Bioinformatics (MTAT.03.239)

Course info

• The first meeting will take place on February 10.
• Lectures: Mondays 12:15 - 14:00, Narva mnt 18 - 1022
• Practice sessions/Consultations: Wednesdays 14:15 - 16:00, Narva mnt 18 - 1019 (No session on March 18)
• Project selection: TBD
• BIIT (Bioinformatics, Algorithmics, and Data Mining group) group website : http://biit.cs.ut.ee/

Contacts

• Course forum: Piazza
• Homework submissions: Homeworks page
• Course materials: https://github.com/kauralasoo/MTAT.03.239_Bioinformatics
• Lecturers: Kaur Alasoo (kaur.alasoo [at] ut.ee), Erik Abner, Priit Adler

Pre-requisites

Although the course has no official pre-requisites, basic programming and data analysis skills are required to successfully complete the homework and project assignments.

Learning objectives

• You will learn how to transfer the theoretical skills that you have learned in Data Mining, Neural Networks and Algorithmics courses to practical data analysis problems, with a particular focus on biology.
• You will know how to assess the quality of data via exploratory analysis (clustering, PCA) and know how to detect and when to remove outlier samples.
• You will understand the basic concepts of information flow in biological systems (genetic variant -> TF binding -> gene expression -> protein expression -> cellular phenotypes/imaging -> organismal phenotypes ) and what are the main biological and computational approaches to analyse it.

Grading and requirements

The grade is calculated from the total number of points (max 100). The points can be earned as follows:

• Homeworks (50 points): there will be 10 homeworks, each worth 5 points;
• Group project and presentation at the poster session (30 points);
• Written exam (20 points);
• Additional points can be earned from bonus tasks within homeworks;

In order to pass the course the student must get at least 50% from homeworks (threshold 25 points), at least 50% from the project (threshold 15 points) and at least 50% from the exam (threshold 10 points).

Bioinformatics seminar

In parallel to the Bioinformatics course, we will also organise the MTAT.03.242 Bioinformatics seminar this semester. While the course gives a basic introduction to each topic, the focus of the seminar will be on critically reviewing and discussing recently published bioinformatics research papers. To ensure that the seminar complements the course, the papers selected for the seminar will be based on the topics covered in the course. More information can be found on the seminar website.