Torbjørn Rognes

Image of Torbjørn Rognes
Norwegian version of this page
Phone +47 22844787
Mobile phone +4790755587
Room 223
Username
Visiting address Gaustadalléen 30D NEMKO-building 0373 Oslo
Postal address Postboks 1080 Blindern 0316 Oslo

I am a professor of bioinformatics leading the Research Group for Biomedical Informatics (BMI) at the Department of Informatics, University of Oslo. I am also affiliated with the new Centre for Bioinformatics. In addition, I work as a research scientist at the Department of Microbiology at Rikshospitalet, Oslo University Hospital (OUS).

Scientific interests

I work on problems in bioinformatics, in particular those related to analysis of DNA and protein sequences. Parallelisation of algorithms for sequence comparisons, searching and clustering of large databases are some of the things I've worked a lot with.

Through the position at the hospital, I've also worked quite a bit with applied bioinformatics, often related to characterisation of genes involved in DNA repair.

Recently, I have developed methods and tools for microbiome bioinformatics, where we analyse sequencing data from amplicon sequencing of rRNAs to determine the composition of microorganisms in samples.

Research projects

VSEARCH: Open and free 64-bit multithreaded tool for processing metagenomic sequences

SWIPE: Smith-Waterman database searches with inter-sequence SIMD parallelisation

SWARM: A robust and fast clustering method for amplicon-based studies

Publika: Publication database for Oslo University Hospital

Available master thesis projects that I may supervise

Please look at the list of all available master thesis projects at BMI.

Current master students

  • Miriam Tamara Grødeland Aarag (with Karin Lagesen)
  • Henrik Høybakk Olsvik (with Trine B. Rounge)
  • Ignar Rumbavicious (with Trine B. Rounge)
  • Håvard Tolås Trondsen (with Sinan Uğur Umu and Trine B. Rounge)

Former master students

  • Akuzike Banda (with Khuzwayo C. Jere, Chrispin Chaguza, Arox W. Kamng’ona)
  • Sindre Grønmyr (2019, with Junbai Wang and Magnar Bjørås)
  • Karina Borlaug (2019, with Rolf Skotheim)
  • Torgeir P. Tynes (2018)
  • Kristoffer Mjelva (2018)
  • Andreas Glasø Skifjeld (2018, with Karin Lagesen)
  • Aila Aspås (2018, with Karin Lagesen)
  • Sebastian Søberg (2017, with Karin Lagesen)
  • Sean Christian Dutch (2017)
  • Victor Synnes (2017, with Torstein Tengs)
  • Tuva Kristine Thoresen (2015) Fast, Parallel Tools for Genome-wide Analysis of Genomic Divergence (with Geir Kjetil Sandve)
  • Mimi Tantono (2015) Parallelisation of Hierarchical Clustering Algorithms for Metagenomics
  • Reidar A. Brenna (2015) A journey to the core - of man and machine alike (with Jon Hjelmervik, SINTEF)
  • Jorun Ramstad (2015) Protein Alignment on the Intel Xeon Phi Coprocessor (with Jon Hjelmervik, SINTEF)
  • Jakob T. Frielingsdorf (2015) Improving optimal sequence alignments through a SIMD-accelerated library
  • Sabba Ifzal (2015) Reproducibility and reusability pf genome assembly evaluation (with Lex Nederbragt, Geir Kjetil Sandve and Ksenia Khelik)
  • Anders Ramsvik Bragstad (2013) Dynamic benchmarking in bioinformatics (with Geir Kjetil Sandve)
  • Runar Furenes (2013) Genome Assembly: Scaffolding Guided by Related Genomes
  • Matias Holte (2013) Assessment of genomic variant calling methods through simulations
  • 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 (with Einar A. Rødland)
  • Arne Olaf Godtland (2007) Aligning of short sequences to whole genomes and a program to verify PCR primers (with 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 (with 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

Please see the list of all former BMI students for links to their master thesis publications.

Current PhD students

  • Roberto Rossini (with Jonas Paulsen)
  • Jonas Christoffer Lindstrøm (with Hilde L. Nilsen)

Former PhD students

  • Eva Lena Fjeld Estensmo (with Håvard Kauserud and others) (2020)
  • Ksenia Khelik (with Lex Nederbragt, Geir Kjetil Sandve and Karin Lagesen) (2019)
  • Srinidhi Varadharajan (with Asbjørn Vøllestad and others) (2019)
  • Pubudu Samarakoon (with Dag Undlien and Robert Lyle) (2017)
  • Bjarne Johannessen (with Rolf Skotheim) (2016)
  • Håvard Aanes (with Peter Alestrøm) (2014)
  • Sabry Razick (with Ian Donaldson) (2012)
  • Sigve Nakken (with Eivind Hovig) (2010)
  • Gard O.S. Thomassen (2010)
  • Karin Lagesen (with Dave W. Ussery) (2008)

Courses where I have the main responsibility

  • IN4030 Introduction to bioinformatics

Courses where I am contributing

  • INF5380 / INF9380 - High Performance Computing in Bioinformatics
  • IN-BIOS5000IN-BIOS9000 - Genome Sequencing Technologies, Assembly, Variant Calling and Statistical Genomics
  •  
  • BIO9905MERG1 - Bioinformatics for Environmental Sequencing (DNA metabarcoding)
  • BIOS4010 - Methods in molecular biology and biochemistry I
  • MBV-INF4410 / MBV-INF9410 / BIOS-IN5410 / BIOS-IN9410 - Bioinformatics for molecular biology
  • IN3130 - Algorithms: Design and Efficiency

Courses that I have contributed to earlier

  • 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 / MBV-INF9410 / MBV-INF9410A Applied readings in mathematics
  • MBV9100BTS / MNBTS400 / MNBTS9000 Molecular biology research course
  • MF9210 Laboratory course in molecular biology

Talks

23 October 2014 - Open access from a researcher’s perspective. Open Access Week, Medical Library, University of Oslo.

My profile on other sites

Tags: Life sciences, Bioinformatics, Algorithms, Parallelisation, Microbiome
Published Nov. 4, 2010 2:15 PM - Last modified Aug. 19, 2021 11:21 AM