Torbjørn Rognes

• Lång, Emma Helena; Lång, Anna Ulrika; Blicher, Pernille; Rognes, Torbjørn; Dommersnes, Paul Gunnar & Bøe, Stig Ove (2024). Topology-guided polar ordering of collective cell migration. Science Advances. ISSN 2375-2548. 10(16), s. 1–14. doi: 10.1126/sciadv.adk4825. Fulltekst i vitenarkiv
• Istvan, Paula; Birkeland, Einar Elvbakken; Avershina, Ekaterina; Kværner, Ane Sørlie; Bemanian, Vahid & Pardini, Barbara [Vis alle 11 forfattere av denne artikkelen] (2024). Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nature Communications. ISSN 2041-1723. 15(1), s. 1–12. doi: 10.1038/s41467-024-46033-0. Fulltekst i vitenarkiv
• Rumbavicius, Ignas; Rounge, Trine Ballestad & Rognes, Torbjørn (2023). HoCoRT: host contamination removal tool. BMC Bioinformatics. ISSN 1471-2105. 24(1). doi: 10.1186/s12859-023-05492-w. Fulltekst i vitenarkiv
• Kalyanasundaram, Sumana; Lefol, Yohan Pierre; Gundersen, Sveinung; Rognes, Torbjørn; Alsøe, Lene & Nilsen, Hilde [Vis alle 9 forfattere av denne artikkelen] (2023). hGSuite HyperBrowser: A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks. PLOS ONE. ISSN 1932-6203. 18(7). doi: 10.1371/journal.pone.0286330. Fulltekst i vitenarkiv
• Rossini, Roberto; Kumar, Vipin; Mathelier, Anthony; Rognes, Torbjørn & Paulsen, Jonas (2022). MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biology. ISSN 1465-6906. 23(1). doi: 10.1186/s13059-022-02815-7. Fulltekst i vitenarkiv Vis sammendrag

  DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.

• Rognes, Torbjørn; Scheffer, Lonneke; Greiff, Victor & Sandve, Geir Kjetil (2022). CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. Bioinformatics. ISSN 1367-4803. 38(17), s. 4230–4232. doi: 10.1093/bioinformatics/btac505. Fulltekst i vitenarkiv
• Kværner, Ane Sørlie; Birkeland, Einar Elvbakken; Bucher-Johannessen, Cecilie; Vinberg, Elina; Nordby, Jan Inge & Kangas, Harri [Vis alle 27 forfattere av denne artikkelen] (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. ISSN 1471-2407. 21. doi: 10.1186/s12885-021-08640-8. Fulltekst i vitenarkiv
• Mahé, Frédéric; Czech, Lucas; Stamatakis, Alexandros; Quince, Christopher; de Vargas, Colomban & Dunthorn, Micah [Vis alle 7 forfattere av denne artikkelen] (2021). Swarm v3: towards tera-scale amplicon clustering. Bioinformatics. ISSN 1367-4803. 38(1), s. 267–269. doi: 10.1093/bioinformatics/btab493. Fulltekst i vitenarkiv
• Eriksson, Anna Maria; Leikfoss, Ingvild Sørum; Abrahamsen, Greger; Gjerstad, Vibeke Sundvold; Mesel Isom, Martine & Keshari, Pankaj [Vis alle 12 forfattere av denne artikkelen] (2021). Exploring the role of the multiple sclerosis susceptibility gene CLEC16A in T cells. Scandinavian Journal of Immunology. ISSN 0300-9475. 94(1). doi: 10.1111/sji.13050. Fulltekst i vitenarkiv
• Snipen, Lars; Angell, Inga-Leena; Rognes, Torbjørn & Rudi, Knut (2021). Reduced metagenome sequencing for strain-resolution taxonomic profiles. Microbiome. ISSN 2049-2618. 9(1). doi: 10.1186/s40168-021-01019-8. Fulltekst i vitenarkiv
• Farooq, Amna; Grønmyr, Sindre; Omer, Ali Avan; Rognes, Torbjørn; Scheffler, Katja & Bjørås, Magnar [Vis alle 7 forfattere av denne artikkelen] (2020). HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data. Computational and Structural Biotechnology Journal. ISSN 2001-0370. 18, s. 2877–2889. doi: 10.1016/j.csbj.2020.09.038. Fulltekst i vitenarkiv
• Khelik, Ksenia; Sandve, Geir Kjetil; Nederbragt, Alexander Johan & Rognes, Torbjørn (2020). NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinformatics. ISSN 1471-2105. 21(1). doi: 10.1186/s12859-020-3414-0. Fulltekst i vitenarkiv
• Safavi, Shiva; Larouche, Ariane; Zahn, Astrid; Patenaude, Anne-Marie; Domanska, Diana Ewa & Dionne, Kiersten [Vis alle 17 forfattere av denne artikkelen] (2020). The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID. NAR Cancer. ISSN 2632-8674. 2(3). doi: 10.1093/narcan/zcaa019. Fulltekst i vitenarkiv
• Khelik, Ksenia; Lagesen, Karin; Sandve, Geir Kjetil; Rognes, Torbjørn & Nederbragt, Alexander Johan (2017). NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinformatics. ISSN 1471-2105. 18(1), s. 1–14. doi: 10.1186/s12859-017-1748-z. Fulltekst i vitenarkiv
• Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix & Lirussi, Lisa [Vis alle 16 forfattere av denne artikkelen] (2017). Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1. Scientific Reports. ISSN 2045-2322. 7(1). doi: 10.1038/s41598-017-07314-5. Fulltekst i vitenarkiv
• Rognes, Torbjørn; Flouri, Tomáš; Nichols, Ben; Quince, Christopher & Mahé, Frédéric (2016). VSEARCH: A versatile open source tool for metagenomics. PeerJ. ISSN 2167-8359. 4(10). doi: 10.7717/peerj.2584. Fulltekst i vitenarkiv Vis sammendrag

  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 the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods. When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results. VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. Discussion. VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.

• Namouchi, Amine; Gomez Munoz, Marta; Frye, Stephan Alfons; Moen, Line Victoria; Rognes, Torbjørn & Tonjum, Tone [Vis alle 7 forfattere av denne artikkelen] (2016). The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress. BMC Genomics. ISSN 1471-2164. 17:791, s. 1–13. doi: 10.1186/s12864-016-3132-1. Fulltekst i vitenarkiv Vis sammendrag

  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 new virulence factors and pathways that play a role in the survival of the tubercle bacillus. The main goal of this study was to map the regulatory networks of differentially expressed (DE) transcripts in Mtb upon various forms of genotoxic stress. We exposed Mtb cells to oxidative (H2O2 or paraquat), nitrosative (DETA/NO), or alkylation (MNNG) stress or mitomycin C, inducing double-strand breaks in the DNA. Total RNA was isolated from treated and untreated cells and subjected to high-throughput deep sequencing. The data generated was analysed to identify DE genes encoding mRNAs, non-coding RNAs (ncRNAs), and the genes potentially targeted by ncRNAs. Results: The most significant transcriptomic alteration with more than 700 DE genes was seen under nitrosative stress. In addition to genes that belong to the replication, recombination and repair (3R) group, mainly found under mitomycin C stress, we identified DE genes important for bacterial virulence and survival, such as genes of the type VII secretion system (T7SS) and the proline-glutamic acid/proline-proline-glutamic acid (PE/PPE) family. By predicting the structures of hypothetical proteins (HPs) encoded by DE genes, we found that some of these HPs might be involved in mycobacterial genome maintenance. We also applied a state-of-the-art method to predict potential target genes of the identified ncRNAs and found that some of these could regulate several genes that might be directly involved in the response to genotoxic stress. Conclusions: Our study reflects the complexity of the response of Mtb in handling genotoxic stress. In addition to genes involved in genome maintenance, other potential key players, such as the members of the T7SS and PE/PPE gene family, were identified. This plethora of responses is detected not only at the level of DE genes encoding mRNAs but also at the level of ncRNAs and their potential targets.

• Kopylova, Evguenia; Navas-Molina, Jose A.; Mercier, Céline; Xu, Zhenjiang Zech; Mahé, Frédéric & He, Yan [Vis alle 10 forfattere av denne artikkelen] (2016). Open-source sequence clustering methods improve the state of the art. mSystems. ISSN 2379-5077. 1(1). doi: 10.1128/mSystems.00003-15. Fulltekst i vitenarkiv Vis sammendrag

  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. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH’s most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release.

• Samarakoon, Pubudu Saneth; Sorte, Hanne Sørmo; Stray-Pedersen, Asbjørg; Rødningen, Olaug Kristin; Rognes, Torbjørn & Lyle, Robert (2016). cnvScan: A CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data. BMC Genomics. ISSN 1471-2164. 17(51). doi: 10.1186/s12864-016-2374-2. Fulltekst i vitenarkiv
• Ougland, Rune; Rognes, Torbjørn; Klungland, Arne & Larsen, Elisabeth (2015). Non-homologous functions of the AlkB homologs. Journal of Molecular Cell Biology. ISSN 1674-2788. 7(6), s. 494–504. doi: 10.1093/jmcb/mjv029.
• Yang, Mingyi; Lin, Xiaolin; Rowe, Alexander D.; Rognes, Torbjørn; Eide, Lars & Bjørås, Magnar (2015). Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway. Scientific Reports. ISSN 2045-2322. 5. doi: 10.1038/srep17409. Fulltekst i vitenarkiv
• Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban & Dunthorn, Micah (2015). Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ. ISSN 2167-8359. 3. doi: 10.7717/peerj.1420. Fulltekst i vitenarkiv
• Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban & Dunthorn, Micah (2015). Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ Preprints. ISSN 2167-9843. 3. doi: 10.7287/peerj.preprints.1222v2.
• Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban & Dunthorn, Micah (2014). Swarm: robust and fast clustering method for amplicon-based studies. PeerJ Preprints. ISSN 2167-9843. 2. doi: 10.7287/peerj.preprints.386v1.
• Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban & Dunthorn, Micah (2014). Swarm: robust and fast clustering method for amplicon-based studies. PeerJ. ISSN 2167-8359. 2014(1). doi: 10.7717/peerj.593. Fulltekst i vitenarkiv Vis sammendrag

  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 by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.

• Aanes, Håvard; Winata, Cecilia L.; Moen, Lars Fredrik; Østrup, Olga; Mathavan, Sinnakaruppan & Collas, Philippe [Vis alle 8 forfattere av denne artikkelen] (2014). Normalization of RNA-Sequencing Data from Samples with Varying mRNA Levels. PLOS ONE. ISSN 1932-6203. 9(2). doi: 10.1371/journal.pone.0089158.
• Booth, James A.; Thomassen, Gard O Sundby; Rowe, Alexander D.; Weel-Sneve, Ragnhild; Lagesen, Karin & Kristiansen, Knut Ivan [Vis alle 9 forfattere av denne artikkelen] (2013). Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response. Scientific Reports. ISSN 2045-2322. 3. doi: 10.1038/srep03053. Fulltekst i vitenarkiv
• Backe, Paul Hoff; Simm, Roger; Lærdahl, Jon Kristen; Dalhus, Bjørn; Fagerlund, Annette & Økstad, Ole Andreas Løchen [Vis alle 10 forfattere av denne artikkelen] (2013). A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures. Journal of Structural Biology. ISSN 1047-8477. 183(1), s. 66–75. doi: 10.1016/j.jsb.2013.04.007. Fulltekst i vitenarkiv
• Søberg, Kristoffer; Jahnsen, Tore; Rognes, Torbjørn; Skålhegg, Bjørn Steen & Lærdahl, Jon Kristen (2013). Evolutionary Paths of the cAMP-Dependent Protein Kinase (PKA) Catalytic Subunits. PLOS ONE. ISSN 1932-6203. 8(4). doi: 10.1371/journal.pone.0060935. Fulltekst i vitenarkiv
• Weel-Sneve, Ragnhild; Kristiansen, Knut Ivan; Odsbu, Ingvild; Dalhus, Bjørn; Booth, James & Rognes, Torbjørn [Vis alle 8 forfattere av denne artikkelen] (2013). Single Transmembrane Peptide DinQ Modulates Membrane-Dependent Activities. PLoS Genetics. ISSN 1553-7390. 9(2). doi: 10.1371/journal.pgen.1003260. Fulltekst i vitenarkiv
• Ougland, Rune; Lando, David; Jonson, Ida; Dahl, John Arne; Moen, Marivi & Nordstrand, Line Mari [Vis alle 11 forfattere av denne artikkelen] (2012). ALKBH1 Is a Histone H2A Dioxygenase Involved in Neural Differentiation. Stem Cells. ISSN 1066-5099. 30(12), s. 2672–2682. doi: 10.1002/stem.1228. Fulltekst i vitenarkiv
• Søberg, Kristoffer; Larsen, Anja C V; Diskar, Mandy; Backe, Paul Hoff; Bjørås, Magnar & Jahnsen, Tore [Vis alle 10 forfattere av denne artikkelen] (2012). Identification and Characterization of Novel Mutations in the Human Gene Encoding the Catalytic Subunit Calpha of Protein Kinase A (PKA). PLOS ONE. ISSN 1932-6203. 7(4). doi: 10.1371/journal.pone.0034838. Fulltekst i vitenarkiv
• Nordstrand, Line Mari; Furu, Kari; Paulsen, Jonas; Rognes, Torbjørn & Klungland, Arne (2012). Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes. Nucleic Acids Research (NAR). ISSN 0305-1048. 40(21), s. 10950–10963. doi: 10.1093/nar/gks839. Fulltekst i vitenarkiv
• Yang, Mingyi; Aamodt, Randi; Dalhus, Bjørn; Balasingham, Seetha ; Helle, Ina Høydal & Andersen, Pernille Strøm [Vis alle 10 forfattere av denne artikkelen] (2011). The ada operon of Mycobacterium tuberculosis encodes two DNA methyltransferases for inducible repair of DNA alkylation damage. DNA Repair. ISSN 1568-7864. 10(6), s. 595–602. doi: 10.1016/j.dnarep.2011.03.007.
• Lærdahl, Jon Kristen; Korvald, Hanne; Nilsen, Line; Dahl-Michelsen, Kristin; Rognes, Torbjørn & Bjørås, Magnar [Vis alle 7 forfattere av denne artikkelen] (2011). Schizosaccharomyces pombe encodes a mutated AP endonuclease 1. DNA Repair. ISSN 1568-7864. 10(3), s. 296–305. doi: 10.1016/j.dnarep.2010.11.014.
• Rognes, Torbjørn (2011). Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinformatics. ISSN 1471-2105. 12. doi: 10.1186/1471-2105-12-221. Fulltekst i vitenarkiv
• Thomassen, Gard O Sundby; Sneve, Ragnhild; Rowe, Alexander D.; Booth, James; Lindvall, Jessica M. & Lagesen, Karin [Vis alle 9 forfattere av denne artikkelen] (2010). Tiling Array Analysis of UV Treated Escherichia coli Predicts Novel Differentially Expressed Small Peptides. PLOS ONE. ISSN 1932-6203. 5(12). doi: 10.1371/journal.pone.0015356. Fulltekst i vitenarkiv Vis sammendrag

  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 in E. coli. This study provides a more complete insight into the transcriptome and the UV irradiation response of this microorganism. Results We detected a number of novel differentially expressed transcripts in addition to the expected SOS response genes (such as sulA, recN, uvrA, lexA, umuC and umuD) in the UV treated cells. Several of the differentially expressed transcripts might play important roles in regulation of the cellular response to UV damage. We have predicted 23 novel small peptides from our set of detected non-gene transcripts. Further, three of the predicted peptides were cloned into protein expression vectors to test the biological activity. All three constructs expressed the predicted peptides, in which two of them were highly toxic to the cell. Additionally, a remarkably high overlap with previously in-silico predicted non-coding RNAs (ncRNAs) was detected. Generally we detected a far higher transcriptional activity than the annotation suggests, and these findings correspond with previous transcription mappings from E. coli and other organisms. Conclusions Here we demonstrate that the E. coli transcriptome consists of far more transcripts than the present annotation suggests, of which many transcripts seem important to the bacterial stress response. Sequence alignment of promoter regions suggest novel regulatory consensus sequences for some of the upregulated genes. Finally, several of the novel transcripts identified in this study encode putative small peptides, which are biologically active.

• Nordstrand, Line Mari; Svärd, Jessica; Larsen, Elisabeth; Nilsen, Anja; Ougland, Rune & Furu, Kari [Vis alle 11 forfattere av denne artikkelen] (2010). Mice Lacking Alkbh1 Display Sex-Ratio Distortion and Unilateral Eye Defects. PLOS ONE. ISSN 1932-6203. 5(11). doi: 10.1371/journal.pone.0013827. Fulltekst i vitenarkiv
• Møllersen, Linda; Rowe, Alexander D.; Larsen, Elisabeth; Rognes, Torbjørn & Klungland, Arne (2010). Continuous and Periodic Expansion of CAG Repeats in Huntington's Disease R6/1 Mice. PLoS Genetics. ISSN 1553-7390. 6(12). doi: 10.1371/journal.pgen.1001242. Fulltekst i vitenarkiv
• Fensgård, Øyvind; Kassahun, Henok; Izabela Agnieszka, Bombik; Rognes, Torbjørn; Lindvall, Jessica Margareta & Nilsen, Hilde (2010). A Two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways. Aging. ISSN 1945-4589. Fulltekst i vitenarkiv Vis sammendrag

  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 to persistent transcription-blocking DNA damage, although the relevant lesions have not been identified. Here we show that loss of NTH-1, the only Base Excision Repair (BER) enzyme known to initiate repair of oxidative DNA damage inC. elegans, restores normal lifespan of the short-lived NER deficient xpa-1 mutant. Loss of NTH-1 leads to oxidative stress and global expression profile changes that involve upregulation of genes responding to endogenous stress and downregulation of ILS. A similar, but more extensive, transcriptomic shift is observed in the xpa-1 mutant whereas loss of both NTH-1 and XPA-1 elicits a different profile with downregulation of Aurora-B and Polo-like kinase 1 signaling networks as well as DNA repair and DNA damage response genes. The restoration of normal lifespan and absence oxidative stress responses in nth-1;xpa-1 indicate that BER contributes to generate transcription blocking lesions from oxidative DNA damage. Hence, our data strongly suggests that the DNA lesions relevant for aging are repair intermediates resulting from aberrant or attempted processing by BER of lesions normally repaired by NER.

• Ambur, Ole Herman; Davidsen, Tonje; Frye, Stephan Alfons; Balasingham, Seetha ; Lagesen, Karin & Rognes, Torbjørn [Vis alle 7 forfattere av denne artikkelen] (2009). Genome dynamics in major bacterial pathogens. FEMS Microbiology Reviews. ISSN 0168-6445. 33(3), s. 453–470. doi: 10.1111/j.1574-6976.2009.00173.x. Fulltekst i vitenarkiv
• Robertson, AB; Klungland, A; Rognes, T & Leiros, Ingar (2009). DNA Repair in Mammalian Cells. Cellular and Molecular Life Sciences (CMLS). ISSN 1420-682X. 66(6), s. 981–993. doi: 10.1007/s00018-009-8736-z.
• Skotheim, Rolf Inge; Thomassen, Gard O Sundby; Eken, Marthe; Lind, Guro Elisabeth; Micci, Francesca & Ribeiro, FR [Vis alle 11 forfattere av denne artikkelen] (2009). A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Molecular Cancer. ISSN 1476-4598. 8. doi: 10.1186/1476-4598-8-5. Fulltekst i vitenarkiv
• Nakken, Sigve; Rødland, Einar Andreas; Rognes, Torbjørn & Hovig, Eivind (2009). Large-scale inference of the point mutational spectrum in human segmental duplications. BMC Genomics. ISSN 1471-2164. 10. doi: 10.1186/1471-2164-10-43. Fulltekst i vitenarkiv
• Thomassen, Gard O Sundby; Rowe, Alexander D.; Lagesen, Karin; Lindvall, Jessica Margareta & Rognes, Torbjørn (2009). Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays. PLOS ONE. ISSN 1932-6203. 4(6). Fulltekst i vitenarkiv
• Nakken, Sigve; Rognes, Torbjørn & Hovig, Eivind (2009). The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts. Nucleic Acids Research (NAR). ISSN 0305-1048. 37(17), s. 5749–5756. doi: 10.1093/nar/gkp590. Fulltekst i vitenarkiv
• Cameron, Jamie; Holla, Øystein Lunde; Lærdahl, Jon Kristen; Kulseth, Mari Ann; Ranheim, Trine & Rognes, Torbjørn [Vis alle 8 forfattere av denne artikkelen] (2008). Characterization of novel mutations in the catalytic domain of the PCSK9 gene. Journal of Internal Medicine. ISSN 0954-6820. 263(4), s. 420–431. doi: 10.1111/j.1365-2796.2007.01915.x.
• Cameron, J; Holla, OL; Laerdahl, JK; Kulseth, MA; Ranheim, T & Rognes, Torbjørn [Vis alle 8 forfattere av denne artikkelen] (2008). Characterization of novel mutations in the catalytic domain of the PCSK9 gene. Journal of Internal Medicine. ISSN 0954-6820. 263(4), s. 420–431. doi: 10.1111/j.1365-2796.2007.01915.x.
• Klungland, Arne; Lærdahl, Jon Kristen & Rognes, Torbjørn (2007). OGG1: From Structural Analysis to the Knockout Mouse. I Evans, Mark D. & Cooke, Marcus S. (Red.), Oxidative Damage to Nucleic Acids. Springer Science+Business Media B.V.. ISSN 9780387729732. s. 67–80.
• Nakken, Sigve; Alseth, Ingrun & Rognes, Torbjørn (2007). Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes. Neuroscience. ISSN 0306-4522. 145. doi: 10.1016/j.neuroscience.2006.09.004.
• Dalhus, Bjørn; Helle, Ina Høydal; Backe, Paul Hoff; Alseth, Ingrun; Rognes, Torbjørn & Bjørås, Magnar [Vis alle 7 forfattere av denne artikkelen] (2007). Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats. Nucleic Acids Research (NAR). ISSN 0305-1048. 35(7), s. 2451–2459. doi: 10.1093/nar/gkm039. Fulltekst i vitenarkiv
• Lagesen, K; Hallin, P; Rødland, Einar Andreas; Staerfeldt, HH; Rognes, T & Ussery, DW (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research (NAR). ISSN 0305-1048. 35. doi: 10.1093/nar/gkm160. Fulltekst i vitenarkiv Vis sammendrag

  The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server.

• Røyrvik, Ellen Christine; Ahlquist, Terje Cruickshank; Rognes, Torbjørn & Lothe, Ragnhild A (2007). Slip Slidin' Away: A Duodecennial Review of Targeted Genes in Mismatch Repair Deficient Colorectal Cancer. Critical reviews in oncogenesis. ISSN 0893-9675. 13(1), s. 229–257. doi: 10.1615/CritRevOncog.v13.i3.20.
• Alseth, Ingrun; Rognes, Torbjørn; Lindbäck, Toril; Solberg, Inger; Robertsen, Kristin & Kristiansen, Knut Ivan [Vis alle 10 forfattere av denne artikkelen] (2006). A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD. Molecular Microbiology. ISSN 0950-382X. 59(5), s. 1602–1609. Fulltekst i vitenarkiv Vis sammendrag

  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 coli tag alkA mutant to screen for 3-methyladenine DNA glycosylase genes in genomic libraries of the soil bacterium Bacillus cereus. Three genes were recovered: alkC, alkD and alkE. The amino acid sequence of AlkE is homologous to the E. coli AlkA sequence. AlkC and AlkD represent novel proteins without sequence similarity to any protein of known function. However, iterative and indirect sequence similarity searches revealed that AlkC and AlkD are distant homologues of each other within a new protein superfamily that is ubiquitous in the prokaryotic kingdom. Homologues of AlkC and AlkD were also identified in the amoebas Entamoeba histolytica and Dictyostelium discoideum, but no other eukaryotic counterparts of the superfamily were found. The alkC and alkD genes were expressed in E. coli and the proteins were purified to homogeneity. Both proteins were found to be specific for removal of N-alkylated bases, and showed no activity on oxidized or deaminated base lesions in DNA. B. cereus AlkC and AlkD thus define novel families of alkylbase DNA glycosylases within a new protein superfamily.

• Thomassen, Gard O. S.; Rosok, Oystein & Rognes, Torbjørn (2006). Computational prediction of microRNAs encoded in viral and other genomes. Journal of Biomedicine and Biotechnology. ISSN 1110-7243. Fulltekst i vitenarkiv
• Alseth, Ingrun; Rognes, Torbjørn; Lindbäck, Toril; Solberg, Inger; Robertsen, Kristin & Kristiansen, Knut Ivan [Vis alle 10 forfattere av denne artikkelen] (2006). A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD. Molecular Microbiology. ISSN 0950-382X. 59. doi: 10.1111/j.1365-2958.2006.05044.x. Fulltekst i vitenarkiv
• Sætrom, Pål; Sneve, Ragnhild; Kristiansen, Knut Ivan; Snøve, Ola; Grünfeld, Thomas & Rognes, Torbjørn [Vis alle 7 forfattere av denne artikkelen] (2005). Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. Nucleic Acids Research (NAR). ISSN 0305-1048. 33, s. 3263–3270. Fulltekst i vitenarkiv
• Sæbø, Per Eystein; Andersen, SM; Myrseth, Jon; Lærdahl, Jon Kristen & Rognes, Torbjørn (2005). PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology. Nucleic Acids Research (NAR). ISSN 0305-1048. 33. doi: 10.1093/nar/gki423. Fulltekst i vitenarkiv
• Davidsen, Tonje; Rødland, Einar Andreas; Lagesen, Karin; Seeberg, Erling Christen; Rognes, Torbjørn & Tønjum, Tone (2004). Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Research (NAR). ISSN 0305-1048. 32(3), s. 1050–1058. Fulltekst i vitenarkiv

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• Istvan, Paula; Birkeland, Einar Elvbakken; Rognes, Torbjørn & Rounge, Trine Ballestad (2021). Profiling gut viruses from metagenomes of Bowel Cancer Screening participants.
• Safavi, Shiva; Larouche, Ariane; Zahn, Astrid; Patenaude, Anne-Marie; Domanska, Diana & Dionne, Kiersten [Vis alle 17 forfattere av denne artikkelen] (2021). Erratum: The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID (NAR Cancer (2020) 2:3 (zcaa019) DOI: 10.1093/narcan/zcaa019). NAR Cancer. ISSN 2632-8674. 3(1). doi: 10.1093/NARCAN/ZCAA045.
• Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix & Lirussi, Lisa [Vis alle 16 forfattere av denne artikkelen] (2017). Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1 .
• Dalhus, Bjørn; Backe, Paul Hoff; Lærdahl, Jon Kristen; Rowe, Alexander D.; Blicher, Pernille & Forstrøm, Rune Johansen [Vis alle 8 forfattere av denne artikkelen] (2015). Helse Sør-Øst Core Facility for Structural Biology and Bioinformatics.
• Hovig, Eivind & Rognes, Torbjørn (2015). Bioinformatikk - å forstå teksten. I Hessen, Dag Olav; Lie, Thore & Stenseth, Nils Christian (Red.), Mendels arv - Genetikkens æra. Gyldendal Norsk Forlag A/S. ISSN 978-82-05-45818-5. s. 329–354.
• Andersen, Pernille Strøm; Backe, Paul Hoff; Lærdahl, Jon Kristen; Rowe, Alexander; Forstrøm, Rune Johansen & Rognes, Torbjørn [Vis alle 8 forfattere av denne artikkelen] (2014). Helse Sør-Øst Core Facility for Structural Biology and Bioinformatics.
• Rognes, Torbjørn (2014). Open access from a researcher’s perspective.
• Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Lagesen, Karin; Khelik, Ksenia; Rognes, Torbjørn & Jentoft, Sissel [Vis alle 7 forfattere av denne artikkelen] (2012). Improving the cod genome with the use of multi-platform sequencing data.
• Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Khelik, Ksenia; Lagesen, Karin; Rounge, Trine Ballestad & Star, Bastiaan [Vis alle 13 forfattere av denne artikkelen] (2012). Challenges and Opportunities for Improving the Atlantic Cod Genome Assembly and Annotation.
• Ambur, Ole Herman; Alfsnes, Kristian; Hovland, Eirik; Homberset, Håvard; Lærdahl, Jon Kristen & Frye, Stephan Alfons [Vis alle 9 forfattere av denne artikkelen] (2010). Mechanisms of neisserial transformation and the evolution of sexual reproduction.
• Fensgård, Øyvind; Lindvall, Jessica Margareta; Kassahun, Henok; Rognes, Torbjørn & Nilsen, Hilde (2009). Microarray analysis of BER mutants.
• Fensgård, Øyvind; Lindvall, Jessica; Kassahun, Henok; Rognes, Torbjørn & Nilsen, Hilde (2009). Microarray analysis of BER mutants.
• Rognes, Torbjørn (2006). PARALIGN: Rapid Sequence Similarity Searches Utilizing Several Levels of Parallelism.
• Robertsen, Kristin; Kristoffersen, Anja Bråthen & Rognes, Torbjørn (2006). Phylogenetic profiles for identifying new DNA-repair proteins.
• Davidsen, Tonje; Rødland, Einar Andreas; Lagesen, Karin; Frye, Stephan Alfons; Ambur, Ole Herman & Rognes, Torbjørn (2003). Biased distribution of bacterial DNA uptake sequences towards genome maintenance genes.
• Davidsen, Tonje; Frye, Stephan Alfons; Balasingham, Seetha; Assalkhou, Reza; Rognes, Torbjørn & Bjørås, Magnar [Vis alle 8 forfattere av denne artikkelen] (2002). Genome maintenance in Neisseria meningitidis: the role of base excision repair.
• Nakken, Sigve & Rognes, Torbjørn (2010). Inference of molecular mechanisms from sequence patterns in human DNA variation. Unipub forlag.
• Thomassen, Gard O Sundby & Rognes, Torbjørn (2010). Design, analysis and applications of custom high-density oligonucleotide microarrays. Unipub forlag. ISSN 978-82-8072-495-3.
• Lagesen, Karin & Rognes, Torbjørn (2008). Computational characterization of ribosomal RNAs in prokaryotes. Unipub forlag. ISSN 978-82-8072-773-2.

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