• Acoustic classification in multifrequency echosounder data using deep convolutional neural networks 

      Brautaset, Olav; Waldeland, Anders Ueland; Johnsen, Espen; Malde, Ketil; Eikvil, Line; Salberg, Arnt-Børre; Handegard, Nils Olav (Peer reviewed; Journal article, 2020)
      Acoustic target classification is the process of assigning observed acoustic backscattering intensity to an acoustic category. A deep learning strategy for acoustic target classification using a convolutional network is ...
    • Automatic interpretation of otoliths using deep learning 

      Moen, Endre; Handegard, Nils Olav; Allken, Vaneeda; Albert, Ole Thomas; Harbitz, Alf; Malde, Ketil (Journal article; Peer reviewed, 2018)
      The age structure of a fish population has important implications for recruitment processes and population fluctuations, and is a key input to fisheries-assessment models. The current method of determining age structure ...
    • Automatic interpretation of salmon scales using deep learning 

      Vabø, Rune; Moen, Endre; Smolinski, Szymon; Husebø, Åse; Handegard, Nils Olav; Malde, Ketil (Peer reviewed; Journal article, 2021)
      For several fish species, age and other important biological information is manually inferred from visual scrutinization of scales, and reliable automatic methods are not widely available. Here, we apply Convolutional ...
    • Characterization of a novel RXR receptor in the salmon louse (Lepeophtheirus salmonis, Copepoda) regulating growth and female reproduction 

      Eichner, Christiane; Dalvin, Sussie Trine; Skern-Mauritzen, Rasmus; Malde, Ketil; Kongshaug, Heidi; Nilsen, Frank (Journal article; Peer reviewed, 2015-02-14)
      Nuclear receptors have crucial roles in all metazoan animals as regulators of gene transcription. A wide range of studies have elucidated molecular and biological significance of nuclear receptors but there are still a ...
    • A deep learning-based method to identify and count pelagic and mesopelagic fishes from trawl camera images 

      Allken, Vaneeda; Rosen, Shale Pettit; Handegard, Nils Olav; Malde, Ketil (Peer reviewed; Journal article, 2021)
      Fish counts and species information can be obtained from images taken within trawls, which enables trawl surveys to operate without extracting fish from their habitat, yields distribution data at fine scale for better ...
    • EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua) 

      Edvardsen, Rolf B.; Malde, Ketil; Mittelholzer, Christian; Taranger, Geir Lasse; Nilsen, Frank (Journal article; Peer reviewed, 2010-06-28)
      The Atlantic cod, Gadus morhua, is an important species both for traditional fishery and increasingly also in fish farming. The Atlantic cod is also under potential threat from various environmental changes such as pollution ...
    • EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua) 

      Edvardsen, Rolf B.; Malde, Ketil; Mittelholzer, Christian; Taranger, Geir Lasse; Nilsen, Frank (Journal article; Peer reviewed, 2010-06-28)
      The Atlantic cod, Gadus morhua, is an important species both for traditional fishery and increasingly also in fish farming. The Atlantic cod is also under potential threat from various environmental changes such as pollution ...
    • Fisheries acoustics and Acoustic Target Classification - Report from the COGMAR/CRIMAC workshop on machine learning methods in fisheries acoustics 

      Handegard, Nils Olav; Andersen, Lars Nonboe; Brautaset, Olav; Choi, Changkyu; Eliassen, Inge Kristian; Heggelund, Yngve; Hestnes, Arne Johan; Malde, Ketil; Osland, Håkon; Ordonez, Alba; Patel, Ruben; Pedersen, Geir; Umar, Ibrahim; Engeland, Tom Van; Vatnehol, Sindre (Rapport fra havforskningen;2021 - 25, Research report, 2021)
      This report documents a workshop organised by the COGMAR and CRIMAC projects. The objective of the workshop was twofold. The first objective was to give an overview of ongoing work using machine learning for Acoustic Target ...
    • Genome sequencing Part 1. Final report, April 2013 

      Skern-Mauritzen, Rasmus; Malde, Ketil; Furmanek, Tomasz; Nilsen, Frank (Rapport fra Havforskningen;Nr. 11-2013, Working paper, 2013)
    • Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations 

      Jansson, Eeva; Besnier, Francois; Malde, Ketil; André, Carl; Dahle, Geir; Glover, Kevin (Peer reviewed; Journal article, 2020)
      Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a ...
    • Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis 

      Besnier, Francois; Kent, Matthew; Skern-Mauritzen, Rasmus; Lien, Sigbjørn; Malde, Ketil; Edvardsen, Rolf B.; Taylor, Simon; Ljungfeldt, Lina; Nilsen, Frank; Glover, Kevin A. (Journal article; Peer reviewed, 2014-10-26)
      Background The salmon louse, Lepeophtheirus salmonis, is an ectoparasite of salmonids that causes huge economic losses in salmon farming, and has also been causatively linked with declines of wild salmonid populations. ...
    • Increasing Sequence Search Sensitivity with Transitive Alignments 

      Malde, Ketil; Furmanek, Tomasz (Journal article; Peer reviewed, 2013-02-14)
      Sequence alignment is an important bioinformatics tool for identifying homology, but searching against the full set of available sequences is likely to result in many hits to poorly annotated sequences providing very little ...
    • Judging a salmon by its spots: Environmental variation is the primary determinant of spot patterns in Salmo salar 

      Jørgensen, Katarina Mariann; Solberg, Monica Favnebøe; Besnier, Francois; Thorsen, Anders; Fjelldal, Per Gunnar; Skaala, Øystein; Malde, Ketil; Glover, Kevin (Journal article; Peer reviewed, 2018)
      In fish, morphological colour changes occur from variations in pigment concentrations and in the morphology, density, and distribution of chromatophores in the skin. However, the underlying mechanisms remain unresolved in ...
    • Machine intelligence and the data-driven future of marine science 

      Malde, Ketil; Handegard, Nils Olav; Eikvil, Line; Salberg, Arnt Børre (Peer reviewed; Journal article, 2019)
      Oceans constitute over 70% of the earth’s surface, and the marine environment and ecosystems are central to many global challenges. Not only are the oceans an important source of food and other resources, but they also ...
    • Machine Learning + Marine Science: Critical Role of Partnerships in Norway 

      Handegard, Nils Olav; Eikvil, Line; Jenssen, Robert; Kampffmeyer, Michael; Salberg, Arnt Børre; Malde, Ketil (Others, 2021)
      In this essay, we review some recent advances in developing machine learning (ML) methods for marine science applications in Norway. We focus mostly on deep learning (DL) methods and review the challenges we have faced in ...
    • Maternal 3’UTRs: from egg to onset of zygotic transcription in Atlantic cod 

      Kleppe, Lene; Edvardsen, Rolf B.; Kuhl, Heiner; Malde, Ketil; Furmanek, Tomasz; Drivenes, Øyvind; Reinhardt, Richard; Taranger, Geir Lasse; Wargelius, Anna (Journal article; Peer reviewed, 2012-09-01)
      Background Zygotic transcription in fish embryos initiates around the time of gastrulation, and all prior development is initiated and controlled by maternally derived messenger RNAs. Atlantic cod egg and embryo viability ...
    • Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis. 

      Dalvin, Sussie; Skaftnesmo, Kai Ove; Malde, Ketil; Glover, Kevin; Leong, Jong S; Koop, Ben F.; Edvardsen, Rolf Brudvik; Sandlund, Nina (Peer reviewed; Journal article, 2019)
      Lepeophtheirus salmonis is a naturally occurring marine parasite of salmonid fishes in the Northern hemisphere, and a major problem in salmonid aquaculture. In addition to the direct effects on host fish, L. salmonis may ...
    • The salmon louse genome: Copepod features and parasitic adaptations 

      Skern-Mauritzen, Rasmus; Malde, Ketil; Eichner, Christiane; Dondrup, Michael; Furmanek, Tomasz; Besnier, Francois; Komisarczuk, Anna Zofia; Nuhn, Michael; Dalvin, Sussie; Edvardsen, Rolf Brudvik; Klages, Sven; Huettel, Bruno; Stueber, Kurt; Grotmol, Sindre; Karlsbakk, Egil Erlingsson; Kersey, Paul; Leong, Jong S; Glover, Kevin Alan; Reinhardt, Richard; Lien, Sigbjørn; Jonassen, Inge; Koop, Ben F; Nilsen, Frank (Peer reviewed; Journal article, 2021)
      Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically ...
    • Simulating a population genomics data set using FlowSim 

      Malde, Ketil (Journal article; Peer reviewed, 2014-01-31)
      Background The field of population genetics use the genetic composition of populations to study the effects of ecological and evolutionary factors, including selection, genetic drift, mating structure, and migration. Until ...
    • The genome sequence of Atlantic cod reveals a unique immune system 

      Star, Bastiaan; Nederbragt, Alexander J.; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone F.; Rounge, Trine B.; Paulsen, Jonas; Solbakken, Monica H.; Sharma, Animesh; Wetten, Ola F.; Lanzén, Anders; Winer, Roger; Knight, James; Vogel, Jan-Hinnerk; Aken, Bronwen; Andersen, Øivind; Lagesen, Karin; Tooming-Klunderud, Ave; Edvardsen, Rolf B.; Tina, Kirubakaran G.; Espelund, Mari; Nepal, Chirag; Previti, Christopher; Karlsen, Bård Ove; Moum, Truls; Skage, Morten; Berg, Paul R.; Gjøen, Tor; Kuhl, Heiner; Thorsen, Jim; Malde, Ketil; Reinhardt, Richard; Du, Lei; Johansen, Steinar D.; Searle, Steve; Lien, Sigbjørn; Nilsen, Frank; Jonassen, Inge; Omholt, Stig W.; Stenseth, Nils Christian; Jakobsen, Kjetill S. (Journal article; Peer reviewed, 2011-08-10)
      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 Atlantic cod, showing evidence for complex ...