I am professor in the Scientific Computing and Machine Learning group (SCML) (formerly the BMI group) in the Machine Learning Section at the Department of Informatics, University of Oslo. I am also affiliated with the Centre for Bioinformatics. In addition, I work as a senior 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. Some of the same underlying algorithms and data structures have shown to be effective also in comparing adaptive immune receptor sequences.
Research projects and tools
CompAIRR: Comparison of Adaptive Immune Receptor Repertoires
VSEARCH: Open and free 64-bit multithreaded tool for processing metagenomic sequences
SWARM: A robust and fast clustering method for amplicon-based studies
SWIPE: Smith-Waterman database searches with inter-sequence SIMD parallelisation
Publika: Publication database for Oslo University Hospital
PhD studies
Former PhD students
- Roberto Rossini (with Jonas Paulsen) (2024)
- Jonas Meier Strømme (with Rolf Skotheim and Bjarne Johannesen) (2022)
- 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)
Master studies
I am responsible for the Computational Science: Bioinformatics (CS:Bioinformatics) study programme option at IFI. We also recruit people from the PROSA study programme.
Available master thesis projects that I may supervise
Please look at the list of all available master thesis projects at BMI.
Current master students
- Eric Svebakk (with Diana Domanska and Sinan Umu)
- Theo Gascogne (with Sinan Umu and Diana Domanska)
- Una Mathiesen Langeland (with Karin Lagesen and Trine B. Rounge)
- Arnas Rumbavicius (with Adnan Hashim and John Arne Dahl)
- Igor Momcilovic (with Marcin W. Wojewodzic)
- Sara Dugalic (with Marcin W. Wojewodzic)
- Bendik Berg (with Jonas Paulsen)
- Sander Brekke Lønnebakke (with Skarphéðinn Halldórsson and Einar Vik-Mo)
Former master students
- Behnoosh Ashrafi (2023, with James Booth and Magnar Bjørås)
- Tiril Gjerstad (2023, with Ole Christian Lingjærde and others)
- Daniel Kristiansen (2023, with Jonas Paulsen)
- Amund Isaksen (2023, with Bjarne Johannessen and Rolf I. Skotheim)
- Hugo Nørholm (2023, with Marcin W. Wojewodzic)
- Nurettin Yarar (2023, with Marcin W. Wojewodzic)
- Simon Nordvold Barak (2023, with Paula Istvan and Trine B. Rounge)
- Ignar Rumbavicious (2022, with Trine B. Rounge)
- Håvard Tolås Trondsen (2022, with Sinan Uğur Umu and Trine B. Rounge)
- Miriam Tamara Grødeland Aarag (2021, with Karin Lagesen)
- Henrik Høybakk Olsvik (2021, with Trine B. Rounge)
- 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/SCML students for links to their master thesis publications.
Courses
Courses where I have the main responsibility
- IN4030 Introduction to bioinformatics
- IN-BIOS5000 / IN-BIOS9000 - Genome Sequencing Technologies, Assembly, Variant Calling and Statistical Genomics
Courses where I am contributing regularly
- BIOS4010 - Methods in molecular biology and biochemistry I
- BIOS-IN5410 / BIOS-IN9410 - Bioinformatics for molecular biology
- BIO9905MERG1 - Bioinformatics for Environmental Sequencing (DNA metabarcoding)
Courses that I have contributed to earlier
- IN3130 - Algorithms: Design and Efficiency
- 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
- INF5380 / INF9380 - High Performance Computing in Bioinformatics
- KJB492 Bioinformatics
- MBV4010 Methods in molecular biology and biochemistry I
- MBV-INF4410 / MBV-INF9410 / MBV-INF9410A Bioinformatics for Molecular Biology
- 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.