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Journal articles
  • Kleppe, Lene; Edvardsen, Rolf; Furmanek, Tomasz; Andersson, Eva; Juanchich, Amélie; Wargelius, Anna. 2017. bmp15l, figla, smc1bl, and larp6l are preferentially expressed in germ cells in Atlantic salmon (Salmo salar L.). Molecular Reproduction and Development. 84: 76-87. doi: 10.1002/mrd.22755
  • Sørhus, Elin; Incardona, John P.; Furmanek, Tomasz; Goetz, Giles W.; Scholz, Nathaniel; Meier, Sonnich; Edvardsen, Rolf; Jentoft, Sissel. 2017. Novel adverse outcome pathways revealed by chemical genetics in a developing marine fish. eLIFE. 6:e20707: 1-30. Published 2017-01-24. doi: 10.7554/eLife.20707
  • Bizuayehu, Teshome Tilahun; Furmanek, Tomasz; Karlsen, Ørjan; van der Meeren, Terje; Edvardsen, Rolf; Rønnestad, Ivar; Hamre, Kristin; Johansen, Steinar Daae; Babiak, Igor. 2016. First feed affects the expressions of microRNA and their targets in Atlantic cod. British Journal of Nutrition. 115: 1145-1154. Published 2016-02-09. doi: 10.1017/S0007114516000155
  • Crespo, Diego; Assis, Luiz H. C.; Furmanek, Tomasz; Bogerd, Jan; Schulz, Rüdiger W. 2016. Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis. Molecular and Cellular Endocrinology. 437: 237-251. doi: 10.1016/j.mce.2016.08.033
  • Kjærner-Semb, Erik Nordtorp; Ayllon, Fernando; Furmanek, Tomasz; Wennevik, Vidar; Dahle, Geir; Niemelä, Eero; Ozerov, Mikhail; Vähä, Juha-Pekka; Glover, Kevin; Rubin, Carl J.; Wargelius, Anna; Edvardsen, Rolf. 2016. Atlantic salmon populations reveal adaptive divergence of immune related genes - A duplicated genome under selection. BMC Genomics. 17:610: 1-12. doi: 10.1186/s12864-016-2867-z
  • Sørhus, Elin; Incardona, John P.; Furmanek, Tomasz; Jentoft, Sissel; Meier, Sonnich; Edvardsen, Rolf. 2016. Developmental transcriptomics in Atlantic haddock: Illuminating pattern formation and organogenesis in non-model vertebrates. Developmental Biology. 411: 301-313. doi: 10.1016/j.ydbio.2016.02.012
  • Valen, Ragnhild; Eilertsen, Mariann; Edvardsen, Rolf; Furmanek, Tomasz; Rønnestad, Ivar; van der Meeren, Terje; Karlsen, Ørjan; Nilsen, Tom Ole; Helvik, Jon Vidar. 2016. The two-step development of a duplex retina involves distinct events of cone and rod neurogenesis and differentiation. Developmental Biology. 416: 389-401. doi: 10.1016/j.ydbio.2016.06.041
  • Ayllon, Fernando; Kjærner-Semb, Erik Nordtorp; Furmanek, Tomasz; Wennevik, Vidar; Solberg, Monica Favnebøe; Dahle, Geir; Taranger, Geir Lasse; Glover, Kevin; Almén, Markus Sällman; Rubin, Carl J.; Edvardsen, Rolf; Wargelius, Anna. 2015. The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon(Salmo salar L.) Males. PLoS Genetics. 11:e1005628. doi: 10.1371/journal.pgen.1005628
  • Penglase, Samuel; Edvardsen, Rolf; Furmanek, Tomasz; Rønnestad, Ivar; Karlsen, Ørjan; van der Meeren, Terje; Hamre, Kristin. 2015. Diet affects the redox system in developing Atlantic cod (Gadus morhua) larvae. Redox Biology. 5: 308-318. Published 2015-06-12. doi: 10.1016/j.redox.2015.06.003
  • Wargelius, Anna; Furmanek, Tomasz; Montfort, Jérôme; Le Cam, Aurélie; Kleppe, Lene; Juanchich, Amélie; Edvardsen, Rolf; Taranger, Geir Lasse; Bobe, Julien. 2015. A comparison between egg trancriptomes of cod and salmon reveals species-specific traits in eggs for each species. Molecular Reproduction and Development. 82: 397-404. doi: 10.1002/mrd.22487
  • 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. 18: 39-44. doi: 10.1016/j.margen.2014.06.008
  • Kleppe, Lene; Edvardsen, Rolf; Furmanek, Tomasz; Taranger, Geir Lasse; Wargelius, Anna. 2014. Global transcriptome analysis identifies regulated transcripts and pathways activated during oogenesis and early embryogenesis in atlantic cod. Molecular Reproduction and Development. 81: 619-635. doi: 10.1002/mrd.22328
  • Wang, Shou; Furmanek, Tomasz; Kryvi, Harald; Krossøy, Christel; Totland, Geir Kåre; Grotmol, Sindre; Wargelius, Anna. 2014. Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation. BMC Genomics. 15:141. doi: 10.1186/1471-2164-15-141
  • Karlsen, Bård Ove; Klingan, Kevin; Emblem, Åse; Jørgensen, Tor Erik; Jüterbock, Alexander; Furmanek, Tomasz; Hoarau, Galice; Johansen, Steinar; Nordeide, Jarle Tryti; Moum, Truls Borg. 2013. Genomic divergence between the migratory and stationary ecotypes of Atlantic cod. Molecular Ecology. 22: 5098-5111. doi: 10.1111/mec.12454
  • Malde, Ketil; Furmanek, Tomasz. 2013. Increasing Sequence Search Sensitivity with Transitive Alignments. PLoS ONE. 8. 7 pages. doi: 10.1371/journal.pone.0054422
  • Wang, Shou; Kryvi, Harald; Grotmol, Sindre; Wargelius, Anna; Krossøy, Christel; Epple, Matthias; Neues, Frank; Furmanek, Tomasz; Totland, Geir Kåre. 2013. Mineralization of the vertebral bodies in Atlantic salmon (Salmo salar L.) is initiated segmentally in the form of hydroxyapatite crystal accretions in the notochord sheath. Journal of Anatomy. 223: 159-170. Published 2013-05-27. doi: 10.1111/joa.12067
  • Bizuayehu, Teshome; Lanes, Carlos Fredrico Ceccon; Furmanek, Tomasz; Karlsen, Bård Ove; Fernandes, Jorge; Johansen, Steinar; Babiak, Igor. 2012. Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development. BMC Genomics. 13. 14 pages. doi: 10.1186/1471-2164-13-11
  • 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. 13. 14 pages. doi: 10.1186/1471-2164-13-443
  • Johansen, Steinar Daae; Karlsen, Bård Ove; Furmanek, Tomasz; Andreassen, morten; Jørgensen, Tor Erik; Bizuayehu, Teshome; Breines, Ragna; Emblem, Åse; Kettunen, Paivi; Luukko, Keijo; Edvardsen, Rolf; Nordeide, Jarle Tryti; Coucheron, Dag-Hugo; Moum, Truls. 2011. RNA deep sequencing of the Atlantic cod transcriptome. Comparative Biochemistry and Physiology - Part D:Genomics and Proteomics. 6: 18-22. doi: 10.1016/j.cbd.2010.04.005
  • Kettunen, Paivi; Furmanek, Tomasz; Chaulagain, Rajib; Kvinnsland, Inger Hals; Luukko, Keijo. 2011. Developmentally regulated expression of intracellular Fgf11-13, hormone-like Fgf15 and canonical Fgf16,-17 and-20 mRNAs in the developing mouse molar tooth. Acta Odontologica Scandinavica. 69: 360-366. doi: 10.3109/00016357.2011.568968
  • Coucheron, Dag H.; Andreassen, Morten; Karlsen, Bård O.; Furmanek, Tomasz; Jørgensen, Tor Erik; Emblem, Åse; Breines, Ragna; Nordeide, Jarle Tryti; Johansen, Steinar D.; Moum, Truls; Nederbragt, Alexander J.; Stenseth, Nils Christian; Jakobsen, Kjetill S. 2009. Large-scale sequence analyses of Atlantic cod. New Biotechnology. 25: 263-271.
  • Johansen, Steinar; Coucheron, Dag-Hugo; Andreassen, morten; Karlsen, Bård Ove; Furmanek, T; Jorgensen, TE; Jørgensen, Tor Erik; Emblem, A; Emblem, Åse; Breines, Ragna; Nordeide, JT; Moum, Truls; Nederbragt, AJ; Stenseth, Nils Christian; Jakobsen, KS. 2009. Large-scale sequence analyses of Atlantic cod. New Biotechnology. 25: 263-271. doi: 10.1016/j.nbt.2009.03.014
  • Luukko, Keijo; Moe, Kyaw; Sijaona, Angelina Clarisa; Furmanek, Tomasz; Kvinnsland, Inger Hals; Midtbø, Marit; Kettunen, Paivi. 2008. Secondary induction and the development of tooth nerve supply. Annals of Anatomy. 190: 178-187. doi: 10.1016/j.aanat.2007.10.003
  • Oltedal, Leif; Haglerød, Camilla; Furmanek, Tomasz; Davanger, Svend. 2008. Vesicular release of glutamate from hippocampal neurons in culture: an immunocytochemical assay. Experimental Brain Research. 184: 479-492. doi: 10.1007/s00221-007-1118-6
  • Kettunen, Paivi; Spencer-Dene, Bradley; Furmanek, Tomasz; Kvinnsland, Inger Hals; Dickson, Clive; Thesleff, Irma; Luukko, Keijo. 2007. Fgfr2b mediated epithelial-mesenchymal interactions coordinate tooth morphogenesis and dental trigeminal axon patterning. Mechanisms of Development. 124: 868-883. doi: 10.1016/j.mod.2007.09.003
  • Ellingsen, Ståle; Laplante, Mary; Kønig, Melanie; Furmanek, Tomasz Michal; Kikuta, Hiroshi; Høivik, Erling Andre; Becker, Thomas S. 2005. Large-scale enhancer detection in the zebrafish genome. Development. 132: 3799-3811. doi: 10.1242/dev.01951
  • Fjeld, Karianne; Kettunen, Paivi; Furmanek, Tomasz Michal; Kvinnsland, Inger Rebekka Hals; Luukko, Keijo. 2005. Dynamic expression of Wnt signaling-related Dickkopf1,-2, and-3 mRNAs in the developing mouse tooth. Developmental Dynamics. 233: 161-166. doi: 10.1002/dvdy.20285
  • Kettunen, Paivi; Løes, Sigbjørn Suk; Furmanek, Tomasz Michal; Fjeld, Karianne; Kvinnsland, Inger Rebekka Hals; Behar, Oded; Yagi, Takeshi; Fujisawa, Hajime; Vainio, Seppo; Taniguchi, Masahiko; Luukko, Keijo. 2005. Coordination of trigeminal axon navigation and patterning with tooth organ formation: epithelial-mesenchymal interactions, and epithelial Wnt4 and Tgfβ1 regulate semaphorin 3a expression in the dental mesenchyme. Development. 132: 323-334. doi: 10.1242/dev.01541
  • Luukko, Keijo Aukusti; Loes, Sigbjorn; Furmanek, Tomasz; Fjeld, Karianne; Hals Kvinnsland, Inger; Kettunen, Paivi Johanna. 2003. Identification of a novel putative signaling center, the tertiary enamel knot in the postnatal mouse molar tooth. Mechanisms of Development. 120: 270-276.
  • Luukko, Keijo; Løes, Sigbjørn Suk; Furmanek, Tomasz; Fjeld, Karianne; Kvinnsland, Inger Hals; Kettunen, Paivi. 2003. Identification of a novel putative signaling center, the tertiary enamel knot in the postnatal mouse molar tooth. Mechanisms of Development. 120: 270-276. doi: 10.1016/S0923-4773(02)00458-6
Reports and theses
  • Furmanek, Tomasz. 2003. 3D visualization and quantification of viability and gene expression in thick tissue samples. 82 pages.

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