Torbjørn Rognes

Førsteamanuensis - Forskningsgruppen for biomedisinsk informatikk

English

E-post torognes@ifi.uio.no

Telefon +47-22844787 +47-22852410

Mobiltelefon +47-90755587

Faks +47-22852401

Rom 10468

Brukernavn

Besøksadresse Gaustadalléen 23B Ole-Johan Dahls hus 0373 OSLO

Postadresse Postboks 1080 Blindern 0316 OSLO

Last ned visittkort

Jeg arbeider med bioinformatikk og er førsteamanuensis i gruppen for Biomedisinsk Informatikk (BMI) ved Institutt for informatikk, Universitetet i Oslo og forsker ved Avdeling for Mikrobiologi, Rikshospitalet, Oslo Universitetssykehus (OUS). Jeg er gruppeleder for bioinformatikkgruppen i Centre for Molecular Biology and Neuroscience (CMBN). I tillegg arbeider jeg for selskapet Sencel Bioinformatics AS, et datterselskap av PubGene, Inc.

Faglige interesser

Jeg forsker på problemstillinger i bioinformatikk, spesielt de som dreier seg om analyse av DNA- og proteinsekvenser. Parallellisering av algoritmer for sekvenssammenligninger og søking i store datamengder har jeg arbeidet mye med. Særlig har jeg jobbet mye med parallellisering i form av SIMD-teknologi.

Gjennom stillingen ved OUS har jeg også arbeidet en del med anvendt bioinformatikk, ofte knyttet til karakterisering av gener involvert i DNA-reparasjon.

I det siste har jeg arbeidet en del med data fra dypsekvensering, spesielt med metoder for mapping av korte sekvenser mot et referansegenom.

Ledige masteroppgaver jeg kan være veileder for

Masterstudenter

Runar Furenes
Matias Holte
Anders Ramsvik Bragstad (sammen med Geir Kjetil Sandve)

Tidligere masterstudenter

Bjørnar A. Ruud (2011) Parallel alignment of short sequence reads on graphics processors
Espen Hannisdal (2010) Effective comparison of genetic sequences on parallel computer architectures
Daniel Johan Hammer Nebdal (2008) Presenting overrepresented words (sammen med Einar Rødland)
Arne Olaf Godtland (2007) Aligning of short sequences to whole genomes and a program to verify PCR primers (sammen med Anja B. Kristoffersen)
Lise Henriksen (2007) Database of Genes Involved in DNA Repair
Geir Ivar Jerstad (2006) Merging the physical properties of DNA with genomic annotations in Ensembl (sammen med Eivind Hovig)
Josef Thingnes (2004) Identifisering av ikkje-kodande RNA ved hjelp av samvariansmodellar
Gard O. S. Thomassen (2004) Detection of non-coding RNA genes by searching for transcription signals in intergenic regions

Emner jeg har deltatt i undervisningen i

INF325 Introduction to bioinformatics
INF2300 Introduction to bioinformatics
INF3350 Introduction to bioinformatics
INF4130 Algorithms: design and efficiency
INF4350 Introduction to bioinformatics
INF5330 Bioinformatics
INF5340 Algorithms in bioinformatics
KJB492 Bioinformatics
MBV4010 Methods in molecular biology and biochemistry I
MBV-INF4410/9410/9410A Applied readings in mathematics / Bioinformatics for Molecular Biology
MF9210 Laboratory course in molecular biology
MNBTS400 / MNBTS9000 Molecular biology research course

Emneord: bioinformatikk, algoritmer, parallellisering, sekvenser, DNA, protein

Lærdahl, Jon Kristen; Korvald, Hanne; Nilsen, Line; Dahl-Michelsen, Kristin; Rognes, Torbjørn; Bjørås, Magnar & Alseth, Ingrun (2011). Schizosaccharomyces pombe encodes a mutated AP endonuclease 1. DNA Repair. ISSN 1568-7864. 10(3), s 296- 305 . doi: 10.1016/j.dnarep.2010.11.014
Rognes, Torbjørn (2011). Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation . BMC Bioinformatics. ISSN 1471-2105. 12 . doi: 10.1186/1471-2105-12-221
Yang, Mingyi; Aamodt, Randi; Dalhus, Bjørn; Balasingham, Seetha; Helle, Ina Høydal; Andersen, Pernille Strøm; Tønjum, Tone et al. (2011). The ada operon of Mycobacterium tuberculosis encodes two DNA methyltransferases for inducible repair of DNA alkylation damage. DNA Repair. ISSN 1568-7864. 10(6), s 595- 602 . doi: 10.1016/j.dnarep.2011.03.007
Fensgård, Øyvind; Kassahun, Henok; Izabela Agnieszka, Bombik; Rognes, Torbjørn; Lindvall, Jessica Margareta & Nilsen, Hilde (2010). A Two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways. . Aging. ISSN 1945-4589.
Møllersen, Linda; Rowe, Alexander D.; Larsen, Elisabeth; Rognes, Torbjørn & Klungland, Arne (2010). Continuous and Periodic Expansion of CAG Repeats in Huntington's Disease R6/1 Mice. PLoS Genetics. ISSN 1553-7390. 6(12) . doi: 10.1371/journal.pgen.1001242
Nordstrand, Line Mari; Svärd, Jessica; Larsen, Elisabeth; Nilsen, Anja; Ougland, Rune; Furu, Kari; Lien, Guro Flor et al. (2010). Mice Lacking Alkbh1 Display Sex-Ratio Distortion and Unilateral Eye Defects. PLoS ONE. ISSN 1932-6203. 5(11) . doi: 10.1371/journal.pone.0013827
Thomassen, Gard O Sundby; Sneve, Ragnhild; Rowe, Alexander D.; Booth, James; Lindvall, Jessica M.; Lagesen, Karin; Kristiansen, Knut Ivan et al. (2010). Tiling Array Analysis of UV Treated Escherichia coli Predicts Novel Differentially Expressed Small Peptides. PLoS ONE. ISSN 1932-6203. 5(12) . doi: 10.1371/journal.pone.0015356
Ambur, Ole Herman; Davidsen, Tonje; Frye, Stephan Alfons; Balasingham, Seetha; Lagesen, Karin; Rognes, Torbjørn & Tønjum, Tone (2009). Genome dynamics in major bacterial pathogens. FEMS Microbiology Reviews. ISSN 0168-6445. 33(3), s 453- 470 . doi: 10.1111/j.1574-6976.2009.00173.x
Nakken, Sigve; Rognes, Torbjørn & Hovig, Eivind (2009). The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts . Nucleic Acids Research. ISSN 0305-1048. 37(17), s 5749- 5756 . doi: 10.1093/nar/gkp590
Nakken, Sigve; Rødland, Einar Andreas; Rognes, Torbjørn & Hovig, Eivind (2009). Large-scale inference of the point mutational spectrum in human segmental duplications. BMC Genomics. ISSN 1471-2164. 10 . doi: 10.1186/1471-2164-10-43
Robertson, AB; Klungland, A; Rognes, T & Leiros, Ingar (2009). DNA Repair in Mammalian Cells. Cellular and Molecular Life Sciences. ISSN 1420-682X. 66(6), s 981- 993 . doi: 10.1007/s00018-009-8736-z
Skotheim, Rolf Inge; Thomassen, Gard O Sundby; Eken, Marthe; Lind, Guro Elisabeth; Micci, Francesca; Ribeiro, FR; Cerveira, N et al. (2009). A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis . Molecular Cancer. ISSN 1476-4598. 8 . doi: 10.1186/1476-4598-8-5
Thomassen, Gard O Sundby; Rowe, Alexander D.; Lagesen, Karin; Lindvall, Jessica Margareta & Rognes, Torbjørn (2009). Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays . PLoS ONE. ISSN 1932-6203. 4(6)
Cameron, J; Holla, OL; Laerdahl, JK; Kulseth, MA; Ranheim, T; Rognes, Torbjørn; Berge, KE et al. (2008). Characterization of novel mutations in the catalytic domain of the PCSK9 gene. Journal of Internal Medicine. ISSN 0954-6820. 263(4), s 420- 431 . doi: 10.1111/j.1365-2796.2007.01915.x
Cameron, Jamie; Holla, Øystein Lunde; Lærdahl, Jon Kristen; Kulseth, Mari Ann; Ranheim, Trine; Rognes, Torbjørn; Berge, Knut Erik et al. (2008). Characterization of novel mutations in the catalytic domain of the PCSK9 gene. Journal of Internal Medicine. ISSN 0954-6820. 263(4), s 420- 431 . doi: 10.1111/j.1365-2796.2007.01915.x
Dalhus, Bjørn; Helle, Ina Høydal; Backe, Paul Hoff; Alseth, Ingrun; Rognes, Torbjørn; Bjørås, Magnar & Lærdahl, Jon Kristen (2007). Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats . Nucleic Acids Research. ISSN 0305-1048. 35(7), s 2451- 2459 . doi: 10.1093/nar/gkm039
Klungland, Arne; Lærdahl, Jon Kristen & Rognes, Torbjørn (2007). OGG1: From Structural Analysis to the Knockout Mouse, In Mark D. Evans & Marcus S. Cooke (ed.), Oxidative Damage to Nucleic Acids. Springer Science+Business Media B.V.. ISBN 9780387729732. Chapter 5. s 67 - 80
Lagesen, K; Hallin, P; Rødland, Einar Andreas; Staerfeldt, HH; Rognes, T & Ussery, DW (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research. ISSN 0305-1048. 35 . doi: 10.1093/nar/gkm160
Nakken, Sigve; Alseth, Ingrun & Rognes, Torbjørn (2007). Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes. Neuroscience. ISSN 0306-4522. 145 . doi: 10.1016/j.neuroscience.2006.09.004
Alseth, Ingrun; Rognes, Torbjørn; Lindbäck, Toril; Solberg, Inger; Robertsen, Kristin; Kristiansen, Knut Ivan; Mainieri, Davide et al. (2006). A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD. Molecular Microbiology. ISSN 0950-382X. 59 . doi: 10.1111/j.1365-2958.2006.05044
Alseth, Ingrun; Rognes, Torbjørn; Lindbäck, Toril; Solberg, Inger; Robertsen, Kristin; Kristiansen, Knut Ivan; Mainieri, Davide et al. (2006). A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD. Molecular Microbiology. ISSN 0950-382X. 59(5), s 1602- 1609
Thomassen, Gard O. S.; Rosok, Oystein & Rognes, Torbjørn (2006). Computational prediction of microRNAs encoded in viral and other genomes. Journal of Biomedicine and Biotechnology. ISSN 1110-7243.
Sæbø, Per Eystein; Andersen, SM; Myrseth, Jon; Lærdahl, Jon Kristen & Rognes, Torbjørn (2005). PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology. Nucleic Acids Research. ISSN 0305-1048. 33 . doi: 10.1093/nar/gki423
Sætrom, Pål; Sneve, Ragnhild; Kristiansen, Knut Ivan; Snøve, Ola; Grünfeld, Thomas; Rognes, Torbjørn & Seeberg, Erling Christen (2005). Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. Nucleic Acids Research. ISSN 0305-1048. 33, s 3263- 3270
Davidsen, Tonje; Rødland, Einar Andreas; Lagesen, Karin; Seeberg, Erling Christen; Rognes, Torbjørn & Tønjum, Tone (2004). Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Research. ISSN 0305-1048. 32(3), s 1050- 1058

Se alle arbeider i Cristin

Ambur, Ole Herman; Alfsnes, Kristian; Hovland, Eirik; Homberset, Håvard; Lærdahl, Jon Kristen; Frye, Stephan Alfons; Rognes, Torbjørn et al. (2010). Mechanisms of neisserial transformation and the evolution of sexual reproduction.
Nakken, Sigve & Rognes, Torbjørn (2010). Inference of molecular mechanisms from sequence patterns in human DNA variation.
Thomassen, Gard O Sundby & Rognes, Torbjørn (2010). Design, analysis and applications of custom high-density oligonucleotide microarrays.
Fensgård, Øyvind; Lindvall, Jessica Margareta; Kassahun, Henok; Rognes, Torbjørn & Nilsen, Hilde (2009). Microarray analysis of BER mutants.
Fensgård, Øyvind; Lindvall, Jessica; Kassahun, Henok; Rognes, Torbjørn & Nilsen, Hilde (2009). Microarray analysis of BER mutants.
Lagesen, Karin & Rognes, Torbjørn (2008). Computational characterization of ribosomal RNAs in prokaryotes .
Robertsen, Kristin; Kristoffersen, Anja Bråthen & Rognes, Torbjørn (2006). Phylogenetic profiles for identifying new DNA-repair proteins.
Rognes, Torbjørn (2006). PARALIGN: Rapid Sequence Similarity Searches Utilizing Several Levels of Parallelism.