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Items: 1 to 50 of 150

1.

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.

Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D.

Nucleic Acids Res. 2019 Oct 4. pii: gkz841. doi: 10.1093/nar/gkz841. [Epub ahead of print]

PMID:
31584084
2.

Whole transcriptome analysis of the Atlantic cod vaccine response reveals subtle changes in adaptive immunity.

Solbakken MH, Jentoft S, Reitan T, Mikkelsen H, Jakobsen KS, Seppola M.

Comp Biochem Physiol Part D Genomics Proteomics. 2019 Sep;31:100597. doi: 10.1016/j.cbd.2019.100597. Epub 2019 May 28.

3.

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod.

Riiser ES, Haverkamp THA, Varadharajan S, Borgan Ø, Jakobsen KS, Jentoft S, Star B.

Environ Microbiol. 2019 Jul;21(7):2576-2594. doi: 10.1111/1462-2920.14652. Epub 2019 May 23.

PMID:
31091345
4.

Vision using multiple distinct rod opsins in deep-sea fishes.

Musilova Z, Cortesi F, Matschiner M, Davies WIL, Patel JS, Stieb SM, de Busserolles F, Malmstrøm M, Tørresen OK, Brown CJ, Mountford JK, Hanel R, Stenkamp DL, Jakobsen KS, Carleton KL, Jentoft S, Marshall J, Salzburger W.

Science. 2019 May 10;364(6440):588-592. doi: 10.1126/science.aav4632.

PMID:
31073066
5.

Disentangling the immune response and host-pathogen interactions in Francisella noatunensis infected Atlantic cod.

Solbakken MH, Jentoft S, Reitan T, Mikkelsen H, Gregers TF, Bakke O, Jakobsen KS, Seppola M.

Comp Biochem Physiol Part D Genomics Proteomics. 2019 Jun;30:333-346. doi: 10.1016/j.cbd.2019.04.004. Epub 2019 Apr 13.

6.

Disentangling structural genomic and behavioural barriers in a sea of connectivity.

Barth JMI, Villegas-Ríos D, Freitas C, Moland E, Star B, André C, Knutsen H, Bradbury I, Dierking J, Petereit C, Righton D, Metcalfe J, Jakobsen KS, Olsen EM, Jentoft S.

Mol Ecol. 2019 Mar;28(6):1394-1411. doi: 10.1111/mec.15010. Epub 2019 Mar 15.

7.

Long-read sequence capture of the haemoglobin gene clusters across codfish species.

Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S.

Mol Ecol Resour. 2019 Jan;19(1):245-259. doi: 10.1111/1755-0998.12955. Epub 2018 Dec 4.

PMID:
30329222
8.

The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication.

Varadharajan S, Sandve SR, Gillard GB, Tørresen OK, Mulugeta TD, Hvidsten TR, Lien S, Asbjørn Vøllestad L, Jentoft S, Nederbragt AJ, Jakobsen KS.

Genome Biol Evol. 2018 Oct 1;10(10):2785-2800. doi: 10.1093/gbe/evy201.

9.

A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations.

Riiser ES, Haverkamp THA, Borgan Ø, Jakobsen KS, Jentoft S, Star B.

Front Microbiol. 2018 Jul 13;9:1561. doi: 10.3389/fmicb.2018.01561. eCollection 2018.

10.

Independent losses of a xenobiotic receptor across teleost evolution.

Eide M, Rydbeck H, Tørresen OK, Lille-Langøy R, Puntervoll P, Goldstone JV, Jakobsen KS, Stegeman J, Goksøyr A, Karlsen OA.

Sci Rep. 2018 Jul 10;8(1):10404. doi: 10.1038/s41598-018-28498-4.

11.

Mitochondrial genome variation of Atlantic cod.

Jørgensen TE, Karlsen BO, Emblem Å, Breines R, Andreassen M, Rounge TB, Nederbragt AJ, Jakobsen KS, Nymark M, Ursvik A, Coucheron DH, Jakt LM, Nordeide JT, Moum T, Johansen SD.

BMC Res Notes. 2018 Jun 19;11(1):397. doi: 10.1186/s13104-018-3506-3.

12.

The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes.

Malmstrøm M, Britz R, Matschiner M, Tørresen OK, Hadiaty RK, Yaakob N, Tan HH, Jakobsen KS, Salzburger W, Rüber L.

Genome Biol Evol. 2018 Apr 1;10(4):1088-1103. doi: 10.1093/gbe/evy058.

13.

Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats.

Tørresen OK, Brieuc MSO, Solbakken MH, Sørhus E, Nederbragt AJ, Jakobsen KS, Meier S, Edvardsen RB, Jentoft S.

BMC Genomics. 2018 Apr 10;19(1):240. doi: 10.1186/s12864-018-4616-y.

14.

Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord.

Vader A, Laughinghouse HD 4th, Griffiths C, Jakobsen KS, Gabrielsen TM.

Environ Microbiol. 2018 Feb;20(2):890-902. doi: 10.1111/1462-2920.14035. Epub 2018 Jan 12.

PMID:
29266690
15.

De novo gene evolution of antifreeze glycoproteins in codfishes revealed by whole genome sequence data.

Baalsrud HT, Tørresen OK, Hongrø Solbakken M, Salzburger W, Hanel R, Jakobsen KS, Jentoft S.

Mol Biol Evol. 2017 Dec 5. doi: 10.1093/molbev/msx311. [Epub ahead of print]

16.

Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions.

Berg PR, Star B, Pampoulie C, Bradbury IR, Bentzen P, Hutchings JA, Jentoft S, Jakobsen KS.

Heredity (Edinb). 2017 Dec;119(6):418-428. doi: 10.1038/hdy.2017.54. Epub 2017 Sep 20.

17.

Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth.

Baalsrud HT, Voje KL, Tørresen OK, Solbakken MH, Matschiner M, Malmstrøm M, Hanel R, Salzburger W, Jakobsen KS, Jentoft S.

Sci Rep. 2017 Aug 11;7(1):7956. doi: 10.1038/s41598-017-08286-2.

18.

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.

Star B, Boessenkool S, Gondek AT, Nikulina EA, Hufthammer AK, Pampoulie C, Knutsen H, André C, Nistelberger HM, Dierking J, Petereit C, Heinrich D, Jakobsen KS, Stenseth NC, Jentoft S, Barrett JH.

Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):9152-9157. doi: 10.1073/pnas.1710186114. Epub 2017 Aug 7.

19.

Genome architecture enables local adaptation of Atlantic cod despite high connectivity.

Barth JMI, Berg PR, Jonsson PR, Bonanomi S, Corell H, Hemmer-Hansen J, Jakobsen KS, Johannesson K, Jorde PE, Knutsen H, Moksnes PO, Star B, Stenseth NC, Svedäng H, Jentoft S, André C.

Mol Ecol. 2017 Sep;26(17):4452-4466. doi: 10.1111/mec.14207. Epub 2017 Jul 19.

PMID:
28626905
20.

Linking species habitat and past palaeoclimatic events to evolution of the teleost innate immune system.

Solbakken MH, Voje KL, Jakobsen KS, Jentoft S.

Proc Biol Sci. 2017 Apr 26;284(1853). pii: 20162810. doi: 10.1098/rspb.2016.2810.

21.

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod.

Tørresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, Walenz BP, Knight J, Ekholm JM, Peluso P, Edvardsen RB, Tooming-Klunderud A, Skage M, Lien S, Jakobsen KS, Nederbragt AJ.

BMC Genomics. 2017 Jan 18;18(1):95. doi: 10.1186/s12864-016-3448-x.

22.

Whole genome sequencing data and de novo draft assemblies for 66 teleost species.

Malmstrøm M, Matschiner M, Tørresen OK, Jakobsen KS, Jentoft S.

Sci Data. 2017 Jan 17;4:160132. doi: 10.1038/sdata.2016.132.

23.

Successive Losses of Central Immune Genes Characterize the Gadiformes' Alternate Immunity.

Solbakken MH, Rise ML, Jakobsen KS, Jentoft S.

Genome Biol Evol. 2016 Dec 31;8(11):3508-3515. doi: 10.1093/gbe/evw250.

24.

Using Prokaryotes for Carbon Capture Storage.

Hicks N, Vik U, Taylor P, Ladoukakis E, Park J, Kolisis F, Jakobsen KS.

Trends Biotechnol. 2017 Jan;35(1):22-32. doi: 10.1016/j.tibtech.2016.06.011. Epub 2016 Oct 3.

PMID:
27712920
25.

Evolution of the immune system influences speciation rates in teleost fishes.

Malmstrøm M, Matschiner M, Tørresen OK, Star B, Snipen LG, Hansen TF, Baalsrud HT, Nederbragt AJ, Hanel R, Salzburger W, Stenseth NC, Jakobsen KS, Jentoft S.

Nat Genet. 2016 Oct;48(10):1204-10. doi: 10.1038/ng.3645. Epub 2016 Aug 22.

PMID:
27548311
26.

Genomic characterization of the Atlantic cod sex-locus.

Star B, Tørresen OK, Nederbragt AJ, Jakobsen KS, Pampoulie C, Jentoft S.

Sci Rep. 2016 Aug 8;6:31235. doi: 10.1038/srep31235.

27.

Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika.

Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W.

Mol Ecol. 2016 Dec;25(24):6143-6161. doi: 10.1111/mec.13767. Epub 2016 Aug 26.

PMID:
27452499
28.

Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions.

Solbakken MH, Tørresen OK, Nederbragt AJ, Seppola M, Gregers TF, Jakobsen KS, Jentoft S.

Sci Rep. 2016 Apr 29;6:25211. doi: 10.1038/srep25211.

29.

The Atlantic salmon genome provides insights into rediploidization.

Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS.

Nature. 2016 May 12;533(7602):200-5. doi: 10.1038/nature17164. Epub 2016 Apr 18.

PMID:
27088604
30.

Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod.

Berg PR, Star B, Pampoulie C, Sodeland M, Barth JM, Knutsen H, Jakobsen KS, Jentoft S.

Sci Rep. 2016 Mar 17;6:23246. doi: 10.1038/srep23246.

31.

Chloroplast phylogeny of Triticum/Aegilops species is not incongruent with an ancient homoploid hybrid origin of the ancestor of the bread wheat D-genome.

Sandve SR, Marcussen T, Mayer K, Jakobsen KS, Heier L, Steuernagel B, Wulff BB, Olsen OA.

New Phytol. 2015 Oct;208(1):9-10. doi: 10.1111/nph.13487. Epub 2015 May 21. No abstract available.

32.

Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.).

Berg PR, Jentoft S, Star B, Ring KH, Knutsen H, Lien S, Jakobsen KS, André C.

Genome Biol Evol. 2015 May 20;7(6):1644-63. doi: 10.1093/gbe/evv093.

33.

Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains.

Stüken A, Riobó P, Franco J, Jakobsen KS, Guillou L, Figueroa RI.

Front Microbiol. 2015 May 1;6:404. doi: 10.3389/fmicb.2015.00404. eCollection 2015.

34.

Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-independent High Throughput Sequencing: A Case Report.

Siddiqui H, Lagesen K, Nederbragt AJ, Eri LM, Jeansson SL, Jakobsen KS.

Open Microbiol J. 2014 Dec 31;8:148-53. doi: 10.2174/1874285801408010148. eCollection 2014.

35.

From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae).

Marcussen T, Heier L, Brysting AK, Oxelman B, Jakobsen KS.

Syst Biol. 2015 Jan;64(1):84-101. doi: 10.1093/sysbio/syu071. Epub 2014 Oct 3.

36.

Use of high throughput sequencing and light microscopy show contrasting results in a study of phytoplankton occurrence in a freshwater environment.

Xiao X, Sogge H, Lagesen K, Tooming-Klunderud A, Jakobsen KS, Rohrlack T.

PLoS One. 2014 Aug 29;9(8):e106510. doi: 10.1371/journal.pone.0106510. eCollection 2014.

37.

Ancient hybridizations among the ancestral genomes of bread wheat.

Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M; International Wheat Genome Sequencing Consortium,, Jakobsen KS, Wulff BB, Steuernagel B, Mayer KF, Olsen OA.

Science. 2014 Jul 18;345(6194):1250092. doi: 10.1126/science.1250092.

38.

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust EV, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AG, Slamovits CH, Smith DR, Smith GJ, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ.

PLoS Biol. 2014 Jun 24;12(6):e1001889. doi: 10.1371/journal.pbio.1001889. eCollection 2014 Jun. No abstract available.

39.

Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.

Star B, Nederbragt AJ, Hansen MH, Skage M, Gilfillan GD, Bradbury IR, Pampoulie C, Stenseth NC, Jakobsen KS, Jentoft S.

PLoS One. 2014 Mar 7;9(3):e89676. doi: 10.1371/journal.pone.0089676. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e103170.

40.

Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

Haverkamp TH, Hammer Ø, Jakobsen KS.

PLoS One. 2014 Jan 24;9(1):e85990. doi: 10.1371/journal.pone.0085990. eCollection 2014.

41.

The chloroplast genome of the diatom Seminavis robusta: new features introduced through multiple mechanisms of horizontal gene transfer.

Brembu T, Winge P, Tooming-Klunderud A, Nederbragt AJ, Jakobsen KS, Bones AM.

Mar Genomics. 2014 Aug;16:17-27. doi: 10.1016/j.margen.2013.12.002. Epub 2013 Dec 21.

42.

Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location.

Star B, Haverkamp TH, Jentoft S, Jakobsen KS.

BMC Microbiol. 2013 Nov 9;13:248. doi: 10.1186/1471-2180-13-248.

43.

Unraveling the evolution of the Atlantic cod's (Gadus morhua L.) alternative immune strategy.

Malmstrøm M, Jentoft S, Gregers TF, Jakobsen KS.

PLoS One. 2013 Sep 3;8(9):e74004. doi: 10.1371/journal.pone.0074004. eCollection 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/18b70612-fd3d-46ce-a04b-652d18c82d5b.

44.

From green to red: horizontal gene transfer of the phycoerythrin gene cluster between Planktothrix strains.

Tooming-Klunderud A, Sogge H, Rounge TB, Nederbragt AJ, Lagesen K, Glöckner G, Hayes PK, Rohrlack T, Jakobsen KS.

Appl Environ Microbiol. 2013 Nov;79(21):6803-12. doi: 10.1128/AEM.01455-13. Epub 2013 Aug 30.

45.

Evolution and distribution of saxitoxin biosynthesis in dinoflagellates.

Orr RJ, Stüken A, Murray SA, Jakobsen KS.

Mar Drugs. 2013 Aug 8;11(8):2814-28. doi: 10.3390/md11082814. Review.

46.

Evolutionary acquisition and loss of saxitoxin biosynthesis in dinoflagellates: the second "core" gene, sxtG.

Orr RJ, Stüken A, Murray SA, Jakobsen KS.

Appl Environ Microbiol. 2013 Apr;79(7):2128-36. doi: 10.1128/AEM.03279-12. Epub 2013 Jan 18.

47.

[Carcinoids and 68Ga-DOTANOC PET/CT].

Borghammer P, Arveschoug AK, Hjorthaug K, Kindt SE, Jakobsen KS.

Ugeskr Laeger. 2013 Jan 7;175(1-2):58. Danish. No abstract available.

PMID:
23305644
48.

When naked became armored: an eight-gene phylogeny reveals monophyletic origin of theca in dinoflagellates.

Orr RJ, Murray SA, Stüken A, Rhodes L, Jakobsen KS.

PLoS One. 2012;7(11):e50004. doi: 10.1371/journal.pone.0050004. Epub 2012 Nov 19.

49.

Gene flow, recombination, and selection in cyanobacteria: population structure of geographically related Planktothrix freshwater strains.

Sogge H, Rohrlack T, Rounge TB, Sønstebø JH, Tooming-Klunderud A, Kristensen T, Jakobsen KS.

Appl Environ Microbiol. 2013 Jan;79(2):508-15. doi: 10.1128/AEM.02417-12. Epub 2012 Nov 2.

50.

Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data.

Frisli T, Haverkamp TH, Jakobsen KS, Stenseth NC, Rudi K.

J Appl Microbiol. 2013 Jan;114(1):141-51. doi: 10.1111/jam.12035. Epub 2012 Nov 1.

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