A5050465824- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Parasite Biology and Host Interactions
- Genomics and Phylogenetic Studies
- Marine Ecology and Invasive Species
- Parasites and Host Interactions
- RNA Research and Splicing
- Planarian Biology and Electrostimulation
- Circular RNAs in diseases
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Insect and Arachnid Ecology and Behavior
- Environmental DNA in Biodiversity Studies
- Marine Bivalve and Aquaculture Studies
- Aquaculture disease management and microbiota
- Helminth infection and control
- Extracellular vesicles in disease
- Marine Biology and Environmental Chemistry
- Protist diversity and phylogeny
- Physiological and biochemical adaptations
- Genetics, Aging, and Longevity in Model Organisms
- Tardigrade Biology and Ecology
- Cephalopods and Marine Biology
- Trace Elements in Health
UiT The Arctic University of Norway
2021-2025
Centre for Arctic Gas Hydrate, Environment and Climate
2022-2024
Stockholm University
2018-2022
Science for Life Laboratory
2018-2022
Oslo University Hospital
2015-2020
Norwegian Cancer Society
2017
University of Oslo
2011-2014
Schiller International University
2008
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides single access point to 44 resources and >18 million ncRNA from wide range organisms types. now also includes secondary (2D) structure information for >13 sequences, making the world's largest 2D database. The diagrams are displayed using R2DT, new visualization method uses consistent, reproducible recognizable layouts related RNAs. sequence similarity search has been updated with faster interface...
Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences conserved across the kingdom. In addition, unique mechanistically well understood features can clearly distinguish bona fide miRNAs from myriad other small generated by cells. However, making this distinction is not a common practice and, thus, surprisingly, heterogeneous quality of available miRNA...
The aim of this study was to identify microRNAs in urinary exosomes that are differently expressed prostate cancer patients and healthy donors. For purpose, RNA extracted from 20 9 males the were analyzed by next generation sequencing. Interestingly, 5 – miR-196a-5p, miR-34a-5p, miR-143-3p, miR-501-3p miR-92a-1-5p significantly downregulated patients. Furthermore, RT-qPCR analysis an independent cohort 28 19 confirmed miR-196a-5p samples. These results suggest specific might serve as...
Abstract Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances different directions. New protocols for sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or include internal controls spike-in sequences. microRNA reference databases were developed with foci, either prioritizing accuracy (low number false positives) completeness negatives). Additionally, other molecules well...
Abstract We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for annotation nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers flatworms. 2.1 now consists 75 spanning over ∼800 million years animal evolution, contains a total number 16 670 microRNAs from 1549 families. Over 6000 were added in this using ∼550...
Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and often assumed to be causally associated with organismal innovations radiations. The 2R hypothesis suggests two WGD events (1R 2R) occurred during early vertebrate evolution. However, the timing of relative divergence gnathostomes (jawed vertebrates) cyclostomes (jawless hagfishes lampreys) unresolved whether these underlie phenotypic diversification remains elusive. Here we present...
Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable body fluids as extracellular RNAs. In this study, we used sequencing (RNA-seq) to investigate the profile of small non-coding (sncRNA) human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included Norwegian population-based Janus Serum Bank (JSB). found that core repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting (piRNA), 411 transfer (tRNA), 24 nucleolar (snoRNA),...
ABSTRACT The prevalent porcine helminth, Ascaris suum , compromises pig health and reduces farm productivity worldwide. closely related human parasite, A. lumbricoides infects more than 800 million people representing a disease burden of 1.31 disability‐adjusted life years. infections are often chronic in nature, the parasites have profound ability to modulate their hosts' immune responses. This study provides first in‐depth characterisation extracellular vesicles (EVs) from different...
The ectoparasitic Monogenea comprise a major part of the obligate parasitic flatworm diversity. Although genomic adaptations to parasitism have been studied in endoparasitic tapeworms (Cestoda) and flukes (Trematoda), no representative has investigated yet. We present high-quality draft genome Gyrodactylus salaris, an economically important monogenean ectoparasite wild Atlantic salmon (Salmo salar). A total 15,488 gene models were identified, which 7,102 functionally annotated. controversial...
(1935). Studies in the mechanism of Wever and Bray effect. Acta Oto-Laryngologica: Vol. 22, No. 3, pp. 477-486.
Abstract The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in field small RNA research. Simultaneously, number samples per miRNA-seq study continues to increase resulting vast amount that requires accurate, fast and user-friendly analysis methods. Since previous release sRNAtoolbox 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements its usability...
Recent studies on microRNA (miRNA) evolution focused mainly the comparison of miRNA complements between animal clades. However, miRNAs within such groups is poorly explored despite availability comparable data that in some cases lack only a few key taxa. For flatworms (Platyhelminthes), are available for free-living and all major parasitic lineages, except Monogenea. We present complement monogenean flatworm Gyrodactylus salaris facilitates comprehensive analysis Platyhelminthes. Using newly...
We present here miRTrace, the first algorithm to trace microRNA sequencing data back their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately (> 99%) assigns real simulated 14 important animal plant groups, sensitively detects parasitic infection in mammals, discovers primate origin of single cells. Applying our over 700 public datasets, we...
Abstract Aging is a key risk factor for chronic diseases of the elderly. MicroRNAs regulate post-transcriptional gene silencing through base-pair binding on their target mRNAs. We identified nonlinear changes in age-related microRNAs by analyzing whole blood from 1334 healthy individuals. observed larger influence age as compared to sex and provide evidence shift 5’ mature form miRNAs aging. The addition 3059 diseased patients uncovered pan-disease disease-specific alterations aging...
We have identified and validated a spaceflight-associated microRNA (miRNA) signature that is shared by rodents humans in response to simulated, short-duration long-duration spaceflight. Previous studies miRNAs regulate rodent responses spaceflight low-Earth orbit, we confirmed the expression of these proposed reacting simulated conditions. Moreover, astronaut samples from NASA Twins Study signatures miRNA sequencing, single-cell RNA sequencing (scRNA-seq), assay for transposase accessible...
Over the last few years, number of microRNAs in human genome has become a controversially debated issue. Several publications reported thousands putative novel not included curated microRNA gene database MirGeneDB and repository miRBase. Recently, by using sequencing ∼300 tissues cell lines, RNA atlas, an expanded inventory annotations, was published, reporting microRNAs. We, developers established prediction tools hosts MirGeneDB, raise concerns about frequently applied functional...
Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their tissues, we hypothesized regulation may play major role the cognitive success this group. We thus profiled messenger RNAs and small three cephalopod species including 18 tissues Octopus vulgaris. show innovation soft-bodied is an expansion microRNA (miRNA) gene repertoire. These...
The annotation of microRNAs depends on the availability transcriptomics data and expert knowledge. This has led to a gap between novel genomes high-quality microRNA complements. Using >16,000 from manually curated gene database MirGeneDB, we generated trained covariance models for all conserved families. These are available in our tool MirMachine, which annotates within genomes. We successfully applied MirMachine range animal species, including those with large genome duplications extinct...
Abstract Molecular markers for tracing animal sample origins and compositions are critical applications such as parasite detection, contamination screening, authentication. Among these, microRNAs have emerged promising candidates due to their deep conservation, near‐hierarchical evolution, stability. I here review the suitability of taxonomic also phylogenetic show how careful annotation efforts establishment curated microRNA gene database MirGeneDB tools like MirMachine revitalized...
Abstract We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to new server and creation computational mirror, we have expanded database with addition 33 invertebrate species, including representatives 5 previously unsampled phyla, 6 mammal species. now contains entries for 21 822 genes (5160 these from species) belonging 1743 families. The inclusion species allowed us refine both evolutionary node appearance number genes/families,...
Robust markers of invasiveness may help reduce the overtreatment in situ carcinomas. Breast cancer is a heterogeneous disease and biological mechanisms for carcinogenesis vary between subtypes. Stratification by subtype therefore necessary to identify relevant robust signatures invasive disease. We have identified microRNA (miRNA) alterations during breast progression two separate datasets used stratification external validation strengthen findings. analyzed (METABRIC AHUS) consisting total...