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

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53 departments in 7 faculties
NTNU Library
Museum of Natural History and Archaeology
58 000 student applications a year
– of which 9000 have NTNU as their first choice
20 000 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
555 000 m 2 owned and rented premises
NTNU, May 2006

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

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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

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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)

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Uracil DNA glycosylase involved in both
DNA repair and somatic hypermutation

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• National program for functional genomics
– Technology platforms
– Research projects
• FUGE I 2002-2006
• FUGE II 2007-2011, 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)
• …

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• The Nord-Trøndelag Health Survey
– HUNT 1 - 1984-1986
• Health survey - 75.000 participants (20+)
– HUNT 2 - 1995-1997
• Health survey + blood - 65.000 participants (20+)
• Health survey - 9.000 participants (13-19)
• 46.000 participated in both HUNT 1 and HUNT 2
– HUNT 3 - 2006-2008

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• 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 22.000 probes
100
• Processing
90
80
– Regulated genes
– Regulatory motifs
– Network
70
60
50
40
30
20
10
0
0 3 6 9 12 15 18 21
S-phase
G1-phase
G2-phase
24 27 30 33

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

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• 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

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• 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

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• 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)