News
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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.
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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.
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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.
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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
The latest publications from the Centre
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
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
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
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CARMA
Software for extraction of DNA copy number motifs in cancer
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Chimeraviz
Chimeraviz manages data from fusion gene finders and provides useful visualization tools.
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CompAIRR
Comparison of Adaptive Immune Receptor Repertoires
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Genomic HyperBrowser
Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets
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immuneML
immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires
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MoDLE
MoDLE: High-performance stochastic modeling of DNA loop extrusion interactions
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ScaR
ScaR — a tool for sensitive detection of known fusion transcripts: establishing prevalence of fusions in testicular germ cell tumors
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Swarm
Highly-scalable and high-resolution amplicon clustering
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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
