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
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
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
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
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
VSEARCH: a versatile open source tool for metagenomics
PeerJ, 4, e2584
DOI 10.7717/peerj.2584, PubMed 27781170
The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress
BMC Genomics, 17 (1), 791
DOI 10.1186/s12864-016-3132-1, PubMed 27724857
Open-Source Sequence Clustering Methods Improve the State Of the Art
mSystems, 1 (1)
DOI 10.1128/mSystems.00003-15, PubMed 27822515
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
Swarm v2: highly-scalable and high-resolution amplicon clustering
PeerJ, 3, e1420
DOI 10.7717/peerj.1420, PubMed 26713226
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
Non-homologous functions of the AlkB homologs
J Mol Cell Biol, 7 (6), 494-504
DOI 10.1093/jmcb/mjv029, PubMed 26003568
Publications 2014
Swarm: robust and fast clustering method for amplicon-based studies
PeerJ, 2, e593
DOI 10.7717/peerj.593, PubMed 25276506
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
Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response
Sci Rep, 3, 3053
DOI 10.1038/srep03053, PubMed 24157950
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
Single transmembrane peptide DinQ modulates membrane-dependent activities
PLoS Genet, 9 (2), e1003260
DOI 10.1371/journal.pgen.1003260, PubMed 23408903
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
ALKBH1 is a histone H2A dioxygenase involved in neural differentiation
Stem Cells, 30 (12), 2672-82
DOI 10.1002/stem.1228, PubMed 22961808
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
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
BMC Bioinformatics, 12, 221
DOI 10.1186/1471-2105-12-221, PubMed 21631914
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
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
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
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
Mice lacking Alkbh1 display sex-ratio distortion and unilateral eye defects
PLoS One, 5 (11), e13827
DOI 10.1371/journal.pone.0013827, PubMed 21072209
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
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
Genome dynamics in major bacterial pathogens
FEMS Microbiol Rev, 33 (3), 453-70
DOI 10.1111/j.1574-6976.2009.00173.x, PubMed 19396949
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
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
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
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
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
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
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