Publications

Next-Generation Sequencing - Peer reviewed publications

​2016

First feed affects expression of microRNAs and their targets in Atlantic cod. Bizuayehu TT, Furmanek T, Karlsen Ø, van der Meeren T, Edvardsen RB, Rønnestad I, Hamre K, Johansen SD, Babiak I. (2016). British Journal of Nutrition 115: 1145-1154.

Next generation sequencing of microRNAs from isogenic neuroblastoma cell lines isolated before and after treatment. Roth SA, Knutsen E, Fiskaa T, Utnes P, Bhawsar S, Løkke C, Johansen SD, Flægstad T, Einvik C. (2016). Cancer Letters 372: 128-136.

Differentially expressed microRNAs and selected mRNA targets in benign meningioma tumors uncover shared biomarkers with malignant tumors. El-Gewely MR, Andreassen M, Walquist M, Ursvik A, Knutsen E, Nystand M, Coucheron DH, Smistad Myrmel K, Henning R, Johansen SD. (2016). Cancers 8: 3.

Lessons learned from the study of non-cancerous meningioma tumorsEl-Gewely MR, Henning R, Johansen SD. (2016). Atlas of Science (http://www.atlasofscience.org; May 30, 2016).

Substantial Downregulation of Myogenic Transcripts in Skeletal Muscle of Atlantic Cod during the Spawning Period. Nagasawa K, Sarropoulou E, Edvardsen V, Fernandes JM (2016). PLoS One 11: e0148374.

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.Olsen JL, Rouzé P, Verhelst B, Lin YC, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Boström C, Chovatia M, Grimwood J, Jenkins JW, Jueterbock A, Mraz A, Stam WT, Tice H, Bornberg-Bauer E, Green PJ, Pearson GA, Procaccini G, Duarte CM, Schmutz J, Reusch TB, Van de Peer Y (2016). Nature 530: 331-335. (Level 2)​

2015

Performance comparison and data analysis strategies for microRNA profiling in cancer research. Knutsen E, Perander M, Fiskaa T, Johansen SD. (2015). Next Generation Sequencing in Cancer Research – from Basepairs to Bedsides. Volume 2). Springer International Publishing Switzerland, pages 239-265.

Temperature during early development has long-term effects on microRNA expression in Atlantic cod. Bizuayehu TT, Johansen SD, Puvanendran V, Toften H, Babiak I. (2015). BMC Genomics, 16: 305.

2014

An evolutionary preserved intergenic spacer in gadiform mitogenomes generates a long noncoding RNA. Jørgensen TE, Bakke I, Ursvik A, Andreassen M, Moum T, Johansen SD. (2014). BMC Evolutionary Biology 14: 182. (Level 2)

 Mitogenome sequence variation in migratory and stationary ecotypes of North-east Atlantic cod. Karlsen BO, Emblem A, Jørgensen TE, Klingan KA, Nordeide JT, Moum T, Johansen SD (2014). Marine Genomics 15: 103-108.

Sea anemones possess dynamic mitogenome structures. Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, Johansen SD. (2014). Molecular Phylogenetics and Evolution 75: 184-193. (Level 2)

MicroRNA in teleost fish. Bizuayehu TT, Babiak I. (2014). Genome Biology and Evolution 6: 1911-1937.

Thermal plasticity of the miRNA transcriptome during Senegalese sole development. Campos C, Sundaram AY, Valente LM, Conceição LE, Engrola S, Fernandes JM. (2014).BMC Genomics 15: 525.

Profiling of the embryonic Atlantic halibut (Hippoglossus hippoglossus L.) transcriptome reveals maternal transcripts as potential markers of embryo quality. Mommens M,Fernandes JM, Tollefsen KE, Johnston IA, Babiak I (2014). BMC Genomics 15: 829.

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification. Smolina I, Kollias S, Poortvliet M, Nielsen TG, Lindeque P, Castellani C, Møller EF, Blanco-Bercial L, Hoarau G (2014). Molecular Ecology Resources 14: 1072-1079. (Level 2)​

2013

Characterization of novel precursor miRNAs using next generation sequencing and prediction of miRNA targets in Atlantic halibut. Bizuayehu TT, Fernandes JM, Johansen SD, Babiak I (2013). PLoS One 8: e61378.

Performance comparison of digital microRNA profiling technologies applied on human breast cancer cell lines. Knutsen E, Fiskaa T, Ursvik A, Jørgensen TE, Perander M, Lund E, Seternes OM, Johansen SD, Andreassen M (2013). PLoS One 8: e75813.

Genomic divergence between the migratory and stationary ecotypes of Atlantic cod. Karlsen BO, Klingan K, Emblem Å, Jørgensen TE, Jueterbock A, Furmanek T, Hoarau G, Johansen SD, Nordeide JT, Moum T (2013). Molecular Ecology 22: 5098-5111. (Level 2)

Transcriptome of Atlantic cod (Gadus morhua L.) early embryos from farmed and wild broodstocks. Lanes CF, Bizuayehu TT, de Oliveira Fernandes JM, Kiron V, Babiak I (2013). Marine Biotechnology 15: 677-694.​

2012

Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development. Bizuayehu TT, Lanes CF, Furmanek T, Karlsen BO, Fernandes JM, Johansen SD, Babiak I. (2012). BMC Genomics 13: 11. 

Digital marine bioprospecting: mining new neurotoxin drug candidates from the transcriptomes of cold-water sea anemones. Urbarova I, Karlsen BO, Okkenhaug S, Seternes OM, Johansen SD, Emblem A. (2012). Marine Drugs 10: 2265-2279.

Sex-Biased miRNA Expression in Atlantic Halibut (Hippoglossus hippoglossus) Brain and Gonads. Bizuayehu TT, Babiak J, Norberg B, Fernandes JM, Johansen SD, Babiak I. (2012). Sexual Development 25: 257-266.

Mitogenome polymorphism in a single branch sample revealed by SOLiD deep sequencing of the Lophelia pertusa coral genome. Emblem Å, Karlsen BO, Evertsen J, Miller DJ, Moum T, Johansen SD. (2012). Gene 506: 344-349.​

2011

The genome sequence of Atlantic cod reveals a unique immune system. Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel JH, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, Nepal C, Previti C, Karlsen BO, Moum T, Skage M, Berg PR, Gjøen T, Kuhl H, Thorsen J, Malde K, Reinhardt R, Du L, Johansen SD, Searle S, Lien S, Nilsen F, Jonassen I, Omholt SW, Stenseth NC, Jakobsen KS. (2011). Nature 477: 207-210. (Level 2)

Characterization of mitochondrial mRNAs in codfish reveals unique features compared to mammals. Coucheron DH, Nymark M, Breines R, Karlsen BO, Andreassen M, Jørgensen TE, Moum T, Johansen SD. (2011). Current Genetics 57: 213-222.

RNA deep sequencing of the Atlantic cod transcriptome. Johansen SD, Karlsen BO, Furmanek T, Andreassen M, Jørgensen TE, Bizuayehu TT, Breines R, Emblem A, Kettunen P, Luukko K, Edvardsen RB, Nordeide JT, Coucheron DH, Moum T. (2011). Comparative Biochemistry and Physiology Part D Genomics and Proteomics 6: 18-22.

2010

Approaching marine bioprospecting in hexacorals by RNA deep sequencing. Johansen SD, Emblem A, Karlsen BO, Okkenhaug S, Hansen H, Moum T, Coucheron DH, Seternes OM. (2010). New Biotechnology 27: 267-275.

2009

Large-scale sequence analyses of Atlantic cod. Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T, Jørgensen TE, Emblem A, Breines R, Nordeide JT, Moum T, Nederbragt AJ, Stenseth NC, Jakobsen KS. (2009). New Biotechnology 25: 263-271.