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NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads.

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

BMC Bioinformatics. 2020 Feb 21;21(1):66. doi: 10.1186/s12859-020-3414-0.


Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1.

Alsøe L, Sarno A, Carracedo S, Domanska D, Dingler F, Lirussi L, SenGupta T, Tekin NB, Jobert L, Alexandrov LB, Galashevskaya A, Rada C, Sandve GK, Rognes T, Krokan HE, Nilsen H.

Sci Rep. 2017 Aug 3;7(1):7199. doi: 10.1038/s41598-017-07314-5.


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.


Open-Source Sequence Clustering Methods Improve the State Of the Art.

Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, Zhou HW, Rognes T, Caporaso JG, Knight R.

mSystems. 2016 Feb 9;1(1). pii: e00003-15. eCollection 2016 Jan-Feb.


VSEARCH: a versatile open source tool for metagenomics.

Rognes T, Flouri T, Nichols B, Quince C, Mahé F.

PeerJ. 2016 Oct 18;4:e2584. eCollection 2016.


The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress.

Namouchi A, Gómez-Muñoz M, Frye SA, Moen LV, Rognes T, Tønjum T, Balasingham SV.

BMC Genomics. 2016 Oct 10;17(1):791.


cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data.

Samarakoon PS, Sorte HS, Stray-Pedersen A, Rødningen OK, Rognes T, Lyle R.

BMC Genomics. 2016 Jan 14;17:51. doi: 10.1186/s12864-016-2374-2.


Swarm v2: highly-scalable and high-resolution amplicon clustering.

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M.

PeerJ. 2015 Dec 10;3:e1420. doi: 10.7717/peerj.1420. eCollection 2015.


Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway.

Yang M, Lin X, Rowe A, Rognes T, Eide L, Bjørås M.

Sci Rep. 2015 Nov 30;5:17409. doi: 10.1038/srep17409.


Non-homologous functions of the AlkB homologs.

Ougland R, Rognes T, Klungland A, Larsen E.

J Mol Cell Biol. 2015 Dec;7(6):494-504. doi: 10.1093/jmcb/mjv029. Epub 2015 May 23. Review.


Swarm: robust and fast clustering method for amplicon-based studies.

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M.

PeerJ. 2014 Sep 25;2:e593. doi: 10.7717/peerj.593. eCollection 2014.


Normalization of RNA-sequencing data from samples with varying mRNA levels.

Aanes H, Winata C, Moen LF, Østrup O, Mathavan S, Collas P, Rognes T, Aleström P.

PLoS One. 2014 Feb 25;9(2):e89158. doi: 10.1371/journal.pone.0089158. eCollection 2014.


Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response.

Booth JA, Thomassen GO, Rowe AD, Weel-Sneve R, Lagesen K, Kristiansen KI, Bjørås M, Rognes T, Lindvall JM.

Sci Rep. 2013 Oct 25;3:3053. doi: 10.1038/srep03053.


A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures.

Backe PH, Simm R, Laerdahl JK, Dalhus B, Fagerlund A, Okstad OA, Rognes T, Alseth I, Kolstø AB, Bjørås M.

J Struct Biol. 2013 Jul;183(1):66-75. doi: 10.1016/j.jsb.2013.04.007. Epub 2013 Apr 25.


Evolutionary paths of the cAMP-dependent protein kinase (PKA) catalytic subunits.

Søberg K, Jahnsen T, Rognes T, Skålhegg BS, Laerdahl JK.

PLoS One. 2013 Apr 12;8(4):e60935. doi: 10.1371/journal.pone.0060935. Print 2013.


Single transmembrane peptide DinQ modulates membrane-dependent activities.

Weel-Sneve R, Kristiansen KI, Odsbu I, Dalhus B, Booth J, Rognes T, Skarstad K, Bjørås M.

PLoS Genet. 2013;9(2):e1003260. doi: 10.1371/journal.pgen.1003260. Epub 2013 Feb 7.


Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes.

Nordstrand LM, Furu K, Paulsen J, Rognes T, Klungland A.

Nucleic Acids Res. 2012 Nov;40(21):10950-63. doi: 10.1093/nar/gks839. Epub 2012 Sep 10.


ALKBH1 is a histone H2A dioxygenase involved in neural differentiation.

Ougland R, Lando D, Jonson I, Dahl JA, Moen MN, Nordstrand LM, Rognes T, Lee JT, Klungland A, Kouzarides T, Larsen E.

Stem Cells. 2012 Dec;30(12):2672-82. doi: 10.1002/stem.1228.


Identification and characterization of novel mutations in the human gene encoding the catalytic subunit Calpha of protein kinase A (PKA).

Søberg K, Larsen AC, Diskar M, Backe PH, Bjørås M, Jahnsen T, Laerdahl JK, Rognes T, Herberg FW, Skålhegg BS.

PLoS One. 2012;7(4):e34838. doi: 10.1371/journal.pone.0034838. Epub 2012 Apr 13.


Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.

Rognes T.

BMC Bioinformatics. 2011 Jun 1;12:221. doi: 10.1186/1471-2105-12-221.


The ada operon of Mycobacterium tuberculosis encodes two DNA methyltransferases for inducible repair of DNA alkylation damage.

Yang M, Aamodt RM, Dalhus B, Balasingham S, Helle I, Andersen P, Tønjum T, Alseth I, Rognes T, Bjørås M.

DNA Repair (Amst). 2011 Jun 10;10(6):595-602. doi: 10.1016/j.dnarep.2011.03.007. Epub 2011 May 12.


Tiling array analysis of UV treated Escherichia coli predicts novel differentially expressed small peptides.

Thomassen GO, Weel-Sneve R, Rowe AD, Booth JA, Lindvall JM, Lagesen K, Kristiansen KI, Bjørås M, Rognes T.

PLoS One. 2010 Dec 23;5(12):e15356. doi: 10.1371/journal.pone.0015356.


Schizosaccharomyces pombe encodes a mutated AP endonuclease 1.

Laerdahl JK, Korvald H, Nilsen L, Dahl-Michelsen K, Rognes T, Bjørås M, Alseth I.

DNA Repair (Amst). 2011 Mar 7;10(3):296-305. doi: 10.1016/j.dnarep.2010.11.014. Epub 2010 Dec 28.


Continuous and periodic expansion of CAG repeats in Huntington's disease R6/1 mice.

Møllersen L, Rowe AD, Larsen E, Rognes T, Klungland A.

PLoS Genet. 2010 Dec 9;6(12):e1001242. doi: 10.1371/journal.pgen.1001242.


Mice lacking Alkbh1 display sex-ratio distortion and unilateral eye defects.

Nordstrand LM, Svärd J, Larsen E, Nilsen A, Ougland R, Furu K, Lien GF, Rognes T, Namekawa SH, Lee JT, Klungland A.

PLoS One. 2010 Nov 3;5(11):e13827. doi: 10.1371/journal.pone.0013827.


A two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways.

Fensgård Ø, Kassahun H, Bombik I, Rognes T, Lindvall JM, Nilsen H.

Aging (Albany NY). 2010 Mar 31;2(3):133-59.


The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts.

Nakken S, Rognes T, Hovig E.

Nucleic Acids Res. 2009 Sep;37(17):5749-56. doi: 10.1093/nar/gkp590. Epub 2009 Jul 17.


Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays.

Thomassen GO, Rowe AD, Lagesen K, Lindvall JM, Rognes T.

PLoS One. 2009 Jun 17;4(6):e5943. doi: 10.1371/journal.pone.0005943.


Genome dynamics in major bacterial pathogens.

Ambur OH, Davidsen T, Frye SA, Balasingham SV, Lagesen K, Rognes T, Tønjum T.

FEMS Microbiol Rev. 2009 May;33(3):453-70. Review.


Large-scale inference of the point mutational spectrum in human segmental duplications.

Nakken S, Rødland EA, Rognes T, Hovig E.

BMC Genomics. 2009 Jan 22;10:43. doi: 10.1186/1471-2164-10-43.


DNA repair in mammalian cells: Base excision repair: the long and short of it.

Robertson AB, Klungland A, Rognes T, Leiros I.

Cell Mol Life Sci. 2009 Mar;66(6):981-93. doi: 10.1007/s00018-009-8736-z. Review.


A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis.

Skotheim RI, Thomassen GO, Eken M, Lind GE, Micci F, Ribeiro FR, Cerveira N, Teixeira MR, Heim S, Rognes T, Lothe RA.

Mol Cancer. 2009 Jan 19;8:5. doi: 10.1186/1476-4598-8-5.


Slip slidin' away: a duodecennial review of targeted genes in mismatch repair deficient colorectal cancer.

Røyrvik EC, Ahlquist T, Rognes T, Lothe RA.

Crit Rev Oncog. 2007 Dec;13(3):229-57. Review.


Characterization of novel mutations in the catalytic domain of the PCSK9 gene.

Cameron J, Holla OL, Laerdahl JK, Kulseth MA, Ranheim T, Rognes T, Berge KE, Leren TP.

J Intern Med. 2008 Apr;263(4):420-31. doi: 10.1111/j.1365-2796.2007.01915.x. Epub 2008 Feb 2.


RNAmmer: consistent and rapid annotation of ribosomal RNA genes.

Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW.

Nucleic Acids Res. 2007;35(9):3100-8. Epub 2007 Apr 22.


Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats.

Dalhus B, Helle IH, Backe PH, Alseth I, Rognes T, Bjørås M, Laerdahl JK.

Nucleic Acids Res. 2007;35(7):2451-9. Epub 2007 Mar 29.


Computational prediction of microRNAs encoded in viral and other genomes.

Thomassen GO, Røsok O, Rognes T.

J Biomed Biotechnol. 2006;2006(4):95270.


Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes.

Nakken S, Alseth I, Rognes T.

Neuroscience. 2007 Apr 14;145(4):1273-9. Epub 2006 Oct 19. Review.


A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD.

Alseth I, Rognes T, Lindbäck T, Solberg I, Robertsen K, Kristiansen KI, Mainieri D, Lillehagen L, Kolstø AB, Bjørås M.

Mol Microbiol. 2006 Mar;59(5):1602-9.


PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology.

Saebø PE, Andersen SM, Myrseth J, Laerdahl JK, Rognes T.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W535-9.


Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming.

Saetrom P, Sneve R, Kristiansen KI, Snøve O Jr, Grünfeld T, Rognes T, Seeberg E.

Nucleic Acids Res. 2005 Jun 7;33(10):3263-70. Print 2005.


Biased distribution of DNA uptake sequences towards genome maintenance genes.

Davidsen T, Rødland EA, Lagesen K, Seeberg E, Rognes T, Tønjum T.

Nucleic Acids Res. 2004 Feb 11;32(3):1050-8. Print 2004.


DNA repair by bacterial AlkB proteins.

Falnes PØ, Rognes T.

Res Microbiol. 2003 Oct;154(8):531-8. Review.


Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V.

Moe A, Ringvoll J, Nordstrand LM, Eide L, Bjørås M, Seeberg E, Rognes T, Klungland A.

Nucleic Acids Res. 2003 Jul 15;31(14):3893-900.


Base removers and strand scissors: different strategies employed in base excision and strand incision at modified base residues in DNA.

Seeberg E, Luna L, Morland I, Eide L, Johnsen B, Larsen E, Alseth I, Dantzer F, Baynton K, Aamodt R, Kristiansen KI, Rognes T, Klungland A, Bjørås M.

Cold Spring Harb Symp Quant Biol. 2000;65:135-42. Review. No abstract available.


Human DNA glycosylases of the bacterial Fpg/MutM superfamily: an alternative pathway for the repair of 8-oxoguanine and other oxidation products in DNA.

Morland I, Rolseth V, Luna L, Rognes T, Bjørås M, Seeberg E.

Nucleic Acids Res. 2002 Nov 15;30(22):4926-36.


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