The course aims to provide the students with theoretical knowledge and practical instruments for the study of evolution and epidemiology, from a general viewpoint as well as specifically on pathogens. These skills will include experience with phylogenetic approaches and their usage to characterise pathogens and to reconstruct epidemic events from genomic sequences.
Course Prerequisites
Basic knowledge in molecular biology, genetics and evolution. For practical activities, basic knowledge in bioinformatics and statistics will be also required, including command line usage.
Teaching Methods
The course will be taught by frontal lectures and by bioinformatic practical activities. The course material (including lecture slides) will be provided by the Kiro platform. For the practical activities, a laptop is required. Students will be guided in installing and using the required software. Such activities will be aimed to integrate the theoretical knowledge progressively acquired throughout the course, and will be carried out with the assistance by the teacher and a tutor. This will allow to maximise the connections between the understanding of theoretical notions treated during the course and the corresponding practical approaches of analysis.
Assessment Methods
The exam will consist in an oral examination. During the examination, the knowledge and proficiency acquired by the student will be verified, both on general concepts, and through testing the reasoning skills on the subject of the course, also by practical examples. The grade will be averaged with the grade for the examination of the first module scheduled for the first semester.
Texts
There is no mandatory textbook. The teaching material provided and notes will be sufficient. For further reading, the following are suggested: -Fenselstein J. Inferring Phylogenies. Sinauer Associates -Rothman KJ Epidemiology: An Introduction. Oxford University Press
Contents
The course will be subdivided into two main sections. The first section will deal with phylogenetic inference. The theoretical basis and various phylogenetic approaches will be presented, in particular regarding analyses on pathogens. In the second section, the bases of epidemiology will be treated, from a general perspective as well as specifically on infectious diseases. The practicals will allow to acquire skills on how to deal with case examples of topics of the course, thereby integrating frontal lectures.
