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NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads 
Khelik, Ksenia; Sandve, Geir K; Nederbragt, Alexander J; Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
Background Advances in whole genome sequencing strategies have provided the opportunity for genomic and comparative genomic analysis of a vast variety of organisms. The analysis results are highly dependent on the quality ...
HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data 
Farooq, Amna; Grønmyr, Sindre; Omer, Ali Avan; Rognes, Torbjørn; Scheffler, Katja; Bjørås, Magnar; Wang, Junbai (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
DNA methylation (5mC) and hydroxymethylation (5hmC) are chemical modifications of cytosine bases which play a crucial role in epigenetic gene regulation. However, cost, data complexity and unavailability of comprehensive ...
The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID 
Safavi, Shiva; Larouche, Ariane; Zahn, Astrid; Patenaude, Anne-Marie; Domanska, Diana Ewa; Dionne, Kiersten; Rognes, Torbjørn; Dingler, Felix; Kang, Seong-Kwi; Liu, Yan; Johnson, Nathalie; Hébert, Josée; Verdun, Ramiro E.; Rada, Cristina; Vega, Francisco; Nilsen, Hilde; Di Noia, Javier M. (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2020)
Abstract In B lymphocytes, the uracil N-glycosylase (UNG) excises genomic uracils made by activation-induced deaminase (AID), thus underpinning antibody gene diversification and oncogenic chromosomal translocations, ...
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences 
Khelik, Ksenia; Lagesen, Karin; Sandve, Geir K; Rognes, Torbjørn; Nederbragt, Alexander J (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2017)
Background Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the ...
Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG 
Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix; Lirussi, Lisa; Sengupta, Tanima; Tekin, Nuriye Basdag; Jobert, Laure; Alexandrov, Ludmil B.; Galashevskaya, Anastasia; Rada, Cristina; Sandve, Geir Kjetil; Rognes, Torbjørn; Krokan, Hans Einar; Nilsen, Hilde Loge (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2017)
Both a DNA lesion and an intermediate for antibody maturation, uracil is primarily processed by base excision repair (BER), either initiated by uracil-DNA glycosylase (UNG) or by single-strand selective monofunctional ...
VSEARCH: a versatile open source tool for metagenomics 
Rognes, Torbjørn; Flouri, Tomáš; Nichols, Ben; Quince, Christopher; Mahé, Frédéric (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2016)
Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to ...
Open-Source Sequence Clustering Methods Improve the State Of the Art 
Kopylova, Evguenia; Navas-Molina, Jose A.; Mercier, Céline; Xu, Zhenjiang Zech; Mahé, Frédéric; He, Yan; Zhou, Hong-Wei; Rognes, Torbjørn; Caporaso, J. Gregory; Knight, Rob (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2016)
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. ...
The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress 
Namouchi, Amine; Gomez Munoz, Marta; Frye, Stephan Alfons; Moen, Line Victoria; Rognes, Torbjørn; Tonjum, Tone; Balasingham, Seetha (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2016)
Background: As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify ...
cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data 
Samarakoon, Pubudu S; Sorte, Hanne S; Stray-Pedersen, Asbjørg; Rødningen, Olaug K; Rognes, Torbjørn; Lyle, Robert (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2016)
Background With advances in next generation sequencing technology and analysis methods, single nucleotide variants (SNVs) and indels can be detected with high sensitivity and specificity in exome sequencing ...
Swarm v2: highly-scalable and high-resolution amplicon clustering 
Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2015)
Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order ...
Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway 
Yang, Mingyi; Lin, Xiaolin; Rowe, Alexander D.; Rognes, Torbjørn; Eide, Lars; Bjørås, Magnar (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2015)
The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown. We employed RNA sequencing to examine the role of human OXR1 for genome wide transcription ...
Swarm: robust and fast clustering method for amplicon-based studies 
Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2014)
Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues ...
Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response 
Booth, James A.; Thomassen, Gard O Sundby; Rowe, Alexander D.; Weel-Sneve, Ragnhild; Lagesen, Karin; Kristiansen, Knut Ivan; Bjørås, Magnar; Rognes, Torbjørn; Lindvall, Jessica Margareta (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2013)
The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. We ...
A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures 
Backe, Paul Hoff; Simm, Roger; Lærdahl, Jon Kristen; Dalhus, Bjørn; Fagerlund, Annette; Økstad, Ole Andreas Løchen; Rognes, Torbjørn; Alseth, Ingrun; Kolstø, Anne-Brit; Bjørås, Magnar (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2013)
The recently discovered HEAT-like repeat (HLR) DNA glycosylase superfamily is widely distributed in all domains of life. The present bioinformatics and phylogenetic analysis shows that HLR DNA glycosylase superfamily members ...
Evolutionary Paths of the cAMP-Dependent Protein Kinase (PKA) Catalytic Subunits 
Søberg, Kristoffer; Jahnsen, Tore; Rognes, Torbjørn; Skålhegg, Bjørn Steen; Lærdahl, Jon Kristen (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2013)
3',5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase or protein kinase A (PKA) has served as a prototype for the large family of protein kinases that are crucially important for signal transduction in ...
Single Transmembrane Peptide DinQ Modulates Membrane-Dependent Activities 
Weel-Sneve, Ragnhild; Kristiansen, Knut Ivan; Odsbu, Ingvild; Dalhus, Bjørn; Booth, James; Rognes, Torbjørn; Skarstad, Kirsten; Bjørås, Magnar (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2013)
The functions of several SOS regulated genes in Escherichia coli are still unknown, including dinQ. In this work we characterize dinQ and two small RNAs, agrA and agrB, with antisense complementarity to dinQ. Northern ...
Identification and Characterization of Novel Mutations in the Human Gene Encoding the Catalytic Subunit Calpha of Protein Kinase A (PKA) 
Søberg, Kristoffer; Larsen, Anja C V; Diskar, Mandy; Backe, Paul Hoff; Bjørås, Magnar; Jahnsen, Tore; Lærdahl, Jon Kristen; Rognes, Torbjørn; Herberg, Friedrich W.; Skålhegg, Bjørn Steen (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2012)
The genes PRKACA and PRKACB encode the principal catalytic (C) subunits of protein kinase A (PKA) Cα and Cβ, respectively. Cα is expressed in all eukaryotic tissues examined and studies of Cα knockout mice demonstrate a ...
Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes 
Nordstrand, Line Mari; Furu, Kari; Paulsen, Jonas; Rognes, Torbjørn; Klungland, Arne (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2012)
Piwi proteins and Piwi-interacting small RNAs (piRNAs) have known functions in transposon silencing in the male germline of fetal and newborn mice. Both are also present in adult testes; however, their function here remains ...
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation 
Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2011)
Background The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation ...
A Two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways 
Fensgård, Øyvind; Kassahun, Henok; Izabela Agnieszka, Bombik; Rognes, Torbjørn; Lindvall, Jessica Margareta; Nilsen, Hilde (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2010)
Activation of oxidative stress-responses and downregulation of insulin-like signaling (ILS) is seen in Nucleotide Excision Repair (NER) deficient segmental progeroid mice. Evidence suggests that this is a survival response ...
Continuous and Periodic Expansion of CAG Repeats in Huntington's Disease R6/1 Mice 
Møllersen, Linda; Rowe, Alexander D.; Larsen, Elisabeth; Rognes, Torbjørn; Klungland, Arne (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2010)
Huntington's disease (HD) is one of several neurodegenerative disorders caused by expansion of CAG repeats in a coding gene. Somatic CAG expansion rates in HD vary between organs, and the greatest instability is observed ...
Mice Lacking Alkbh1 Display Sex-Ratio Distortion and Unilateral Eye Defects 
Nordstrand, Line Mari; Svärd, Jessica; Larsen, Elisabeth; Nilsen, Anja; Ougland, Rune; Furu, Kari; Lien, Guro Flor; Rognes, Torbjørn; Namekawa, Satoshi H; Lee, Jeannie T; Klungland, Arne (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2010)
Background Eschericia coli AlkB is a 2-oxoglutarate- and iron-dependent dioxygenase that reverses alkylated DNA damage by oxidative demethylation. Mouse AlkB homolog 1 (Alkbh1) is one of eight members of the newly discovered ...
Tiling Array Analysis of UV Treated Escherichia coli Predicts Novel Differentially Expressed Small Peptides 
Thomassen, Gard O Sundby; Sneve, Ragnhild; Rowe, Alexander D.; Booth, James; Lindvall, Jessica M.; Lagesen, Karin; Kristiansen, Knut Ivan; Bjørås, Magnar; Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2010)
Background Despite comprehensive investigation, the Escherichia coli SOS response system is not yet fully understood. We have applied custom designed whole genome tiling arrays to measure UV invoked transcriptional changes ...
A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis 
Skotheim, Rolf I; Thomassen, Gard O; Eken, Marthe; Lind, Guro E; Micci, Francesca; Ribeiro, Franclim R; Cerveira, Nuno; Teixeira, Manuel R; Heim, Sverre; Rognes, Torbjørn; Lothe, Ragnhild A (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Background The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal ...
Large-scale inference of the point mutational spectrum in human segmental duplications 
Nakken, Sigve; Rødland, Einar A; Rognes, Torbjørn; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Background Recent segmental duplications are relatively large (≥ 1 kb) genomic regions of high sequence identity (≥ 90%). They cover approximately 4–5% of the human genome and play important roles in gene ...
Genome dynamics in major bacterial pathogens 
Ambur, Ole Herman; Davidsen, Tonje; Frye, Stephan Alfons; Balasingham, Seetha; Lagesen, Karin; Rognes, Torbjørn; Tønjum, Tone (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Pathogenic bacteria continuously encounter multiple forms of stress in their hostile environments, which leads to DNA damage. With the new insight into biology offered by genome sequences, the elucidation of the gene content ...
Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays 
Thomassen, Gard O Sundby; Rowe, Alexander D.; Lagesen, Karin; Lindvall, Jessica Margareta; Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Background High-density tiling microarrays are a powerful tool for the characterization of complete genomes. The two major computational challenges associated with custom-made arrays are design and analysis. Firstly, ...
The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts 
Nakken, Sigve; Rognes, Torbjørn; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
Specific guanine-rich sequence motifs in the human genome have considerable potential to form four-stranded structures known as G-quadruplexes or G4 DNA. The enrichment of these motifs in key chromosomal regions has suggested ...
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats 
Dalhus, Bjørn; Helle, Ina Høydal; Backe, Paul Hoff; Alseth, Ingrun; Rognes, Torbjørn; Bjørås, Magnar; Lærdahl, Jon Kristen (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2007)
3-methyladenine DNA glycosylases initiate repair of cytotoxic and promutagenic alkylated bases in DNA. We demonstrate by comparative modelling that Bacillus cereus AlkD belongs to a new, fifth, structural superfamily of ...
A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD 
Alseth, Ingrun; Rognes, Torbjørn; Lindbäck, Toril; Solberg, Inger; Robertsen, Kristin; Kristiansen, Knut Ivan; Mainieri, Davide; Lillehagen, Lucy; Kolstø, Anne-Brit; Bjørås, Magnar (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2006)
Soil bacteria are heavily exposed to environmental methylating agents such as methylchloride and may have special requirements for repair of alkylation damage on DNA. We have used functional complementation of an Escherichia ...
Computational prediction of microRNAs encoded in viral and other genomes 
Thomassen, Gard O. S.; Rosok, Oystein; Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2006)
We present an overview of selected computational methods for microRNA prediction. It is especially aimed at viral miRNA detection. As the number of microRNAs increases and the range of genomes encoding miRNAs expands, it ...
PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology 
Sæbø, Per Eystein; Andersen, SM; Myrseth, Jon; Lærdahl, Jon Kristen; Rognes, Torbjørn (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2005)
PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith–Waterman ...
 
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Date Issued2010 - 2020 (23)2005 - 2009 (9)Document TypeTidsskriftartikkel (32)Author
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