Blar i Bergen Open Research Archive på forfatter "Malde, Ketil"

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    • Annotating otoliths with a deep generative model 

      Bojesen, Troels Arnfred; Denechaud, Côme; Malde, Ketil (Journal article; Peer reviewed, 2023)
      Otoliths are a central information source for fish ecology and stock management, conveying important data about age and other life history for individual fish. Traditionally, interpretation of otoliths has required skilled ...

    • Automatic interpretation of otoliths using deep learning 

      Moen, Endre; Handegard, Nils Olav; Allken, Vaneeda; Albert, Ole Thomas; Harbitz, Alf; Malde, Ketil (Peer reviewed; Journal article, 2018-12-17)
      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 (Journal article; Peer reviewed, 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 ...

    • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim 

      Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (Peer reviewed; Journal article, 2010)
      Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 ...

    • 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 (Peer reviewed; Journal article, 2015-02-14)
      Background: 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 ...

    • A contrastive learning approach for individual re-identification in a wild fish population 

      Olsen, Ørjan Langøy; Sørdalen, Tonje Knutsen; Goodwin, Morten; Malde, Ketil; Knausgård, Kristian Muri; Halvorsen, Kim Aleksander Tallaksen (Journal article; Peer reviewed, 2023)
      In both terrestrial and marine ecology, physical tagging is a frequently used method to study population dynamics and behavior. However, such tagging techniques are increasingly being replaced by individual re-identification ...

    • 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 (Journal article; Peer reviewed, 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 ...

    • DeepOtolith v1.0: An Open-Source AI Platform for Automating Fish Age Reading from Otolith or Scale Images 

      Politikos, Dimitris V.; Sykiniotis, Nikolaos; Petasis, Georgios; Dedousis, Pavlos; Ordonez, Alba; Vabø, Rune; Anastasopoulou, Aikaterini; Moen, Endre; Mytilineou, Chryssi; Salberg, Arnt-Børre; Chatzispyrou, Archontia; Malde, Ketil (Journal article; Peer reviewed, 2022-05-29)
      Every year, marine scientists around the world read thousands of otolith or scale images to determine the age structure of commercial fish stocks. This knowledge is important for fisheries and conservation management. ...

    • Filtering duplicate reads from 454 pyrosequencing data 

      Balzer, Susanne Mignon; Malde, Ketil; Grohme, Markus A.; Jonassen, Inge (Peer reviewed; Journal article, 2013)
      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 sequencing and metagenomics. Especially ...

    • The genome sequence of Atlantic cod reveals a unique immune system 

      Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone Fredsvik; Rounge, Trine Ballestad; Paulsen, Jonas; Solbakken, Monica Hongrø; Sharma, Animesh; Wetten, Ola Frang; Lanzén, Anders; Winer, Roger; Knight, James; Vogel, Jan-Hinnerk; Aken, Bronwen; Andersen, Øivind; Lagesen, Karin; Tooming-Klunderud, Ave; Edvardsen, Rolf; Kirubakaran, G. Tina; Espelund, Mari; Nepal, Chirag; Previti, A. Christopher; Karlsen, Bård Ove; Moum, Truls; Skage, Morten; Berg, Paul Ragnar; Gjøen, Tor; Kuhl, Heiner; Thorsen, Jim; Malde, Ketil; Reinhardt, Richard; Du, Lei; Johansen, Steinar Daae; Searle, Steve; Lien, Sigbjørn; Nilsen, Frank; Jonassen, Inge; Omholt, Stig W; Stenseth, Nils Christian; Jakobsen, Kjetill Sigurd (Peer reviewed; Journal article, 2011-09)
      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 ...

    • Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations 

      Jansson, Eeva; Besnier, Francois; Malde, Ketil; André, Carl; Dahle, Geir; Glover, Kevin (Journal article; Peer reviewed, 2020)
      Background 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 ...

    • 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; Taylor, Simon; Ljungfeldt, Lina; Nilsen, Frank; Glover, Kevin (Peer reviewed; Journal article, 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. ...

    • 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 (Peer reviewed; Journal article, 2018-04-12)
      Background. 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 ...

    • Machine learning in marine ecology: an overview of techniques and applications 

      Rubbens, Peter; Brodie, Stephanie; Cordier, Tristan; Desto Barcellos, Diogo; DeVos, Paul; Fernandes-Salvador, Jose A; Fincham, Jennifer; Gomes, Alessandra; Handegard, Nils Olav; Howell, Kerry L.; Jamet, Cédric; Kartveit, Kyrre Heldal; Moustahfid, Hassan; Parcerisas, Clea; Politikos, Dimitris V.; Sauzède, Raphaëlle; Sokolova, Maria; Uusitalo, Laura; Van den Bulcke, Laure; van Helmond, Aloysius; Watson, Jordan T.; Welch, Heather; Beltran-Perez, Oscar; Chaffron, Samuel; Greenberg, David S.; Kühn, Bernhard; Kiko, Rainer; Lo, Madiop; Lopes, Rubens M.; Möller, Klas Ove; Michaels, William; Pala, Ahmet; Romagnan, Jean-Baptiste; Schuchert, Pia; Seydi, Vahid; Villasante, Sebastian; Malde, Ketil; Irisson, Jean-Olivier (Journal article; Peer reviewed, 2023)
      Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific ...

    • Measuring Adversarial Robustness using a Voronoi-Epsilon Adversary 

      Kim, Hyeongji; Parviainen, Pekka; Malde, Ketil (Journal article; Peer reviewed, 2023)
      Previous studies on robustness have argued that there is a tradeoff between accuracy and adversarial accuracy. The tradeoff can be inevitable even when we neglect generalization. We argue that the tradeoff is inherent to ...

    • Repeats and EST analysis for new organisms 

      Malde, Ketil; Jonassen, Inge (Journal article, 2008-01-18)
      Background Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask ...

    • The salmon louse genome may be much larger than sequencing suggests 

      Wyngaard, Grace; Skern-Mauritzen, Rasmus; Malde, Ketil; Prendergast, Rachel; Peruzzi, Stefano (Journal article; Peer reviewed, 2022)
      The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically ...

    • 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 (Journal article; Peer reviewed, 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 ...

    • Systematic exploration of error sources in pyrosequencing flowgram data 

      Balzer, Susanne Mignon; Malde, Ketil; Jonassen, Inge (Peer reviewed; Journal article, 2011)
      Motivation: 454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes to read lengths, performance and cost, but shows higher per-base error rates. Although there are several ...

    • Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species 

      Malde, Ketil; Seliussen, Bjørghild Breistein; Sanchez, Maria Quintela; Dahle, Geir; Besnier, Francois; Skaug, Hans J.; Øien, Nils Inge; Solvang, Hiroko Kato; Haug, Tore; Skern-Mauritzen, Rasmus; Kanda, Naohisa; Pastene, Luis A.; Jonassen, Inge; Glover, Kevin (Peer reviewed; Journal article, 2017-01-13)
      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. An ...