11.30 - 13.00
Practical: Phylogeographic diffusion in continuous space
IMPORTANT NOTE:

It is important to have your own PC for the practical lessons. Remember to take it with you before leaving. Please install the following software on your PC in advance to start your lessons smoothly:

REFERENCES:

1. Data Integration in Bayesian Phylogenetics (2023) Annual Review of Statistics and Its Application
(click here to open).

2. Virus genomes reveal factors that spread and sustained the Ebola epidemic (2017) Nature
( click here to open).

All participants will receive a certificate of attendance at the end of the course (ECTS credits are not awarded)