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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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NTNU key figures
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 m2 owned and rented premises
NTNU, May 2006
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Organizational chart
BOARD
RECTOR
INFORMATION DIV.
TECHNICAL DIV.
ORGANIZATIONAL 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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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
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GeneTools / eGOn
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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)
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Function is context-sensitive
Uracil DNA
glycosylase
involved in both
DNA repair and
somatic
hypermutation
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FUGE – Functional Genomics
• 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
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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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HUNT
• 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 studies
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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
• Processing
– Regulated genes
– Regulatory motifs
– Network
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S-phase
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G1-phase
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G2-phase
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Bioinformatics research areas
• 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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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
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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
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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)