Publications published since 2003 or in press from OUS - Bioinformatics group

55 publications found

Publications in press

Tveten K, Holla OL, Cameron J, Strøm TB, Berge KE, Laerdahl JK, Leren TP
Interaction between the ligand-binding domain of the LDL receptor and the C-terminal domain of PCSK9 is required for PCSK9 to remain bound to the LDL receptor during endosomal acidification
Hum Mol Genet (in press)
PubMed 22156580

Publications 2011

Benam AV, Lång E, Alfsnes K, Fleckenstein B, Rowe AD, Hovland E, Ambur OH, Frye SA, Tønjum T (2011)
Structure-function relationships of the competence lipoprotein ComL and SSB in meningococcal transformation
Microbiology, 157 (Pt 5), 1329-42
PubMed 21330432

Holla ØL, Cameron J, Tveten K, Strøm TB, Berge KE, Laerdahl JK, Leren TP (2011)
Role of the C-terminal domain of PCSK9 in degradation of the LDL receptors
J Lipid Res, 52 (10), 1787-94
PubMed 21771976

Holla ØL, Laerdahl JK, Strøm TB, Tveten K, Cameron J, Berge KE, Leren TP (2011)
Removal of acidic residues of the prodomain of PCSK9 increases its activity towards the LDL receptor
Biochem Biophys Res Commun, 406 (2), 234-8
PubMed 21324305

Korvald H, Mølstad Moe AM, Cederkvist FH, Thiede B, Laerdahl JK, Bjørås M, Alseth I (2011)
Schizosaccharomyces pombe Ofd2 is a nuclear 2-oxoglutarate and iron dependent dioxygenase interacting with histones
PLoS One, 6 (9), e25188
PubMed 21949882

Laerdahl JK, Korvald H, Nilsen L, Dahl-Michelsen K, Rognes T, Bjørås M, Alseth I (2011)
Schizosaccharomyces pombe encodes a mutated AP endonuclease 1
DNA Repair (Amst), 10 (3), 296-305
PubMed 21193357

Melum E, Franke A, Schramm C, Weismüller TJ, Gotthardt DN, Offner FA, Juran BD, Laerdahl JK, Labi V, Björnsson E, Weersma RK, Henckaerts L, Teufel A, Rust C, Ellinghaus E, Balschun T, Boberg KM, Ellinghaus D, Bergquist A, Sauer P, Ryu E, Hov JR, Wedemeyer J, Lindkvist B, Wittig M et al. (2011)
Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci
Nat Genet, 43 (1), 17-9
PubMed 21151127

Rognes T (2011)
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
BMC Bioinformatics, 12, 221
PubMed 21631914

Yang M, Aamodt RM, Dalhus B, Balasingham S, Helle I, Andersen P, Tønjum T, Alseth I, Rognes T, Bjørås M (2011)
The ada operon of Mycobacterium tuberculosis encodes two DNA methyltransferases for inducible repair of DNA alkylation damage
DNA Repair (Amst), 10 (6), 595-602
PubMed 21570366

Publications 2010

Bohlin J, Snipen L, Hardy SP, Kristoffersen AB, Lagesen K, Dønsvik T, Skjerve E, Ussery DW (2010)
Analysis of intra-genomic GC content homogeneity within prokaryotes
BMC Genomics, 11, 464
PubMed 20691090

Falster DS, Nakken S, Bergem-Ohr M, Rødland EA, Breivik J (2010)
Unstable DNA repair genes shaped by their own sequence modifying phenotypes
J Mol Evol, 70 (3), 266-74
PubMed 20213140

Friis C, Wassenaar TM, Javed MA, Snipen L, Lagesen K, Hallin PF, Newell DG, Toszeghy M, Ridley A, Manning G, Ussery DW (2010)
Genomic characterization of Campylobacter jejuni strain M1
PLoS One, 5 (8), e12253
PubMed 20865039

Hov JR, Keitel V, Laerdahl JK, Spomer L, Ellinghaus E, ElSharawy A, Melum E, Boberg KM, Manke T, Balschun T, Schramm C, Bergquist A, Weismüller T, Gotthardt D, Rust C, Henckaerts L, Onnie CM, Weersma RK, Sterneck M, Teufel A, Runz H, Stiehl A, Ponsioen CY, Wijmenga C, Vatn MH et al. (2010)
Mutational characterization of the bile acid receptor TGR5 in primary sclerosing cholangitis
PLoS One, 5 (8), e12403
PubMed 20811628

Lagesen K, Ussery DW, Wassenaar TM (2010)
Genome update: the 1000th genome--a cautionary tale
Microbiology, 156 (Pt 3), 603-8
PubMed 20093288

Møllersen L, Rowe AD, Larsen E, Rognes T, Klungland A (2010)
Continuous and periodic expansion of CAG repeats in Huntington's disease R6/1 mice
PLoS Genet, 6 (12), e1001242
PubMed 21170307

Nordstrand LM, Svärd J, Larsen E, Nilsen A, Ougland R, Furu K, Lien GF, Rognes T, Namekawa SH, Lee JT, Klungland A (2010)
Mice lacking Alkbh1 display sex-ratio distortion and unilateral eye defects
PLoS One, 5 (11), e13827
PubMed 21072209

Thomassen GO, Weel-Sneve R, Rowe AD, Booth JA, Lindvall JM, Lagesen K, Kristiansen KI, Bjørås M, Rognes T (2010)
Tiling array analysis of UV treated Escherichia coli predicts novel differentially expressed small peptides
PLoS One, 5 (12), e15356
PubMed 21203457

Publications 2009

Ambur OH, Davidsen T, Frye SA, Balasingham SV, Lagesen K, Rognes T, Tønjum T (2009)
Genome dynamics in major bacterial pathogens
FEMS Microbiol Rev, 33 (3), 453-70
PubMed 19396949

Cameron J, Holla ØL, Laerdahl JK, Kulseth MA, Berge KE, Leren TP (2009)
Mutation S462P in the PCSK9 gene reduces secretion of mutant PCSK9 without affecting the autocatalytic cleavage
Atherosclerosis, 203 (1), 161-5
PubMed 19022446

Dalhus B, Laerdahl JK, Backe PH, Bjørås M (2009)
DNA base repair--recognition and initiation of catalysis
FEMS Microbiol Rev, 33 (6), 1044-78
PubMed 19659577

Holla ØL, Nakken S, Mattingsdal M, Ranheim T, Berge KE, Defesche JC, Leren TP (2009)
Effects of intronic mutations in the LDLR gene on pre-mRNA splicing: Comparison of wet-lab and bioinformatics analyses
Mol Genet Metab, 96 (4), 245-52
PubMed 19208450

Krokeide SZ, Bolstad N, Laerdahl JK, Bjørås M, Luna L (2009)
Expression and purification of NEIL3, a human DNA glycosylase homolog
Protein Expr Purif, 65 (2), 160-4
PubMed 19121397

Nakken KE, Labori KJ, Rødningen OK, Nakken S, Berge KE, Eiklid K, Raeder MG (2009)
ABCB4 sequence variations in young adults with cholesterol gallstone disease
Liver Int, 29 (5), 743-7
PubMed 19018976

Nakken S, Aussedat O, Kristoffersen AB, Holst-Jensen A, Tengs T (2009)
UniquePrimer - a web utility for design of specific PCR primers and probes
Ann. Microbiol., 59 (2), 391-393

Nakken S, Rognes T, Hovig E (2009)
The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts
Nucleic Acids Res, 37 (17), 5749-56
PubMed 19617376

Nakken S, Rødland EA, Rognes T, Hovig E (2009)
Large-scale inference of the point mutational spectrum in human segmental duplications
BMC Genomics, 10, 43
PubMed 19161616

Nordlund MS, Warren DJ, Laerdahl JK, Paus E (2009)
Studies on multiple forms of proGRP in serum from small cell lung cancer patients
Tumour Biol, 30 (5-6), 265-75
PubMed 19907206

Robertson AB, Klungland A, Rognes T, Leiros I (2009)
DNA repair in mammalian cells: Base excision repair: the long and short of it
Cell Mol Life Sci, 66 (6), 981-93
PubMed 19153658

Skotheim RI, Thomassen GO, Eken M, Lind GE, Micci F, Ribeiro FR, Cerveira N, Teixeira MR, Heim S, Rognes T, Lothe RA (2009)
A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis
Mol Cancer, 8, 5
PubMed 19152679

Thomassen GO, Rowe AD, Lagesen K, Lindvall JM, Rognes T (2009)
Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays
PLoS One, 4 (6), e5943
PubMed 19536279

Ussery DW, Kiil K, Lagesen K, Sicheritz-Pontén T, Bohlin J, Wassenaar TM (2009)
The genus burkholderia: analysis of 56 genomic sequences
Genome Dyn, 6, 140-57
PubMed 19696499

Publications 2008

Cameron J, Holla OL, Laerdahl JK, Kulseth MA, Ranheim T, Rognes T, Berge KE, Leren TP (2008)
Characterization of novel mutations in the catalytic domain of the PCSK9 gene
J Intern Med, 263 (4), 420-31
PubMed 18266662

Cameron J, Holla ØL, Berge KE, Kulseth MA, Ranheim T, Leren TP, Laerdahl JK (2008)
Investigations on the evolutionary conservation of PCSK9 reveal a functionally important protrusion
FEBS J, 275 (16), 4121-33
PubMed 18631360

Larsen E, Kleppa L, Meza TJ, Meza-Zepeda LA, Rada C, Castellanos CG, Lien GF, Nesse GJ, Neuberger MS, Laerdahl JK, William Doughty R, Klungland A (2008)
Early-onset lymphoma and extensive embryonic apoptosis in two domain-specific Fen1 mice mutants
Cancer Res, 68 (12), 4571-9
PubMed 18559501

Publications 2007

Adzhubei AA, Vlasova AV, Hagen-Larsen H, Ruden TA, Laerdahl JK, Høyheim B (2007)
Annotated expressed sequence tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource
BMC Genomics, 8, 209
PubMed 17605782

Dalhus B, Helle IH, Backe PH, Alseth I, Rognes T, Bjørås M, Laerdahl JK (2007)
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats
Nucleic Acids Res, 35 (7), 2451-9
PubMed 17395642

Davidsen T, Amundsen EK, Rødland EA, Tønjum T (2007)
DNA repair profiles of disease-associated isolates of Neisseria meningitidis
FEMS Immunol Med Microbiol, 49 (2), 243-51
PubMed 17284282

Davidsen T, Tuven HK, Bjørås M, Rødland EA, Tønjum T (2007)
Genetic interactions of DNA repair pathways in the pathogen Neisseria meningitidis
J Bacteriol, 189 (15), 5728-37
PubMed 17513474

Hayes B, Laerdahl JK, Lien S, Moen T, Berg P, Hindar K, Davidson WS, Koop BF, Adzhubei A, Hoyheim B (2007)
An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences
Aquaculture, 265 (1-4), 82-90

Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW (2007)
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Nucleic Acids Res, 35 (9), 3100-8
PubMed 17452365

Nakken S, Alseth I, Rognes T (2007)
Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes
Neuroscience, 145 (4), 1273-9
PubMed 17055652

Røyrvik EC, Ahlquist T, Rognes T, Lothe RA (2007)
Slip slidin' away: a duodecennial review of targeted genes in mismatch repair deficient colorectal cancer
Crit Rev Oncog, 13 (3), 229-57
PubMed 18298386

Publications 2006

Adzhubei AA, Laerdahl JK, Vlasova AV (2006)
preAssemble: a tool for automatic sequencer trace data processing
BMC Bioinformatics, 7, 22
PubMed 16417643

Alseth I, Rognes T, Lindbäck T, Solberg I, Robertsen K, Kristiansen KI, Mainieri D, Lillehagen L, Kolstø AB, Bjørås M (2006)
A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD
Mol Microbiol, 59 (5), 1602-9
PubMed 16468998

Rodland EA (2006)
Simes' procedure is 'valid on average'
Biometrika, 93 (3), 742-746

Thomassen GO, Røsok O, Rognes T (2006)
Computational prediction of microRNAs encoded in viral and other genomes
J Biomed Biotechnol, 2006 (4), 95270
PubMed 17057374

Publications 2005

Hagen-Larsen H, Laerdahl JK, Panitz F, Adzhubei A, Høyheim B (2005)
An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)
BMC Genomics, 6, 171
PubMed 16321156

Laerdahl JK, Civcir PU, Bache-Andreassen L, Uggerud E (2005)
Nucleophilic identity substitution reactions. The reaction between hydrogen fluoride and protonated alkyl fluorides
Org Biomol Chem, 4 (1), 135-41
PubMed 16358008

Saebø PE, Andersen SM, Myrseth J, Laerdahl JK, Rognes T (2005)
PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology
Nucleic Acids Res, 33 (Web Server issue), W535-9
PubMed 15980529

Saetrom P, Sneve R, Kristiansen KI, Snøve O, Grünfeld T, Rognes T, Seeberg E (2005)
Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming
Nucleic Acids Res, 33 (10), 3263-70
PubMed 15942029

Publications 2004

Davidsen T, Rødland EA, Lagesen K, Seeberg E, Rognes T, Tønjum T (2004)
Biased distribution of DNA uptake sequences towards genome maintenance genes
Nucleic Acids Res, 32 (3), 1050-8
PubMed 14960717

Ussery DW, Hallin PF, Lagesen K, Coenye T (2004)
Genome update: rRNAs in sequenced microbial genomes
Microbiology, 150 (Pt 5), 1113-5
PubMed 15133066

Ussery DW, Hallin PF, Lagesen K, Wassenaar TM (2004)
Genome update: tRNAs in sequenced microbial genomes
Microbiology, 150 (Pt 6), 1603-6
PubMed 15184546

Publications 2003

Falnes PØ, Rognes T (2003)
DNA repair by bacterial AlkB proteins
Res Microbiol, 154 (8), 531-8
PubMed 14527653

Moe A, Ringvoll J, Nordstrand LM, Eide L, Bjørås M, Seeberg E, Rognes T, Klungland A (2003)
Incision at hypoxanthine residues in DNA by a mammalian homologue of the Escherichia coli antimutator enzyme endonuclease V
Nucleic Acids Res, 31 (14), 3893-900
PubMed 12853604