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Items: 41

1.

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.

2.

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.

3.

Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish.

Lie KK, Tørresen OK, Solbakken MH, Rønnestad I, Tooming-Klunderud A, Nederbragt AJ, Jentoft S, Sæle Ø.

BMC Genomics. 2018 Mar 6;19(1):186. doi: 10.1186/s12864-018-4570-8.

4.

NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences.

Khelik K, Lagesen K, Sandve GK, Rognes T, Nederbragt AJ.

BMC Bioinformatics. 2017 Jul 12;18(1):338. doi: 10.1186/s12859-017-1748-z.

5.

The genomic mosaicism of hybrid speciation.

Elgvin TO, Trier CN, Tørresen OK, Hagen IJ, Lien S, Nederbragt AJ, Ravinet M, Jensen H, Sætre GP.

Sci Adv. 2017 Jun 14;3(6):e1602996. doi: 10.1126/sciadv.1602996. eCollection 2017 Jun.

6.

Coordinates and intervals in graph-based reference genomes.

Rand KD, Grytten I, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK.

BMC Bioinformatics. 2017 May 18;18(1):263. doi: 10.1186/s12859-017-1678-9.

7.

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.

Simovski B, Vodák D, Gundersen S, Domanska D, Azab A, Holden L, Holden M, Grytten I, Rand K, Drabløs F, Johansen M, Mora A, Lund-Andersen C, Fromm B, Eskeland R, Gabrielsen OS, Ferkingstad E, Nakken S, Bengtsen M, Nederbragt AJ, Thorarensen HS, Akse JA, Glad I, Hovig E, Sandve GK.

Gigascience. 2017 Jul 1;6(7):1-12. doi: 10.1093/gigascience/gix032.

8.

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.

9.

Annually resolved North Atlantic marine climate over the last millennium.

Reynolds DJ, Scourse JD, Halloran PR, Nederbragt AJ, Wanamaker AD, Butler PG, Richardson CA, Heinemeier J, Eiríksson J, Knudsen KL, Hall IR.

Nat Commun. 2016 Dec 6;7:13502. doi: 10.1038/ncomms13502.

10.

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
11.

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.

12.

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.

Frank JA, Pan Y, Tooming-Klunderud A, Eijsink VG, McHardy AC, Nederbragt AJ, Pope PB.

Sci Rep. 2016 May 9;6:25373. doi: 10.1038/srep25373.

13.

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.

14.

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
15.

The khmer software package: enabling efficient nucleotide sequence analysis.

Crusoe MR, Alameldin HF, Awad S, Boucher E, Caldwell A, Cartwright R, Charbonneau A, Constantinides B, Edvenson G, Fay S, Fenton J, Fenzl T, Fish J, Garcia-Gutierrez L, Garland P, Gluck J, González I, Guermond S, Guo J, Gupta A, Herr JR, Howe A, Hyer A, Härpfer A, Irber L, Kidd R, Lin D, Lippi J, Mansour T, McA'Nulty P, McDonald E, Mizzi J, Murray KD, Nahum JR, Nanlohy K, Nederbragt AJ, Ortiz-Zuazaga H, Ory J, Pell J, Pepe-Ranney C, Russ ZN, Schwarz E, Scott C, Seaman J, Sievert S, Simpson J, Skennerton CT, Spencer J, Srinivasan R, Standage D, Stapleton JA, Steinman SR, Stein J, Taylor B, Trimble W, Wiencko HL, Wright M, Wyss B, Zhang Q, Zyme E, Brown CT.

F1000Res. 2015 Sep 25;4:900. doi: 10.12688/f1000research.6924.1. eCollection 2015.

16.

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.

17.

Hybrid speciation through sorting of parental incompatibilities in Italian sparrows.

Hermansen JS, Haas F, Trier CN, Bailey RI, Nederbragt AJ, Marzal A, Saetre GP.

Mol Ecol. 2014 Dec;23(23):5831-42. doi: 10.1111/mec.12910. Epub 2014 Oct 7.

PMID:
25208037
18.

On the middle ground between open source and commercial software - the case of the Newbler program.

Nederbragt AJ.

Genome Biol. 2014;15(4):113. Epub 2014 Apr 29. No abstract available.

19.

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.

20.

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.

21.

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.

22.

Alterations of microbiota in urine from women with interstitial cystitis.

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

BMC Microbiol. 2012 Sep 13;12:205. doi: 10.1186/1471-2180-12-205.

23.

Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches.

Logares R, Haverkamp TH, Kumar S, Lanzén A, Nederbragt AJ, Quince C, Kauserud H.

J Microbiol Methods. 2012 Oct;91(1):106-13. doi: 10.1016/j.mimet.2012.07.017. Epub 2012 Jul 28. Review.

PMID:
22849829
24.

Genome fragmentation is not confined to the peridinin plastid in dinoflagellates.

Espelund M, Minge MA, Gabrielsen TM, Nederbragt AJ, Shalchian-Tabrizi K, Otis C, Turmel M, Lemieux C, Jakobsen KS.

PLoS One. 2012;7(6):e38809. doi: 10.1371/journal.pone.0038809. Epub 2012 Jun 18.

25.

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons.

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

BMC Microbiol. 2011 Nov 2;11:244. doi: 10.1186/1471-2180-11-244.

26.

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.

Nature. 2011 Aug 10;477(7363):207-10. doi: 10.1038/nature10342.

27.

Genome evolution of a tertiary dinoflagellate plastid.

Gabrielsen TM, Minge MA, Espelund M, Tooming-Klunderud A, Patil V, Nederbragt AJ, Otis C, Turmel M, Shalchian-Tabrizi K, Lemieux C, Jakobsen KS.

PLoS One. 2011 Apr 26;6(4):e19132. doi: 10.1371/journal.pone.0019132.

28.

Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant.

Brede DA, Snipen LG, Ussery DW, Nederbragt AJ, Nes IF.

J Bacteriol. 2011 May;193(9):2377-8. doi: 10.1128/JB.00183-11. Epub 2011 Mar 11.

29.

A novel totivirus and piscine reovirus (PRV) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (CMS).

Løvoll M, Wiik-Nielsen J, Grove S, Wiik-Nielsen CR, Kristoffersen AB, Faller R, Poppe T, Jung J, Pedamallu CS, Nederbragt AJ, Meyerson M, Rimstad E, Tengs T.

Virol J. 2010 Nov 10;7:309. doi: 10.1186/1743-422X-7-309.

30.

Genomic organization and gene expression of the multiple globins in Atlantic cod: conservation of globin-flanking genes in chordates infers the origin of the vertebrate globin clusters.

Wetten OF, Nederbragt AJ, Wilson RC, Jakobsen KS, Edvardsen RB, Andersen Ø.

BMC Evol Biol. 2010 Oct 20;10:315. doi: 10.1186/1471-2148-10-315.

31.

A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain.

Rounge TB, Rohrlack T, Nederbragt AJ, Kristensen T, Jakobsen KS.

BMC Genomics. 2009 Aug 25;10:396. doi: 10.1186/1471-2164-10-396.

32.

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.

N Biotechnol. 2009 Jun;25(5):263-71. doi: 10.1016/j.nbt.2009.03.014. Epub 2009 Apr 5. Review.

PMID:
19491044
33.

A solid-phase method for preparing human DNA from urine for diagnostic purposes.

Siddiqui H, Nederbragt AJ, Jakobsen KS.

Clin Biochem. 2009 Jul;42(10-11):1128-35. doi: 10.1016/j.clinbiochem.2009.03.010. Epub 2009 Mar 19.

PMID:
19303866
34.

Multiple-locus variable-number tandem repeat analysis of Legionella pneumophila using multi-colored capillary electrophoresis.

Nederbragt AJ, Balasingham A, Sirevåg R, Utkilen H, Jakobsen KS, Anderson-Glenna MJ.

J Microbiol Methods. 2008 May;73(2):111-7. doi: 10.1016/j.mimet.2008.02.007. Epub 2008 Feb 23.

PMID:
18374436
35.

A lophotrochozoan twist gene is expressed in the ectomesoderm of the gastropod mollusk Patella vulgata.

Nederbragt AJ, Lespinet O, van Wageningen S, van Loon AE, Adoutte A, Dictus WJ.

Evol Dev. 2002 Sep-Oct;4(5):334-43.

PMID:
12356263
36.

Novel and conserved roles for orthodenticle/ otx and orthopedia/ otp orthologs in the gastropod mollusc Patella vulgata.

Nederbragt AJ, te Welscher P, van den Driesche S, van Loon AE, Dictus WJ.

Dev Genes Evol. 2002 Aug;212(7):330-7. Epub 2002 Jun 12.

PMID:
12185486
37.

Evolutionary biology: hedgehog crosses the snail's midline.

Nederbragt AJ, van Loon AE, Dictus WJ.

Nature. 2002 Jun 20;417(6891):811-2.

PMID:
12075342
39.

Characterisation of two snail genes in the gastropod mollusc Patella vulgata. Implications for understanding the ancestral function of the snail-related genes in Bilateria.

Lespinet O, Nederbragt AJ, Cassan M, Dictus WJ, van Loon AE, Adoutte A.

Dev Genes Evol. 2002 May;212(4):186-95. Epub 2002 Apr 18.

PMID:
12012233
40.

The stringlike genes of the limpet Patella vulgata.

van der Kooij A, Nederbragt AJ, Goedemans HJ, van Loon AE.

Gene. 1996 Jun 26;172(2):261-5.

PMID:
8682314
41.

Isolation and composition of the constitutive agglutinins from haploid Saccharomyces cerevisiae cells.

Sijmons PC, Nederbragt AJ, Klis FM, Van den Ende H.

Arch Microbiol. 1987 Sep;148(3):208-12.

PMID:
3314767

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