1 Bioinformatics at Norwegian University of Science and Technology Professor Finn Drabløs Department of Cancer Research and Molecular Medicine Finn Drabløs – Bioinformatics

2 53 departments in 7 faculties NTNU Library Museum of Natural History and Archaeology student applications a year – of which 9000 have NTNU as their first choice registered students, 7000 admitted/year 3000 degrees awarded a year 220 doctoral degrees awarded a year 4320 employees 2600 empl. in education and research; 555 professors Budget: NOK 3.6 billion m 2 owned and rented premises NTNU key figures NTNU, May 2006

3 BOARD RECTOR ORGANIZATIONAL DIV.UNIVERSITY LIBRARYMUS. NAT.HIST. & ARCHEOL. INFORMATION DIV.TECHNICAL DIV.FINANCIAL DIV.STUDENT & ACAD. DIV. FACULTIES ARCHITECTURE & FINE ART ARTS INFORM. TECH., MATHEMATICS & ELECTR. ENG. ENGINEERING SCI. & TECHN. MEDICINE NATURAL SCI. & TECHN. SOCIAL SCIENCES & TECHN. MAN. Organizational chart NTNU, May 2006

4 Department of Computer and Information Science Research groups Algorithms, HPC and Graphics (Networks, Evolutionary methods) Computer Architecture and Design (FPGA) Database Systems (Databases for biobanks) Design and Use of Information Systems Information Management (Data integration, Text mining) Information Systems Intelligent Learning Arenas Knowledge-Based Systems Logic and Language Technology (Ontologies) Self-Organizing Systems Software Engineering

5 GeneTools / eGOn

6 Department of Cancer Research and Molecular Medicine DNA Repair and Genome Stability Molecular Biology (mainly related to DNA repair) Proteomics Structure Biology (X-ray) Microarrays (printed, Affymetrix) / Genotyping (Illumina) Bioinformatics Interagon (Bioinformatics company)

7 Function is context-sensitive Uracil DNA glycosylase involved in both DNA repair and somatic hypermutation

8 FUGE – Functional Genomics National program for functional genomics –Technology platforms –Research projects FUGE I FUGE II , 420 MNOK Application deadline April 18, 18:00 –Several technology platforms Bioinformatics technology platform (extension) Microarray technology platform (extension) Biobank technology platform (extension) … –Several research projects miRNA in cell cycle regulation Genome Browser – statistical module (Ensembl) …

9 HUNT The Nord-Trøndelag Health Survey –HUNT Health survey participants (20+) –HUNT Health survey + blood participants (20+) Health survey participants (13-19) participated in both HUNT 1 and HUNT 2 –HUNT

10 Cell cycle studies Cell cycle synchronised (G1) HaCaT cells Status measured with flow cytometry Triplicates at 12 time points (1.5 cycle) Measured with Affymetrix U133A and B –2 x probes Processing –Regulated genes –Regulatory motifs –Network S-phase G1-phase G2-phase

11 Transcription factor and RNA based gene regulation –Finding regulatory motifs in co-regulated genes –Comparing regulatory regions Structure prediction and modelling of protein structures Part of FUGE Bioinformatics platform Bioinformatics research areas Automatic ligand docking Potential ligand binding sites

12 miRNA gene and target prediction Ongoing research activity –FUGE project with University of Bergen, using zebrafish to verify prediction of regulatory features (promoters, enhancers, miRNA) FUGE application: “The roles of microRNAs and transcription factors in gene regulation and tissue specific expression” –Includes cell cycle regulation, international collaboration

13 Composite motif discovery Find motifs (binding sites) that tend to occur together Use general “motif generators” for input –MEME, Pratt, Teiresias Do exhaustive search with efficient search tree pruning for motif combinations with flexible distance and N-of-M matching Lecture Notes in Computer Science 2005

14 Contributions Literature scanning, manual curation –Partly linked to FUGE technology platform Experimental test bench, feedback on usage –Linked to projects on gene regulation (Text mining on protein – protein interactions) (Ontology data linked to e.g. microarray data) –(Medical ontologies with versioning)