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Ketil Malde

Associate Professor
  • E-mailKetil.Malde@uib.no
  • Visitor Address
    HIB - Thormøhlensgt. 55
  • Postal Address
    Postboks 7803
    5020 Bergen
Academic article
  • Brautaset, Olav; Waldeland, Anders Ueland; Johnsen, Espen; Malde, Ketil; Eikvil, Line; Salberg, Arnt-Børre; Handegard, Nils Olav. 2020. Acoustic classification in multifrequency echosounder data using deep convolutional neural networks. ICES Journal of Marine Science.
  • Boitsov, Stepan; Grøsvik, Bjørn Einar; Nesje, Guri; Malde, Ketil; Klungsøyr, Jarle. 2019. Levels and temporal trends of persistent organic pollutants (POPs) in Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) from the southern Barents Sea. Environmental Research. 89-97.
  • Myers, Savannah Carolyn; Thorsen, Anders; Smolinski, Szymon; Godiksen, Jane Aanestad; Malde, Ketil; Handegard, Nils Olav. 2019. An efficient protocol and data set for automated otolith image analysis. Geoscience Data Journal. 1-9.
  • Fields, David M.; Handegard, Nils Olav; Dalen, John; Eichner, Christiane; Malde, Ketil; Karlsen, Ørjan; Skiftesvik, Anne Berit; Durif, Caroline; Browman, Howard. 2019. Airgun blasts used in marine seismic surveys have limited effects on mortality, and no sublethal effects on behaviour or gene expression, in the copepod Calanus finmarchicus. ICES Journal of Marine Science. 2033-2044.
  • Dalvin, Sussie; Skaftnesmo, Kai Ove; Malde, Ketil; Glover, Kevin; Leong, Jong S; Koop, Ben F.; Edvardsen, Rolf Brudvik; Sandlund, Nina. 2018. Microbial communities associated with the parasitic copepod Lepeophtheirus salmonis. . Marine Genomics.
  • Jørgensen, Katarina Mariann; Solberg, Monica Favnebøe; Besnier, Francois; Thorsen, Anders; Fjelldal, Per Gunnar; Skaala, Øystein; Malde, Ketil; Glover, Kevin. 2018. Judging a salmon by its spots: Environmental variation is the primary determinant of spot patterns in Salmo salar. BMC Ecology. 1-13.
  • Allken, Vaneeda; Handegard, Nils Olav; Rosen, Shale; Schreyeck, Tiffanie; Mahiout, Thomas; Malde, Ketil. 2018. Fish species identification using a convolutional neural network trained on synthetic data. ICES Journal of Marine Science. 342-349.
  • Moen, Endre; Handegard, Nils Olav; Allken, Vaneeda; Albert, Ole Thomas; Harbitz, Alf; Malde, Ketil. 2018. Automatic interpretation of otoliths using deep learning. PLOS ONE. 1-14.
  • 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. 2017. Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics. 1-11.
  • Eichner, Christiane; Dalvin, Sussie Trine; Skern-Mauritzen, Rasmus; Malde, Ketil; Kongshaug, Heidi; Nilsen, Frank. 2015. Characterization of a novel RXR receptor in the salmon louse (Lepeophtheirus salmonis, Copepoda) regulating growth and female reproduction. BMC Genomics. 22 pages.
  • Malde, Ketil. 2014. Simulating a population genomics data set using FlowSim. BMC Research Notes.
  • Besnier, Francois; Kent, Matthew Peter; Skern-Mauritzen, Rasmus; Lien, Sigbjørn; Malde, Ketil; Edvardsen, Rolf; Taylor, Simon; Ljungfeldt, Lina; Nilsen, Frank; Glover, Kevin. 2014. Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis. BMC Genomics. 18 pages.
  • Edvardsen, Rolf; Dalvin, Sussie Trine; Furmanek, Tomasz; Malde, Ketil; Mæhle, Stig; Kvamme, Bjørn Olav; Skern-Mauritzen, Rasmus. 2014. Gene expression in five salmon louse (Lepeophtheirus salmonis, Krøyer 1837) tissues. Marine Genomics. 39-44.
  • Malde, Ketil. 2014. Estimating the information value of polymorphic sites using pooled sequences. BMC Genomics. 11 pages.
  • Malde, Ketil; Furmanek, Tomasz. 2013. Increasing Sequence Search Sensitivity with Transitive Alignments. PLOS ONE. 7 pages.
  • Skern-Mauritzen, Rasmus; Malde, Ketil; Besnier, Francois; Nilsen, Frank; Jonassen, Inge; Reinhardt, Richard; Koop, Ben F.; Dalvin, Sussie Trine; Mæhle, Stig; Kongshaug, Heidi; Glover, Kevin. 2013. How does sequence variability affect de novo assembly quality? Journal of Natural History. 901-910.
  • Balzer, Susanne; Malde, Ketil; Grohme, Markus A.; Jonassen, Inge. 2013. Filtering duplicate reads from 454 pyrosequencing data. Bioinformatics. 830-836.
  • Kleppe, Lene; Edvardsen, Rolf; Kuhl, H; Malde, Ketil; Furmanek, Tomasz; Drivenes, O; Reinhardt, R; Taranger, Geir Lasse; Wargelius, Anna. 2012. Maternal 3 ' UTRs: from egg to onset of zygotic transcription in Atlantic cod. BMC Genomics. 14 pages.
  • 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. 2011. The genome sequence of Atlantic cod reveals a unique immune system. Nature. 207-210.
  • Balzer, Susanne; Malde, Ketil; Jonassen, Inge. 2011. Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics. I304-I309.
  • Sagstad, Anita; Grotmol, Sindre; Kryvi, Harald; Krossøy, Christel; Totland, Geir Kåre; Malde, Ketil; Wang, Shou; Hansen, Tom Johnny; Wargelius, Anna Sofie Troedsson. 2011. Identification of vimentin- and elastin-like transcripts specifically expressed in developing notochord of Atlantic salmon (Salmo salar L.). Cell and Tissue Research. 191-202.
  • Edvardsen, Rolf; Malde, Ketil; Mittelholzer, Christian; Taranger, Geir Lasse; Nilsen, Frank. 2011. EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua). Comparative Biochemistry and Physiology - Part D:Genomics and Proteomics. 23-30.
  • Balzer, Susanne; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge. 2010. Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics. i420-i425.
  • Malde, Marian Kjellevold; Bugel, S; Kristensen, M.; Malde, Ketil; Graff, Ingvild Eide; Pedersen, Jan I. 2010. Calcium from salmon and cod bone is well absorbed in young healthy men: a double-blinded randomised crossover design. Nutrition & Metabolism. 9 pages.
  • Patel, Sonal; Malde, Kjetil; Lanzén, Anders; Hetlelid Olsen, Rolf; Nerland, Audun H. 2009. Identification of immune related genes in Atlantic halibut (Hippoglossus hippoglossus L.) following in vivo antigenic and in vitro mitogenic stimulation. Fish and Shellfish Immunology. 729-738.
  • Malde, Ketil. 2008. The effect of sequence quality on sequence alignment. Bioinformatics. 897-900.
  • Malde, Ketil; Jonassen, Inge. 2008. Repeats and EST analysis for new organisms. BMC Genomics. 7 pages.
  • Malde, Ketil; Schneeberger, Korbinian; Coward, Eivind; Jonassen, Inge. 2006. RBR: library-less repeat detection for ESTs. Bioinformatics. 2232-2236.
  • Malde, Ketil; Giegerich, Robert. 2006. Calculating PSSM probabilities with lazy dynamic programming. Journal of functional programming. 75-81.
  • Schneeberger, Korbinian; Malde, Ketil; Coward, Eivind; Jonassen, Inge. 2005. Masking repeats while clustering ESTs. Nucleic Acids Research. 2176-2180.
  • Malde, Ketil; Coward, Eivind; Jonassen, Inge. 2005. A graph based algorithm for generating EST consensus sequences. Bioinformatics. 1371-1375.
  • Malde, Ketil; Coward, Eivind; Jonassen, Inge. 2003. Fast Sequence Clustering Using a Suffix Array Algorithm. Bioinformatics. 1221-1226.
  • Malde, Ketil; Coward, Eivind; Jonasen, Inge. 2003. A Fast Algorithm for EST Clustering using Suffix Arrays. Bioinformatics.
Report
  • Guidi, Lionel; Fernandez Guerra, A.; Canchaya, C; Curry, Ed; Foglini, F.; Irisson, J.-O.; Malde, Ketil; Marshall, C. T.; Obst, M.; Ribeiro, R. P.; Tjiputra, Jerry; Bakker, D. C. E. 2020. Big Data in Marine Science. 6. 6. .
  • Malde, Ketil. 2019. WORKING GROUP ON MACHINE LEARNING IN MARINE SCIENCE (WGMLEARN). .
  • Malde, Ketil; Handegard, Nils Olav; Hammersland, Hege; Michaels, William. 2019. Machine learning to improve marine science for the sustainability of living ocean resources: Report from the 2019 Norway - U.S. Workshop. .
  • Malde, Ketil; Syed, Shaheen. 2018. Report of the Workshop on Machine Learning in Marine Science (WKMLEARN). .
Lecture
  • Allken, Vaneeda; Handegard, Nils Olav; Rosen, Shale; Malde, Ketil. 2019. Using a CNN trained on synthetic data for fish species identification.
  • Allken, Vaneeda; Handegard, Nils Olav; Rosen, Shale; Malde, Ketil. 2019. Using a CNN trained on synthetic data for fish species identification.
  • Malde, Ketil. 2016. Big Data og Big Analysis - hvordan drikke fra brannslangen.
  • Malde, Ketil. 2015. Insitute of Marine Research - a research and advisory institute.
Academic lecture
  • Salberg, Arnt Børre; Eikvil, Line; Malde, Ketil; Handegard, Nils Olav. 2019. The COGMAR project.
  • Handegard, Nils Olav; Allken, Vaneeda; Malde, Ketil. 2018. Drowning in data: Can deep learning approaches be the solution?
  • Malde, Ketil. 2013. Identifying diagnostic SNPs in the presence of sequencing errors.
  • Malde, Ketil. 2013. Can Software Transactional Memory make concurrent programs simple and safe?
  • Edvardsen, Rolf; Mæhle, Stig; Furmanek, Tomasz; Malde, Ketil; Kvamme, Bjørn Olav; Dalvin, Sussie Trine; Skern-Mauritzen, Rasmus. 2012. Transcriptomic analysis of the salmon louse.
  • Skern-Mauritzen, Rasmus; Malde, Ketil; Furmanek, Tomasz; Reinhardt, Richard; Koop, Ben F; Nilsen, Frank. 2012. The Salmon Louse Genome Project.
  • Wargelius, Anna ; Edvardsen, Rolf; Haugen, Trine; Ellingsen, Ståle; Andersson, Eva; Malde, Ketil; Karlsen, Ørjan; Fjelldal, Per Gunnar; Taranger, Geir Lasse; Drivenes, Øyvind. 2012. Attempts to induce sterility in Atlantic salmon by morfolino and zink finger techniques.
  • Kleppe, Lene; Edvardsen, Rolf; Kuhl, Heiner; Malde, Ketil; Furmanek, Tomasz; Drivenes, Øyvind; Reinhardt, Richard; Taranger, Geir Lasse; Wargelius, Anna. 2011. Maternal 3'UTRs: from egg to onset of zygotic transcription in Atlantic cod.
  • Malde, Ketil; O'Sullivan, Bryan. 2009. Using Bloom Filters for Large Scale Gene Sequence Analysis in Haskell.
  • Malde, Ketil; Coward, Eivind; Jonasen, Inge. 2002. A Fast Algorithm for EST Clustering using Suffix Trees.
Short communication
  • Malde, Ketil. 2011. Flower: extracting information from pyrosequencing data. Bioinformatics. 1041-1042.
Doctoral dissertation
  • Malde, Ketil. 2005. Algorithms for the Analysis of Expressed Sequence Tags.
Poster
  • Vabø, Rune; Moen, Endre; Kim, Hyeongji; Handegard, Nils Olav; Malde, Ketil. 2020. Automatic interpretation of salmon scales using deep learning.
  • Godiksen, Jane Aanestad; Geffen, Audrey J.; Folkvord, Arild; Westgaard, Jon-Ivar; Johansen, Torild; Albert, Ole Thomas; Staby, Arved; Harbitz, Alf; Slotte, Aril; Malde, Ketil; Irgens, Christian; Kjesbu, Olav Sigurd. 2019. Otoliths as life history indicators.
  • Handegard, Nils Olav; Malde, Ketil; Tenningen, Maria; Pena, Hector. 2017. Automatisk klassifisering av svømming i not .
  • Malde, Ketil. 2013. A data storage strategy for generic, heterogenous scientific data.
Academic literature review
  • Malde, Ketil; Handegard, Nils Olav; Eikvil, Line; Salberg, Arnt Børre. 2019. Machine intelligence and the data-driven future of marine science. 12 pages.
Article in business/trade/industry journal
  • Boitsov, Stepan; Malde, Ketil; Grøsvik, Bjørn Einar; Nesje, Guri; Klungsøyr, Jarle. 2019. Levels and temporal trends of persistent organic pollutants (POPs) in Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) from the southern Barents Sea. Environmental Research.

More information in national current research information system (CRIStin)