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 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.
"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.
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.
“Many human cancers are rooted in rare germline mutations, but identifying them and understanding their clinical impact is a considerable challenge. We have created a comprehensive bioinformatics workflow that successfully prioritizes cancer-predisposing DNA variants detected from high-throughput sequencing. Importantly, our reporting tool also highlights any variant with implications for prognosis or treatment options”, says Eivind Hovig, Professor and leader of the Centre for Bioinformatics.
The study, financed by the Norwegian Research Council, was recently published in the International Journal of Cancer and can be found here. The bioinformatics tool is named Cancer Predisposition Sequencing Reporter (CPSR), and was established in collaboration with researchers at Oslo University Hospital and researchers from the University of Melbourne in Australia.
“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.
“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.
“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.
The knowledge of corona virus variants in Norway has been insufficient, professor Eivind Hovig, director of the Centre for Bioinformatics, tells Norwegian media.
A position paper on precision medicine in the Nordics, where we have contributed, has been published in Nature, the renowned international journal of science.