Kaisa_2012_3_photo by Veikko Somerpuro

Systems medicine seminar

The topic of Systems Medicine seminar in 2017 is single-cell bioinformatics. Welcome!

Single-cell measurement technologies allow measuring genetic/epigenetic variation, chromosomal aberrations and gene/protein expressions, etc. from thousands of individual cells simultaneously. While single-cell technology has provided unprecedented possibilities to conduct medical research, the vast amount of data creates a number of challenges to data analysis and visualization methods. In this course the main focus is on recent state-of-the-art single-cell publications and especially their bioinformatics. An essential feature of the course is to analyze single-cell data and thus prerequisite is working knowledge of R (or MATLAB, Python, etc.) programming language.

The course starts on Tuesday November 7th 2017 at 12.15 in meeting room 3 in Biomedicum Helsinki (Haartmaninkatu 8). If you have questions, send email to sampsa.hautaniemi@helsinki.

23.10.2017 at 09:00 - 12.12.2017 at 23:59


Here is the course’s teaching schedule. Check the description for possible other schedules.

Tue 7.11.2017
12:00 - 14:00
Tue 14.11.2017
12:00 - 14:00
Tue 21.11.2017
12:00 - 14:00
Tue 28.11.2017
12:00 - 14:00
Tue 5.12.2017
12:00 - 14:00
Tue 12.12.2017
12:00 - 14:00



Master's Programme in Life Science Informatics is responsible for the course.

Module where the course belongs to:

  • Systems biology and medicine

The course is available to students from other degree programmes.

Basic understanding of biology and medicine is recommended.

In this course a systems biology or medicine topic will be chosen and studied through scientific journal articles, student presentations and exercises. After the course a student should be able to understand scientific literature related to the topic of the seminar, understand the methods typically used and solve related research questions by analyzing biomedical data.

Preferably second year of the MSc program.

The course is offered every second year (even years).

This course focuses on understanding a recent research topic in systems medicine or biology. This can be certain mathematical approach, such as recent advances in qualitative modeling of signaling pathways or one methodology, such as t-Distributed Stochastic Neighbor Embedding (tSNE) in single-cell data analysis. The topic of the course is different in different years. In addition to reading and complementing exercises related to articles, students will apply the methods to biomedical data and interpret their results.

Articles, seminar presentations.

Students are given an article to read, a group of students will present its pros and cons another group opposes. All students return exercises related to the article (can be analysis tasks or theoretical). Active participation in discussing the articles and their merits is required.

The following is the current plan for Autumn 2018: assessment practices may evolve from year to year.

Grading scale is PASS/FAIL.

In order to pass, a students needs to return all exercises, present an article and oppose a presentation of another student.

Cannot be taken as a distance learning course, students are required to participate in seminars (at least 90%).

Presentation, being an opponent for another student, completion of exercises.