Rognes group

The group works on microbiome bioinformatics and develops sequence analysis tools.

Research aims

Develop rapid and widely useful tools for sequence analysis by exploiting parallelism, smart data structures and effective algorithms. In particular comparison, searching, clustering and classification of sequences.

Projects

  • Tools for microbiome sequencing data analysis (VSEARCH, Swarm)
  • Tools for rapid sequence comparison (SWIPE)
  • Publication database and associated statistics (Publika)

Research topics

Software

  • VSEARCH: a versatile open-source tool for metagenomics

People

  • Torbjørn Rognes (PI)
  • Tuva Kristine Thoresen (PhD student) (on leave)
  • Henrik Høybakk Olsvik (master student) (with Trine B. Rounge)
  • Akuzike Banda (master student) (with Khuzwayo C. Jere, Chrispin Chaguza, and Arox W. Kamng’ona)
  • Christian Ytterhaug Sæther (master student) (with Alex D. Rowe)

Publications

Publications 2020

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

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

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

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

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 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


 

Published Apr. 2, 2019 2:48 PM - Last modified Jan. 30, 2020 11:42 AM