Timothy Vaughan: Katalogdaten im Frühjahrssemester 2022

NameHerr Dr. Timothy Vaughan
NamensvariantenTim Vaughan
Timothy G. Vaughan
Adresse
Computational Evolution
ETH Zürich, BSS J 2.1
Klingelbergstrasse 48
4056 Basel
SWITZERLAND
E-Mailtimothy.vaughan@bsse.ethz.ch
DepartementBiosysteme
BeziehungDozent

NummerTitelECTSUmfangDozierende
262-0200-00LBayesian Phylodynamics4 KP2G + 2AT. Vaughan
KurzbeschreibungHow fast is COVID-19 spreading at the moment? How fast was Ebola spreading in West Africa? Where and when did these epidemic outbreak start? How can we construct the phylogenetic tree of great apes, and did gene flow occur between different apes? At the end of the course, students will have designed, performed, presented, and discussed their own phylodynamic data analysis to answer such questions.
LernzielAttendees will extend their knowledge of Bayesian phylodynamics obtained in the “Computational Biology” class (636-0017-00L) and will learn how to apply this theory to real world data. The main theoretical concepts introduced are:
* Bayesian statistics
* Phylogenetic and phylodynamic models
* Markov Chain Monte Carlo methods
Attendees will apply these concepts to a number of applications yielding biological insight into:
* Epidemiology
* Pathogen evolution
* Macroevolution of species
InhaltIn the first part of the semester, in each week, we will first present the theoretical concepts of Bayesian phylodynamics. The presentation will be followed by attendees using the software package BEAST v2 to apply these theoretical concepts to empirical data. We use previously published datasets on e.g. Ebola, Zika, Yellow Fever, Apes, and Penguins for analysis. Examples of these practical tutorials are available on https://taming-the-beast.org/.
In the second part of the semester, the students choose an empirical dataset of genetic sequencing data and possibly some non-genetic metadata. They then design and conduct a research project in which they perform Bayesian phylogenetic analyses of their dataset. The weekly class is intended to discuss and monitor progress and to address students’ questions very interactively. At the end of the semester, the students present their research project in an oral presentation. The content of the presentation, the style of the presentation, and the performance in answering the questions after the presentation will be marked.
SkriptAll material will be available on https://taming-the-beast.org/.
LiteraturThe following books provide excellent background material:
• Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST.
• Yang, Z. 2014. Molecular Evolution: A Statistical Approach.
• Felsenstein, J. 2003. Inferring Phylogenies.
More detailed information is available on https://taming-the-beast.org/.
Voraussetzungen / BesonderesThis class builds upon the content which we teach in the Computational Biology class (636-0017-00L). Attendees must have either taken the Computational Biology class or acquired the content elsewhere.