1. Introduction to MBI and euSysbio programmes MBI/euSysbio Orientation Event for Aalto students September 7nd, 2012 Juho Rousu

2. 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. 1 st year Aalto – 2 nd 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 euSysbioMBI

3. Academic staff – MBI/euSysbio at Aalto Prof. Juho Rousu In charge MBI & euSysbio @ Aalto Prof. Erik Aurell euSysbio Director, KTH Prof. Harri Lähdesmäki Prof. Samuel Kaski HIIT Director Dr. Kirsti Laurila Coordinator MBI & euSysbio @ Aalto Ali Faisal Tutor Maria Osmala Tutor Sini Rautio Tutor

4. 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)

5. Where everything happens A – Aalto Otaniemi Campus Most bioinformatics & systems biology courses Information and computer science B – University of Helsinki, Meilahti Campus Biomedical courses C – University of Helsinki, Kumpula Campus Bioinformatics courses, mostly for MBI

6. euSysbio: additional locations B - KTH, Stockholm, Sweden Visit in Autumn 1 st and 2 nd year destination C - IST, Lisbon Portugal Winter school in January/February 2 nd year destination

8. Building blocks of bioinformatics and computational systems biology Data analysis Data mining Statistical modelingSignal processingMachine learning Computational sciences Computer science & Algorithms Software & databasesBiology & medicineBiotechnologyComputational systems biology & Bioinformatics

9. 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, …)

10. 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”

11. 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!