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Centre for Bioinformatics

DNA

Centre for Bioinformatics constitute 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

  • Ten simple rules for quick and dirty scientific programming June 16, 2021 10:48 AM

    “We argue that a quick and dirty style of programming is not necessarily bad: the quicker you code, the more scientific ideas you can potentially test and publish. However, if coding quickly means coding sloppily, then bugs, false conclusions, and article retractions may be the result. Furthermore, if your code becomes increasingly complex and messy over time, then adapting it to new tasks will be difficult, potentially stalling your research progress” says Geir Kjetil Sandve, Professor at the Centre for Bioinformatics.

    The study was recently published in the popular ten simple rules series of PLOS Computational Biology and can be found here.

  • immuneML: a domain-tailored machine learning ecosystem to decipher adaptive immunity June 16, 2021 10:32 AM

    “We have developed a large software framework that provides a broad variety of machine learning modules for discovering patterns in immune data. It implements each step of the machine learning process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows” says Geir Kjetil Sandve, Professor at the Centre for Bioinformatics.

    The study was recently made available on BioRxiv preprint server and can be found here.

    The study has been a large team effort with contributions from national and international collaborators including the group of Victor Greiff, Associate professor at the Department of Immunology.

  • Fine-tuning epigenetic methods to create new knowledge from old samples June 16, 2021 9:33 AM

    “We have succeeded in extracting epigenetic information from scarce DNA from serum archived in the Janus Serum Biobank. This opens up new avenues for what serum banks can be used to achieve” says Trine B Rounge researcher at the Cancer Registry of Norway and Associate Professor at Centre for Bioinformatics.

    The study, financed by Norwegian Cancer Society, was recently published in Clinical Epigenetics and can be found here.

    In a collaborative national and international effort, the researchers conducted a study to test the feasibility of extracting more information from DNA from the Janus samples than was previously anticipated.

  • Insufficient knowledge of virus variants Mar. 10, 2021 11:48 AM

    The knowledge of corona virus variants in Norway has been insufficient, professor Eivind Hovig, director of the Centre for Bioinformatics, tells Norwegian media.

Events

24 Aug.
10:00 AM, Meeting rooms 113 + 115 (former NEMKO building)
31 Aug.
10:00 AM, Meeting rooms 113 + 115 (former NEMKO building)
07 Sep.
10:00 AM, Meeting rooms 113 + 115 (former NEMKO building)
14 Sep.
10:00 AM, Meeting rooms 113 + 115 (former NEMKO building)

Sven Furberg Seminars in Bioinformatics and Statistical Genomics

23 Sep.
2:30 PM, TBA

Dr. Bart Deplancke, Professor at the École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland, will present his current research.

The latest publications from the Centre

Mariampillai JE, Prestgaard EE, Kjeldsen SE, Liestøl K, Grundvold I, Bodegård J, Gjesdal K, Erikssen JE, Skretteberg PT (2021)
Novel insights into stroke risk beyond resting and maximal bicycle exercise systolic blood pressure
J Hypertens (in press)
DOI 10.1097/HJH.0000000000002894, PubMed 34102659

Ramberg H, Richardsen E, de Souza GA, Rakaee M, Stensland ME, Braadland PR, Nygård S, Ögren O, Guldvik IJ, Berge V, Svindland A, Taskén KA, Andersen S (2021)
Proteomic analyses identify major vault protein as a prognostic biomarker for fatal prostate cancer
Carcinogenesis, 42 (5), 685-693
DOI 10.1093/carcin/bgab015, PubMed 33609362

Elvsåshagen T, Shadrin A, Frei O, van der Meer D, Bahrami S, Kumar VJ, Smeland O, Westlye LT, Andreassen OA, Kaufmann T (2021)
The genetic architecture of the human thalamus and its overlap with ten common brain disorders
Nat Commun, 12 (1), 2909
DOI 10.1038/s41467-021-23175-z, PubMed 34006833

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

  • 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

Life Science logo

Oslo University Hospital logo