Aim and content

This is a generic course. This means that the course is reserved for PhD students at the Graduate School of Health and Medical Sciences at UCPH.

Anyone can apply for the course, but if you are not a PhD student at the Graduate School, you will be placed on the waiting list until enrollment deadline. After the enrollment deadline, available seats will be allocated to the waiting list.

The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at NorDoc member faculties. All other participants must pay the course fee.

Learning objectives
A student who has met the objectives of the course will be able to:
1. Interpret phylogenetic trees and networks.
2. Align and curate sequence data.
3. Test a variety of hypotheses of comparative molecular evolution.
4. Perform Bayesian analyses of molecular data relevant to public health.
5. Analyse large numbers of loci for dating evolutionary events.

Content
This course will give students a broad understanding of phylogenetics, phylogenomics, and phylodynamics, via practice in these fields. Starting from the very basics, students will be exposed to depictions of trees and networks, and taught to interpret graphics published on the topic.
The most robust and commonly used methods of inferring phylogenetic trees are explained in detail, with an emphasis on the statistical theory and motivation for each. From the outset the course will be hands-on, placing the students in a position to critically evaluate choices in a project on molecular evolution.
In a mini-project that can range fields of epidemiology, biodiversity, or linguistics, students will be undertake the complete process of phylogenetic analysis from data preparation, through making inferences using sophisticated hierarchical models, finishing with interpretation of results. With a heavy emphasis on hands-on practicals with real data sets, students will learn concepts and practice of sequence alignment, data cleaning and filtering, and inference of phylogeny and molecular evolutionary parameters with a range of methods and software.
In addition to basic methods of inference, students will learn to handle data sets with large numbers of genes and perform molecular dating. The course will therefore also cover the basics of Bayesian inference, common model hierarchies in phylogenetics and examples of their implementation.
Successful students will be able to report their phylogenetic procedures and results clearly and accurately for scientific publication.

Participants
This course is aimed at researchers interested in studying pathogens and biodiversity using genomic data.
Attendees might come from any of a broad range of fields, but must be interested in analyses of multiple taxa, such as viruses, bacteria, plants, and vertebrates.
A prior basic understanding of probability is strongly recommended.

Relevance to graduate programmes
The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:
– Biostatistics and Bioinformatics
– Immunology and Infectious Diseases
– Public Health and Epidemiology

Language
English

Form
Lectures, computer exercises, group mini-project.

Course director
Associate Professor David Duchene
Department of Public Health, Section of Epidemiology
David.duchene@sund.ku.dk

Teachers
Associate Professor David Duchene
Department of Public Health, Section of Epidemiology
David.duchene@sund.ku.dk

Dates
28/10/2024 – 01/11/2024 – 9-15:30 all days

Course location
CSS Building 7

Registration
Please register before 01/10/2024

Expected frequency
Once per year.

Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules.
Applications from other participants will be considered after the last day of enrolment.

Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

Disclaimer:
DDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.