Ingen lysbildetittel

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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
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, 1800
• 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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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

• 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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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
• Part of FUGE Bioinformatics platform

Automatic ligand docking
Potential ligand binding sites
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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)