A5061545123- Fish Ecology and Management Studies
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Marine and fisheries research
- Marine animal studies overview
- Identification and Quantification in Food
- Ichthyology and Marine Biology
- Parasite Biology and Host Interactions
- Algorithms and Data Compression
- Microbial Community Ecology and Physiology
- Aquaculture disease management and microbiota
- Coral and Marine Ecosystems Studies
- Underwater Acoustics Research
- Water Quality Monitoring Technologies
- Wheat and Barley Genetics and Pathology
- Botanical Studies and Applications
- Fish Biology and Ecology Studies
- Adversarial Robustness in Machine Learning
- RNA and protein synthesis mechanisms
- Environmental DNA in Biodiversity Studies
- Domain Adaptation and Few-Shot Learning
- CRISPR and Genetic Engineering
- Animal Genetics and Reproduction
- Neurobiology and Insect Physiology Research
- Protist diversity and phylogeny
Norwegian Institute of Marine Research
2014-2024
University of Bergen
2011-2024
Acoustics (Norway)
2024
Göteborgs Stads
2020
Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster an unusual immune architecture compared to other sequenced vertebrates. The assembly was obtained exclusively by 454 sequencing shotgun paired-end libraries, automated annotation identified 22,154 genes. major histocompatibility (MHC)...
Abstract Oceans constitute over 70% of the earth's surface, and marine environment ecosystems are central to many global challenges. Not only oceans an important source food other resources, but they also play a roles in climate provide crucial ecosystem services. To monitor ensure sustainable exploitation extensive data collection analysis efforts form backbone management programmes on global, regional, or national levels. Technological advances sensor technology, autonomous platforms,...
Abstract Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks the increase amount data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine is needed marine ecology. Then we provide quick primer on techniques vocabulary. built database ∼1000 publications implement such analyse ecology For various types (images, optical spectra, acoustics, omics, geolocations, biogeochemical...
Abstract Motivation: The commercial launch of 454 pyrosequencing in 2005 was a milestone genome sequencing terms performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 base pairs are thus approaching obtained from traditional Sanger sequencing. Study design projects would benefit being able simulate experiments. Results: We explore raw data investigate its characteristics derive empirical distributions for flow values generated by...
Abstract Acoustic-trawl surveys are an important tool for marine stock management and environmental monitoring of life. Correctly assigning the acoustic signal to species or groups is a challenge, recently trawl camera systems have been developed support interpretation data. Examining images from known positions in track provides high resolution ground truth presence species. Here, we develop deploy deep learning neural network automate classification present Deep Vision system. To remedy...
Calcium (Ca) - fortified foods are likely to play an important role in helping the consumer achieve adequate Ca intake, especially for persons with a low intake of dairy products. Fish bones have high content, and huge quantities this raw material available as by-product from fish industry. Previously, emphasis has been on producing quality products by-products by use bacterial proteases. However, documentation nutritional value enzymatically rinsed Ca-rich bone fraction remains unexplored....
Abstract Motivation: 454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes read lengths, performance and cost, but shows higher per-base error rates. Although there are several tools available for noise removal, targeting different application fields, data interpretation would benefit from a better understanding of the types. Results: By exploring raw data, we quantify what extent factors account errors. In addition well-known homopolymer...
Abstract Acoustic target classification is the process of assigning observed acoustic backscattering intensity to an category. A deep learning strategy for using a convolutional network developed, consisting encoder and decoder, which allow use pixel information more abstract features. The can learn features directly from data, learned feature space may include both frequency response school morphology. We tested method on multifrequency data collected between 2007 2018 during Norwegian...
The age structure of a fish population has important implications for recruitment processes and fluctuations, is key input to fisheries-assessment models. current method determining relies on manually reading from otoliths, the process labor intensive dependent specialist expertise. Recent advances in machine learning have provided methods that been remarkably successful variety settings, with potential automate analysis previously required manual curation. Machine models successfully...
Abstract Fish counts and species information can be obtained from images taken within trawls, which enables trawl surveys to operate without extracting fish their habitat, yields distribution data at fine scale for better interpretation of acoustic results, detect that are not retained in the catch due mesh selection. To automate process image-based detection identification, we trained a deep learning algorithm (RetinaNet) on collected trawl-mounted Deep Vision camera system. In this study,...
Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically ecologically important ectoparasitic found on salmonid fish. We present the 695.4 Mbp L. assembly containing ≈60% repetitive regions 13,081 annotated protein-coding genes. The comprises 14 autosomes a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of expected arthropod...
In fish, morphological colour changes occur from variations in pigment concentrations and the morphology, density, distribution of chromatophores skin. However, underlying mechanisms remain unresolved most species. Here, we describe first investigation into genetic environmental basis spot pattern development one world's studied fishes, Atlantic salmon. We reared 920 salmon 64 families domesticated, F1-hybrid wild origin two contrasting environments (Hatchery; tanks for freshwater stage sea...
Abstract Seismic surveys use airguns that emit low frequency high magnitude sound to detect subsea resources and map seabed geology. The effect of seismic blasts on Calanus spp., a key food source for commercially important fish, was assessed in field experiments. Immediate mortality copepods significantly different from controls at distances 5 m or less the airguns. Mortality 1 week after airgun blast higher—by 9% relative controls—in placed 10 but not distance 20 blast. increase...
For several fish species, age and other important biological information is manually inferred from visual scrutinization of scales, reliable automatic methods are not widely available. Here, we apply Convolutional Neural Networks (CNN) with transfer learning on a novel dataset 9056 images Atlantic salmon scales for four different prediction tasks. We predicted origin (wild/farmed), spawning history (previous spawner/non-spawner), river age, sea age. obtained high accuracy (96.70%), (96.40%),...
Efficient clustering is important for handling the large amount of available EST sequences. Most contemporary methods are based on some kind all-against-all comparison, resulting in a quadratic time complexity. A different approach needed to keep up with rapid growth data.A new, fast algorithm presented. Sub-quadratic complexity achieved by using an suffix arrays. prototype implementation has been developed and run benchmark data set. The produced clusterings validated comparing them other...
Abstract Motivation: Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome metagenomics. Especially latter application extremely sensitive errors artificially duplicated reads. Both are common can create a strong bias estimation of diversity composition sample. To date, there several tools that aim remove noise duplicates. Nevertheless, duplicate removal often based on...
Background: In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. [..] minke whale complex [...] migrations have been documented fertile hybrids back-crossed individuals both also identified. However, it is not known whether this represents a event, potentially driven by ecosystem changes Antarctic, or sporadic occurrence happening over an...
Nuclear receptors have crucial roles in all metazoan animals as regulators of gene transcription. A wide range studies elucidated molecular and biological significance nuclear but there are still a large number where the knowledge is very limited. In present study we identified an RXR type receptor salmon louse (Lepeophtheirus salmonis) (i.e. LsRXR). one two partners Ecdysteroid arthropods, for main molting hormone 20-hydroxyecdysone (E20) with array effects arthropods. Five different LsRXR...
This study contributes to advancing the field of automatic fish event recognition in natural underwater videos, addressing current gap studying interaction and competition, including predator-prey relationships mating behaviors. We used corkwing wrasse (Symphodus melops) as a model, marine species commercial importance that reproduces sea-weed nests built cared for by single male. These attract wide range visitors are focal point behavior such spawning, chasing, maintenance. propose deep...
Zygotic transcription in fish embryos initiates around the time of gastrulation, and all prior development is initiated controlled by maternally derived messenger RNAs. Atlantic cod egg embryo viability variable, it hypothesized that early depends upon feature these maternal Both length presence specific motifs 3'UTR RNAs are believed to regulate expression stability transcripts. Therefore, aim this study was characterize overall composition structure most common found eggs pre-zygotic...
Abstract Otoliths are a central information source for fish ecology and stock management, conveying important data about age other life history individual fish. Traditionally, interpretation of otoliths has required skilled expert readers, but recently deep learning classification regression models have been trained to extract from images variety species. Despite high accuracy in many cases, the adoption such fisheries management slow. One reason may be that underlying mechanisms model uses...
Abstract Motivation: The nucleotide sequencing process produces not only the sequence of nucleotides, but also associated quality values. Quality values provide valuable information, are primarily used for trimming sequences and generally ignored in subsequent analyses. Results: This article describes how scoring schemes standard alignment algorithms can be modified to take into account produce improved alignments statistically more accurate scores. A prototype implementation is provided,...