Rognes group

Publications 2024

Yang M, Kaarbø M, Myhre V, Reims HM, Karlsen TH, Wang J, Rognes T, Halvorsen B, Fevang B, Lundin KEA, Aukrust P, Bjørås M, Jørgensen SF (2024)
Altered Genome-Wide DNA Methylation in the Duodenum of Common Variable Immunodeficiency Patients
J Clin Immunol, 44 (6), 133
DOI 10.1007/s10875-024-01726-5, PubMed 38780872

Lång E, Lång A, Blicher P, Rognes T, Dommersnes PG, Bøe SO (2024)
Topology-guided polar ordering of collective cell migration
Sci Adv, 10 (16), eadk4825
DOI 10.1126/sciadv.adk4825, PubMed 38630812

Istvan P, Birkeland E, Avershina E, Kværner AS, Bemanian V, Pardini B, Tarallo S, de Vos WM, Rognes T, Berstad P, Rounge TB (2024)
Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study
Nat Commun, 15 (1), 1791
DOI 10.1038/s41467-024-46033-0, PubMed 38424056

Publications 2023

Rumbavicius I, Rounge TB, Rognes T (2023)
HoCoRT: host contamination removal tool
BMC Bioinformatics, 24 (1), 371
DOI 10.1186/s12859-023-05492-w, PubMed 37784008

Kalyanasundaram S, Lefol Y, Gundersen S, Rognes T, Alsøe L, Nilsen HL, Hovig E, Sandve GK, Domanska D (2023)
hGSuite HyperBrowser: A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks
PLoS One, 18 (7), e0286330
DOI 10.1371/journal.pone.0286330, PubMed 37467208

Publications 2022

Rossini R, Kumar V, Mathelier A, Rognes T, Paulsen J (2022)
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions
Genome Biol, 23 (1), 247
DOI 10.1186/s13059-022-02815-7, PubMed 36451166

Rognes T, Scheffer L, Greiff V, Sandve GK (2022)
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching
Bioinformatics, 38 (17), 4230-4232
DOI 10.1093/bioinformatics/btac505, PubMed 35852318

Publications 2021

Mahé F, Czech L, Stamatakis A, Quince C, de Vargas C, Dunthorn M, Rognes T (2021)
Swarm v3: towards tera-scale amplicon clustering
Bioinformatics, 38 (1), 267-269
DOI 10.1093/bioinformatics/btab493, PubMed 34244702

Kværner AS, Birkeland E, Bucher-Johannessen C, Vinberg E, Nordby JI, Kangas H, Bemanian V, Ellonen P, Botteri E, Natvig E, Rognes T, Hovig E, Lyle R, Ambur OH, de Vos WM, Bultman S, Hjartåker A, Landberg R, Song M, Blix HS, Ursin G, Randel KR, de Lange T, Hoff G, Holme Ø et al. (2021)
The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants
BMC Cancer, 21 (1), 930
DOI 10.1186/s12885-021-08640-8, PubMed 34407780

Eriksson AM, Leikfoss IS, Abrahamsen G, Sundvold V, Isom MM, Keshari PK, Rognes T, Landsverk OJB, Bos SD, Harbo HF, Spurkland A, Berge T (2021)
Exploring the role of the multiple sclerosis susceptibility gene CLEC16A in T cells
Scand J Immunol, 94 (1), e13050
DOI 10.1111/sji.13050, PubMed 34643957

Snipen L, Angell IL, Rognes T, Rudi K (2021)
Reduced metagenome sequencing for strain-resolution taxonomic profiles
Microbiome, 9 (1), 79
DOI 10.1186/s40168-021-01019-8, PubMed 33781324

Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Noia JMD (2021)
Erratum: The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID
NAR Cancer, 3 (1), zcaa045
DOI 10.1093/narcan/zcaa045, PubMed 34316697

Publications 2020

Farooq A, Grønmyr S, Ali O, Rognes T, Scheffler K, Bjørås M, Wang J (2020)
HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data
Comput Struct Biotechnol J, 18, 2877-2889
DOI 10.1016/j.csbj.2020.09.038, PubMed 33163148

Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Di Noia JM (2020)
The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID
NAR Cancer, 2 (3), zcaa019
DOI 10.1093/narcan/zcaa019, PubMed 33554121

Khelik K, Sandve GK, Nederbragt AJ, Rognes T (2020)
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads
BMC Bioinformatics, 21 (1), 66
DOI 10.1186/s12859-020-3414-0, PubMed 32085722

Publications 2017

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 (2017)
Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1
Sci Rep, 7 (1), 7199
DOI 10.1038/s41598-017-07314-5, PubMed 28775312

Khelik K, Lagesen K, Sandve GK, Rognes T, Nederbragt AJ (2017)
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences
BMC Bioinformatics, 18 (1), 338
DOI 10.1186/s12859-017-1748-z, PubMed 28701187

Publications 2016

Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016)
VSEARCH: a versatile open source tool for metagenomics
PeerJ, 4, e2584
DOI 10.7717/peerj.2584, PubMed 27781170

Namouchi A, Gómez-Muñoz M, Frye SA, Moen LV, Rognes T, Tønjum T, Balasingham SV (2016)
The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress
BMC Genomics, 17 (1), 791
DOI 10.1186/s12864-016-3132-1, PubMed 27724857

Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, Zhou HW, Rognes T, Caporaso JG, Knight R (2016)
Open-Source Sequence Clustering Methods Improve the State Of the Art
mSystems, 1 (1)
DOI 10.1128/mSystems.00003-15, PubMed 27822515

Samarakoon PS, Sorte HS, Stray-Pedersen A, Rødningen OK, Rognes T, Lyle R (2016)
cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data
BMC Genomics, 17, 51
DOI 10.1186/s12864-016-2374-2, PubMed 26764020

Publications 2015

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2015)
Swarm v2: highly-scalable and high-resolution amplicon clustering
PeerJ, 3, e1420
DOI 10.7717/peerj.1420, PubMed 26713226

Yang M, Lin X, Rowe A, Rognes T, Eide L, Bjørås M (2015)
Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway
Sci Rep, 5, 17409
DOI 10.1038/srep17409, PubMed 26616534

Ougland R, Rognes T, Klungland A, Larsen E (2015)
Non-homologous functions of the AlkB homologs
J Mol Cell Biol, 7 (6), 494-504
DOI 10.1093/jmcb/mjv029, PubMed 26003568

Publications 2014

Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2014)
Swarm: robust and fast clustering method for amplicon-based studies
PeerJ, 2, e593
DOI 10.7717/peerj.593, PubMed 25276506

Aanes H, Winata C, Moen LF, Østrup O, Mathavan S, Collas P, Rognes T, Aleström P (2014)
Normalization of RNA-sequencing data from samples with varying mRNA levels
PLoS One, 9 (2), e89158
DOI 10.1371/journal.pone.0089158, PubMed 24586560

Publications 2013

Booth JA, Thomassen GO, Rowe AD, Weel-Sneve R, Lagesen K, Kristiansen KI, Bjørås M, Rognes T, Lindvall JM (2013)
Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response
Sci Rep, 3, 3053
DOI 10.1038/srep03053, PubMed 24157950

Backe PH, Simm R, Laerdahl JK, Dalhus B, Fagerlund A, Okstad OA, Rognes T, Alseth I, Kolstø AB, Bjørås M (2013)
A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures
J Struct Biol, 183 (1), 66-75
DOI 10.1016/j.jsb.2013.04.007, PubMed 23623903

Weel-Sneve R, Kristiansen KI, Odsbu I, Dalhus B, Booth J, Rognes T, Skarstad K, Bjørås M (2013)
Single transmembrane peptide DinQ modulates membrane-dependent activities
PLoS Genet, 9 (2), e1003260
DOI 10.1371/journal.pgen.1003260, PubMed 23408903

Søberg K, Jahnsen T, Rognes T, Skålhegg BS, Laerdahl JK (2013)
Evolutionary paths of the cAMP-dependent protein kinase (PKA) catalytic subunits
PLoS One, 8 (4), e60935
DOI 10.1371/journal.pone.0060935, PubMed 23593352

Publications 2012

Ougland R, Lando D, Jonson I, Dahl JA, Moen MN, Nordstrand LM, Rognes T, Lee JT, Klungland A, Kouzarides T, Larsen E (2012)
ALKBH1 is a histone H2A dioxygenase involved in neural differentiation
Stem Cells, 30 (12), 2672-82
DOI 10.1002/stem.1228, PubMed 22961808

Nordstrand LM, Furu K, Paulsen J, Rognes T, Klungland A (2012)
Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes
Nucleic Acids Res, 40 (21), 10950-63
DOI 10.1093/nar/gks839, PubMed 22965116

Publications 2011

Rognes T (2011)
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
BMC Bioinformatics, 12, 221
DOI 10.1186/1471-2105-12-221, 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
DOI 10.1016/j.dnarep.2011.03.007, PubMed 21570366

Publications 2010

Laerdahl JK, Korvald H, Nilsen L, Dahl-Michelsen K, Rognes T, Bjørås M, Alseth I (2010)
Schizosaccharomyces pombe encodes a mutated AP endonuclease 1
DNA Repair (Amst), 10 (3), 296-305
DOI 10.1016/j.dnarep.2010.11.014, PubMed 21193357

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
DOI 10.1371/journal.pone.0015356, PubMed 21203457

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
DOI 10.1371/journal.pgen.1001242, 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
DOI 10.1371/journal.pone.0013827, PubMed 21072209

Fensgård Ø, Kassahun H, Bombik I, Rognes T, Lindvall JM, Nilsen H (2010)
A two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways
Aging (Albany NY), 2 (3), 133-59
DOI 10.18632/aging.100127, PubMed 20382984

Publications 2009

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
DOI 10.1093/nar/gkp590, PubMed 19617376

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
DOI 10.1371/journal.pone.0005943, PubMed 19536279

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
DOI 10.1111/j.1574-6976.2009.00173.x, PubMed 19396949

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
DOI 10.1007/s00018-009-8736-z, PubMed 19153658

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
DOI 10.1186/1471-2164-10-43, PubMed 19161616

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
DOI 10.1186/1476-4598-8-5, PubMed 19152679

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
DOI 10.1111/j.1365-2796.2007.01915.x, PubMed 18266662

Publications 2007

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
DOI 10.1615/critrevoncog.v13.i3.20, PubMed 18298386

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
DOI 10.1093/nar/gkm160, PubMed 17452365

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
DOI 10.1093/nar/gkm039, PubMed 17395642

Publications 2006

Nakken S, Alseth I, Rognes T (2006)
Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes
Neuroscience, 145 (4), 1273-9
DOI 10.1016/j.neuroscience.2006.09.004, PubMed 17055652

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
DOI 10.1111/j.1365-2958.2006.05044.x, PubMed 16468998

Thomassen GO, Røsok O, Rognes T (2006)
Computational prediction of microRNAs encoded in viral and other genomes
J Biomed Biotechnol, 2006 (4), 95270
DOI 10.1155/JBB/2006/95270, PubMed 17057374

Publications 2005

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
DOI 10.1093/nar/gki423, PubMed 15980529

Publications 2001

Rognes T (2001)
ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches
Nucleic Acids Res, 29 (7), 1647-52
DOI 10.1093/nar/29.7.1647, PubMed 11266569

Publications 2000

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
DOI 10.1093/bioinformatics/16.8.699, PubMed 11099256

Publications 1998

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
DOI 10.1093/bioinformatics/14.10.839, PubMed 9927712