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Centre for Bioinformatics

DNA

The Centre for Bioinformatics constitutes the hub of bioinformatics and computational biology. Our competence spans from precision medicine through all aspects of genomics, regardless of species and populations, through to protein structure.

 

News

  • New group leader at the Centre for Bioinformatics May 20, 2022 9:18 AM

    The centre for Bioinformatics is delighted to announce that Dr. Trine Rounge has started as a new group leader at the centre from May 2022. Rounge group aims to unravel the molecular mechanisms that can detect and explain cancer progression at an early stage.

  • MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions Apr. 28, 2022 9:21 PM

    "MoDLE is a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data, and does so orders of magnitude faster than existing approaches. MoDLE's speed opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings", says Jonas Paulsen, professor at the Department of Biosciences.

  • Swarm v3: towards tera-scale amplicon clustering Aug. 16, 2021 2:43 PM

    "The new version 3 of the Swarm software is a major step towards clustering extremely large amplicon datasets used in microbiome studies. It includes extensive improvements that make it about 10 times faster and twice as memory efficient as the previous version. Swarm makes it possible to cluster a huge dataset in reasonable time at one go, unlike other approaches where a large dataset needs to analysed in smaller portions," says Torbjørn Rognes, professor at the Centre for Bioinformatics.

    The work was carried out in an international collaboration and was recently published in the journal Bioinformatics. The open-source tool is freely available on GitHub.

  • A reference material for the genetic structure of Norway published Aug. 11, 2021 8:49 AM

    In a collaboration with deCODE Genetics, we were able to genotype a relatively representative cohort of the Norwegian population to generate a reference material for the genetic structure of Norway. “Somewhat surprisingly, no such study has previously characterized the genetic structure of Norway to any significant detail, and we are thrilled to provide this for future reference”, says professor Eivind Hovig. Among the novel findings is that historically there has been more limited genetic variation in the southern Norwegian counties of Agder, Telemark and Rogaland, indicating a level of genetic isolation.

Sven Furberg Seminars in Bioinformatics and Statistical Genomics

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The latest publications from the Centre

Chetty M, Roomaney I, Oosterwyk C, Manyisa N, Bope CD, Agenbag G, Wonkam A (2022)
Craniofacial, dental, and molecular features of Pyle disease in a South African child
BDJ Open, 8 (1), 28
DOI 10.1038/s41405-022-00120-w, PubMed 36138002

Loughnan RJ, Shadrin AA, Frei O, van der Meer D, Zhao W, Palmer CE, Thompson WK, Makowski C, Jernigan TL, Andreassen OA, Fan CC, Dale AM (2022)
Generalization of cortical MOSTest genome-wide associations within and across samples
Neuroimage, 263, 119632 (in press)
DOI 10.1016/j.neuroimage.2022.119632, PubMed 36115590

Løvestad AH, Repesa A, Costanzi JM, Lagström S, Christiansen IK, Rounge TB, Ambur OH (2022)
Differences in integration frequencies and APOBEC3 profiles of five high-risk HPV types adheres to phylogeny
Tumour Virus Res, 14, 200247 (in press)
DOI 10.1016/j.tvr.2022.200247, PubMed 36100161

Software developed at the centre

  • CARMA

    Software for extraction of DNA copy number motifs in cancer

  • Chimeraviz

    Chimeraviz manages data from fusion gene finders and provides useful visualization tools.

  • CompAIRR

    Comparison of Adaptive Immune Receptor Repertoires

  • Genomic HyperBrowser

    Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets

  • immuneML

    immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires

  • MoDLE

    MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions

  • ScaR

    ScaR — a tool for sensitive detection of known fusion transcripts: establishing prevalence of fusions in testicular germ cell tumors

  • Swarm

    Highly-scalable and high-resolution amplicon clustering

  • VSEARCH

    A versatile open source tool for metagenomics

Collaborations

ELIXIR Norway

ELIXIR Norway is the Norwegian national node of ELIXIR, the pan-European infrastructure for biological information, supporting life science research and its translation to medicine, environment, the bioindustries and society. This organization is a virtual organization where the Center of Bioinformatics hosts the regional Oslo node. It participates to the national help-desk user support, and in that activity also collaborates and coordinates closely with the Helse Sør-Øst-funded Bioinformatics Core facility.

Partners and collaborating organizational units

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