Publications from Bioinformatics group

58 publications found

Publications 2010

Bohlin J, Snipen L, Cloeckaert A, Lagesen K, Ussery D, Kristoffersen AB, Godfroid J (2010)
Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods
BMC Evol Biol, 10, 249
PubMed 20707916

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

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, IBSEN Study Group, Stokkers PC, Vermeire S, Mathew CG, Lie BA, Beuers U, Manns MP, Schreiber S, Schrumpf E, Häussinger D, Franke A, Karlsen TH (2010)
Mutational characterization of the bile acid receptor TGR5 in primary sclerosing cholangitis
PLoS One, 5 (8)
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

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

Blomberg KE, Smith CI, Lindvall JM (2007)
Gene expression signatures in primary immunodeficiencies: the experience from human disease and mouse models
Curr Mol Med, 7 (6), 555-66
PubMed 17896992

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

Emelie K, Blomberg M, Smith CIE, Lindvall JM (2007)
Gene expression signatures in primary immunodeficiencies: The experience from human disease and mouse models
Curr. Mol. Med., 7 (6), 555-566

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

Laerdahl JK, Civcir PU, Bache-Andreassen L, Uggerud E (2006)
Nucleophilic identity substitution reactions. The reaction between hydrogen fluoride and protonated alkyl fluorides
Org Biomol Chem, 4 (1), 135-41
PubMed 16358008

Rodland EA (2006)
Exact distribution of word counts in shuffled sequences. (vol 38, pg 116, 2006)
Adv. Appl. Probab., 38 (2), 580

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

Rodland EA (2006)
Exact distribution of word counts in shuffled sequences
Adv. Appl. Probab., 38 (1), 116-133

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

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

Schwerdtfeger P, Kuhn A, Bast R, Laerdahl JK, Faglioni F, Lazzeretti P (2004)
The vibrational spectrum of camphor from ab initio and density functional theory and parity violation in the C-C*-CO bending mode
Chem. Phys. Lett., 383 (5-6), 496-501

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

Publications 2002

Morland I, Rolseth V, Luna L, Rognes T, Bjørås M, Seeberg E (2002)
Human DNA glycosylases of the bacterial Fpg/MutM superfamily: an alternative pathway for the repair of 8-oxoguanine and other oxidation products in DNA
Nucleic Acids Res, 30 (22), 4926-36
PubMed 12433996

Publications 2001

Rognes T (2001)
ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches
Nucleic Acids Res, 29 (7), 1647-52
PubMed 11266569

Publications 2000

Luna L, Bjørås M, Hoff E, Rognes T, Seeberg E (2000)
Cell-cycle regulation, intracellular sorting and induced overexpression of the human NTH1 DNA glycosylase involved in removal of formamidopyrimidine residues from DNA
Mutat Res, 460 (2), 95-104
PubMed 10882850

Rognes T, Seeberg E (2000)
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
Bioinformatics, 16 (8), 699-706
PubMed 11099256

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 (2000)
Base removers and strand scissors: different strategies employed in base excision and strand incision at modified base residues in DNA
Cold Spring Harb Symp Quant Biol, 65, 135-42
PubMed 12760028

Publications 1999

Alseth I, Eide L, Pirovano M, Rognes T, Seeberg E, Bjørås M (1999)
The Saccharomyces cerevisiae homologues of endonuclease III from Escherichia coli, Ntg1 and Ntg2, are both required for efficient repair of spontaneous and induced oxidative DNA damage in yeast
Mol Cell Biol, 19 (5), 3779-87
PubMed 10207101

Luna L, Bjoras M, Berdal KG, Alseth I, Eide L, Rognes T, Seeberg E (1999)
Genes and enzymes for the removal of oxidative DNA base damage
ALFRED BENZON SYMP SERIES, 44, 272-283

Publications 1998

Lagesen K, Folstad I (1998)
Antler asymmetry and immunity in reindeer
Behav. Ecol. Sociobiol., 44 (2), 135-142

Rognes T, Seeberg E (1998)
SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments
Bioinformatics, 14 (10), 839-45
PubMed 9927712

Publications 1997

Bjorâs M, Luna L, Johnsen B, Hoff E, Haug T, Rognes T, Seeberg E (1997)
Opposite base-dependent reactions of a human base excision repair enzyme on DNA containing 7,8-dihydro-8-oxoguanine and abasic sites
EMBO J, 16 (20), 6314-22
PubMed 9321410