Centre for Bioinformatics

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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

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.

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The latest publications from the Centre

Kidd SG, Bogaard M, Carm KT, Bakken AC, Maltau AMV, Løvf M, Lothe RA, Axcrona K, Axcrona U, Skotheim RI (2022)
In situ expression of ERG protein in the context of tumor heterogeneity identifies prostate cancer patients with inferior prognosis
Mol Oncol (in press)
DOI 10.1002/1878-0261.13225, PubMed 35574900

Helland Å, Russnes HG, Fagereng GL, Al-Shibli K, Andersson Y, Berg T, Bjørge L, Blix E, Bjerkehagen B, Brabrand S, Cameron MG, Dalhaug A, Dietzel D, Dønnem T, Enerly E, Flobak Å, Fluge S, Gilje B, Gjertsen BT, Grønberg BH, Grønås K, Guren T, Hamre H, Haug Å, Heinrich D et al. (2022)
Improving public cancer care by implementing precision medicine in Norway: IMPRESS-Norway
J Transl Med, 20 (1), 225
DOI 10.1186/s12967-022-03432-5, PubMed 35568909

Torgersen K, Rahman Z, Bahrami S, Hindley GFL, Parker N, Frei O, Shadrin A, O'Connell KS, Tesli M, Smeland OB, Munkhaugen J, Djurovic S, Dammen T, Andreassen OA (2022)
Shared genetic loci between depression and cardiometabolic traits
PLoS Genet, 18 (5), e1010161 (in press)
DOI 10.1371/journal.pgen.1010161, PubMed 35560157

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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

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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.