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Bioinformatics atNorwegian University of Science and Technology

Professor Finn DrabløsDepartment of Cancer Research and Molecular Medicine

Finn Drabløs – Bioinformatics

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53 departments in 7 facultiesNTNU LibraryMuseum 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 employees2600 empl. in education and research; 555 professorsBudget: NOK 3.6 billion555 000 m2 owned and rented premises

NTNU key figures

NTNU, May 2006

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BOARD

RECTORORGANIZATIONAL DIV. UNIVERSITY LIBRARY MUS. NAT.HIST. & ARCHEOL.

INFORMATION DIV. TECHNICAL DIV. FINANCIAL DIV. STUDENT & ACAD. DIV.

FACULTIES

ARCHITECTURE & FINE ART

ARTSINFORM. TECH.,MATHEMATICS & ELECTR. ENG.

ENGINEERINGSCI. & TECHN.

MEDICINENATURAL SCI. & TECHN.

SOCIALSCIENCES & TECHN. MAN.

Organizational chart

NTNU, May 2006

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Department of Computer and Information ScienceResearch 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• 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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• 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

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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)