• 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 ...
    • 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 ...
    • 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 ...
    • 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 ...