Introduction to MBI and euSysbio programmes

MBI/euSysbio Orientation Event for Aalto studentsSeptember 7nd, 2012Juho Rousu

Two MSc Programmes

• euSysbio – Computational and Systems Biology– Erasmus Mundus programme jointly offered by KTH, Sweden

and IST, Portugal– Double degree programme, studies in two universities (e.g. 1st

year Aalto – 2nd year KTH or IST, and vice versa)

• MBI – Bioinformatics– In collaboration with University of Helsinki– Degree granted by Aalto

• Common coursebase, different degree structure• Biological studies offered by University of Helsinki for

both programmes• Internships & MSc thesis topics in research groups

euSysbio MBI

Academic staff – MBI/euSysbio at Aalto

Department of Information and Computer Science (ICS)• Merger of

• The Laboratory of Computer and Information Science

• The Laboratory for Theoretical Computer Science

• General research theme:• Advanced computational methods for modelling, analysing, and solving complex tasks in technology and in science

• Three centres of Excellence in Research• CoE in Computational Inference Research (Prof. Samuel Kaski, Prof. Erik Aurell)

• Algorithmic Data Analysis CoE (Prof. Juho Rousu, Jaakko Hollmen)

• CoE in Molecular Systems Immunology and Physiology Research (Prof. Harri Lähdesmäki)

Where everything happens

euSysbio: additional locations

Building blocks of bioinformatics and computational systems biology

Data analysisData mining

Statistical modeling

Signal processing Machine learning Computational sciences

Computer science& Algorithms

Software & databases Biology & medicineBiotechnology

Computational systems biology & Bioinformatics

Related research groups

• Internship positions and thesis topics come from research groups

• ICS department• Computational systems biology (Lähdesmäki)• Kernel Machines, Pattern Analysis, and Computational Biology

(Rousu)• Statistical machine learning and bioinformatics (Kaski)• Parsimonious modelling (Hollmen)

• Other institutes• University of Helsinki (Dozens of biological/biomedical research

groups)• VTT Technical Research Center of Finland (across the road)• Companies (Orion, Valio, …)

Example Thesis topics

• “Computational Comparative Study of blood TCR repertoire: Celiac Disease patients versus Controls”

• “Bayesian Integrative Modelling of Metabolic and Transcriptional Data Using Pathway Information”

• “Modeling the dynamics of human neuromagnetic brain rhythms”

•“Type 1 diabetes biomarkers in human whole blood transcriptome”

•“Effects of computational methods to detect copy number variation in autism research”

• “Computational analysis to reveal combinatorial histone modifications”

• ”Comparison of Metagenomic Data by identifying enriched Pathways in Metabolic Networks”

• ”Performance analysis of inverse covariance estimation methods for inferring biological networks from genomic data”

Closing Words

• MBI&euSysbio programmes are challenging, be prepared to work hard– If your mathematics and statistics skills are dusty, time to brush up

• Obtaining 60 credits per year is not a trivial task– If you feel you are not keeping up with the courses, please be in

contact with us (tutors, Kirsti, Juho) early rather than late • Good grades are important

– to get good internship/MSc thesis opportunities/Phd studies/employment

• Be punctual with deadlines of coursework– late submissions may result to lower grades for courses and thesis– euSysbio: failing to complete enough credits may cause problems

with your scholarship payments• Finally: enjoy Aalto and Finland!