Karin Lagesen

Image of Karin Lagesen
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Visiting address Gaustadalléen 23B Ole Johan Dahls hus 0373 OSLO
Postal address Postboks 1080 Blindern 0316 OSLO
Tags: Annotation, Atlantic cod, Genomics, Programming, Amplicon high throughput sequencing, Bioinformatics, Comparative genomics, DNA sequence analysis, DNA sequencing, High-throughput sequencing, Open-source tools

Publications

  • Siddiqui, Huma; Lagesen, Karin; Nederbragt, Alexander Johan; Eri, Lars Magne; Jeansson, Stig & Jakobsen, Kjetill Sigurd (2014). Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-Independent High Throughput Sequencing: A Case Report. Open Microbiology Journal.  ISSN 1874-2858.  8, s 148- 153 . doi: 10.2174/1874285801408010148
  • Xiao, Xi; Sogge, Hanne; Lagesen, Karin; Tooming-Klunderud, Ave; Jakobsen, Kjetill Sigurd & Rohrlack, Thomas (2014). Use of high throughput sequencing and light microscopy show contrasting results in a study of phytoplankton occurrence in a freshwater environment. PLoS ONE.  ISSN 1932-6203.  9(8) . doi: 10.1371/journal.pone.0106510 Full text in Research Archive
  • 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 (2013). Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response. Scientific Reports.  ISSN 2045-2322.  3 . doi: 10.1038/srep03053 Full text in Research Archive
  • De Muinck, Eric; Lagesen, Karin; Afset, Jan Egil; Didelot, Xavier; Rønningen, Kjersti Skjold; Rudi, Knut; Stenseth, Nils Christian & Trosvik, Pål (2013). Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche . BMC Genomics.  ISSN 1471-2164.  14 . doi: 10.1186/1471-2164-14-81 Full text in Research Archive
  • Tooming-Klunderud, Ave; Sogge, Hanne; Rounge, Trine Ballestad; Nederbragt, Alexander Johan; Lagesen, Karin; Glöckner, Gernot; Hayes, Paul K; Rohrlack, Thomas & Jakobsen, Kjetill Sigurd (2013). From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains. Applied and Environmental Microbiology.  ISSN 0099-2240.  79(21), s 6803- 6812 . doi: 10.1128/AEM.01455-13 Full text in Research Archive
  • Vesth, Tammi; Lagesen, Karin; Acar, Öncel & Ussery, David (2013). CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics. PLoS ONE.  ISSN 1932-6203.  8(4), s 1- 16 . doi: 10.1371/journal.pone.0060120 Full text in Research Archive
  • Jørgensen, Marte Holten; Lagesen, Karin; Mable, Barbara & Brysting, Anne Krag (2012). Using high-throughput sequencing to investigate the evolution of self-incompatibility genes in the Brassicaceae: strategies and challenges. Plant Ecology & Diversity.  ISSN 1755-0874.  5(4), s 473- 484 . doi: 10.1080/17550874.2012.748098
  • Siddiqui, Huma; Lagesen, Karin; Nederbragt, Alexander Johan; Jeansson, Stig & Jakobsen, Kjetill Sigurd (2012). Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiology.  ISSN 1471-2180.  12(205) . doi: 10.1186/1471-2180-12-205 Full text in Research Archive
  • Snipen, Lars; Wassenaar, Trudy M.; Altermann, Eric; Olson, Jonathan; Kathariou, Sophia; Lagesen, Karin; Takamiya, Monica; Knøchel, Susanne; Ussery, David Wayne & Meinersmann, Richard J. (2012). Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli. Microbial Informatics and Experimentation.  ISSN 2042-5783.  2(1) . doi: 10.1186/2042-5783-2-8
  • Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone Fredsvik; Rounge, Trine Ballestad; Paulsen, Jonas; Solbakken, Monica Hongrø; Sharma, Animesh; Wetten, Ola Frang; Lanzén, Anders; Winer, Roger; Knight, James; Vogel, Jan-Hinnerk; Aken, Bronwen; Andersen, Øivind; Lagesen, Karin; Tooming-Klunderud, Ave; Edvardsen, Rolf; Kirubakaran, G. Tina; Espelund, Mari; Nepal, Chirag; Previti, A. Christopher; Karlsen, Bård Ove; Moum, Truls; Skage, Morten; Berg, Paul Ragnar; Gjøen, Tor; Kuhl, Heiner; Thorsen, Jim; Malde, Ketil; Reinhardt, Richard; Du, Lei; Johansen, Steinar Daae; Searle, Steve; Lien, Sigbjørn; Nilsen, Frank; Jonassen, Inge; Omholt, Stig W; Stenseth, Nils Christian & Jakobsen, Kjetill Sigurd (2011). The genome sequence of Atlantic cod reveals a unique immune system. Nature.  ISSN 0028-0836.  477(7363), s 207- 210 . doi: 10.1038/nature10342 Full text in Research Archive
  • Siddiqui, Huma; Nederbragt, Alexander Johan; Lagesen, Karin; Jeansson, Stig & Jakobsen, Kjetill Sigurd (2011). Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiology.  ISSN 1471-2180.  11 . doi: 10.1186/1471-2180-11-244
  • Bohlin, Jon; Snipen, Lars-Gustav; Cloeckaert, A; Lagesen, Karin; Ussery, David Wayne; Kristoffersen, Anja Bråthen & Godfroid, Jacques (2010). Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods. BMC Evolutionary Biology.  ISSN 1471-2148.  10 . doi: 10.1186/1471-2148-10-249
  • Bohlin, Jon; Snipen, Lars-Gustav; Hardy, Simon P.; Kristoffersen, Anja Bråthen; Lagesen, Karin; Dønvik, Torunn; Skjerve, Eystein & Ussery, David Wayne (2010). Analysis of intra-genomic GC content homogeneity within prokaryotes . BMC Genomics.  ISSN 1471-2164.  11 . doi: 10.1186/1471-2164-11-464
  • Friis, C; Wassenaar, TM; Javed, MA; Snipen, Lars-Gustav; Lagesen, Karin; Hallin, PF; Newell, DG; Toszeghy, M; Ridley, A; Manning, G & Ussery, David Wayne (2010). Genomic Characterization of Campylobacter jejuni Strain M1. PLoS ONE.  ISSN 1932-6203.  5(8) . doi: 10.1371/journal.pone.0012253
  • Thomassen, Gard O Sundby; Sneve, Ragnhild; Rowe, Alexander D.; Booth, James; Lindvall, Jessica M.; Lagesen, Karin; Kristiansen, Knut Ivan; Bjørås, Magnar & Rognes, Torbjørn (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
  • Vesth, Tammi; Wassenaar, TM; Hallin, Peter; Snipen, Lars-Gustav; Lagesen, Karin & Ussery, David Wayne (2010). On the Origins of a Vibrio Species . Microbial Ecology.  ISSN 0095-3628.  59(1), s 1- 13 . doi: 10.1007/s00248-009-9596-7
  • Ambur, Ole Herman; Davidsen, Tonje; Frye, Stephan Alfons; Balasingham, Seetha; Lagesen, Karin; Rognes, Torbjørn & Tønjum, Tone (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
  • 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)
  • Ussery, DW; Kiil, K; Lagesen, Karin; Sicheritz-Pontén, T; bohlin, jon & Wassenaar, TM (2009). The Genus Burkholderia: Analysis of 56 Genomic Sequences , In H de Reuse & S Bereswill (ed.),  Microbial Pathogenomics.  S. Karger.  ISBN 978-3-8055-9192-8.  The Genus Burkholderia: Analysis of 56 Genomic Sequences.  s 140 - 157
  • 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.  ISSN 0305-1048.  35 . doi: 10.1093/nar/gkm160
  • Ussery, DW; Hallin, PF; Lagesen, Karin & Wassenaar, TM (2005). Genome update: tRNAs in sequenced microbial genomes. Microbiology.  ISSN 1350-0872.  150, s 1603- 1606
  • Ussery, DW; Hallin, PF; Lagesen, Karin & Coenye, T (2004). Genome update: rRNAs in sequenced microbial genomes. Microbiology.  ISSN 1350-0872.  150, s 1113- 1115
  • 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.  ISSN 0305-1048.  32(3), s 1050- 1058

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  • Slettemeås, Jannice Schau; Norström, Madelaine; Sunde, Marianne; Urdahl, Anne Margrete; Wester, Astrid Lousie; Lagesen, Karin; Simonsen, Gunnar Skov; Ulstad, Charlotte Rosenberg & Sekse, Camilla (2017). Quinolone resistant Escherichia coli from broiler in Norway - characterization, comparison to human isolates and molecular risk assessment.
  • Spilsberg, Bjørn; Lagesen, Karin; Kristoffersen, Anja Bråthen & Holst-Jensen, Arne (2017). Identification and quantification of genetically modified organisms (GMO) from high throughput sequencing data.
  • Evensen, Jonas; Gundersen, Sveinung; Kristoffersen, Anja Bråthen & Lagesen, Karin (2016). STRAINTRACER-DB: A flexible analysis and persistent storage system for sequence and epidemiological data.
  • Holst-Jensen, Arne; Spilsberg, Bjørn; Kristoffersen, Anja Bråthen & Lagesen, Karin (2016). Detection and quantification of genetically modified organisms by use of shotgun whole genome sequencing.
  • Jonsson, Malin E; Torp, Mona; Lagesen, Karin; Kristoffersen, Anja Bråthen; Vigerust, Margrete; Angen, Øystein; Wester, Astrid Lousie; Dahle, Ulf R & Hofshagen, Merete (2016). A pilot study of the sources of campylobacteriosis in Norway.
  • Nederbragt, Alexander Johan & Lagesen, Karin (2016). The Carpentry effort at the University of Oslo.
  • Slettemeås, Jannice Schau; Norström, Madelaine; Sunde, Marianne; Urdahl, Anne Margrete; Wester, Astrid Lousie; Simonsen, Gunnar Skov; Ulstad, Charlotte Rosenberg; Sekse, Camilla & Lagesen, Karin (2016). Quinolone resistant Escherichia coli from broiler in Norway - characterization, comparison to human isolates and molecular risk assessment.
  • Colquhoun, Duncan John; Lagesen, Karin; Vestby, Lene Karine & Gulla, Snorre (2015). Yersiniose – et økende problem i norsk fiskeoppdrett?. Norsk Fiskeoppdrett.  ISSN 0332-7132.  15, s 48- 50
  • Torp, Mona; Kristoffersen, Anja Bråthen; Vigerust, Margrete; Angen, Øistein; Jonsson, Malin E; Lagesen, Karin; Hofshagen, Merete; Wester, Astrid Lousie & Dahle, Ulf R (2015). Sources of campylobacteriosis in Norway - a pilot study.
  • Torp, Mona; Lagesen, Karin; Vigerust, Margrete; Angen, Øystein; Wester, Astrid Louise; Dahle, Ulf R; Jonsson, Malin E; Kristoffersen, Anja Bråthen & Hofshagen, Merete (2014). Sources of campylobacteriosis in Norway - a pilot study.
  • Tørresen, Ole Kristian; Walenz, Brian; Grove, Harald; Lien, Sigbjørn; Knight, James; Star, Bastiaan; Lagesen, Karin; Sandve, Geir Kjetil F.; Skage, Morten; Hansen, Marianne Helén Selander; Klunderud, Ave Tooming; Miller, Jason Rafe; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2014). A new, high quality reference genome assembly for Atlantic cod.
  • Holst-Jensen, Arne; Foam, Napoleon; Kristoffersen, Anja Bråthen; Lagesen, Karin; Spilsberg, Bjørn & Tengs, Torstein (2012). Potential for use of next generation sequencing NGS to detect GMO in food and feed.
  • Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Khelik, Ksenia; Lagesen, Karin; Rounge, Trine Ballestad; Star, Bastiaan; Tina, Kirubakaran G.; Berg, Paul Ragnar; Rognes, Torbjørn; Jentoft, Sissel; Winer, Roger; Dewar, Ken & Jakobsen, Kjetill Sigurd (2012). Challenges and Opportunities for Improving the Atlantic Cod Genome Assembly and Annotation.
  • Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone Fredsvik; Rounge, Trine Ballestad; Solbakken, Monica Hongrø; Paulsen, Jonas; Lagesen, Karin; Tooming-Klunderud, Ave; Tina, Kirubakaran G.; Espelund, Mari; Skage, Morten; Berg, Paul Ragnar; Omholt, Stig W; Stenseth, Nils Christian & Jakobsen, Kjetill Sigurd (2011). The genome of Atlantic cod reveals a unique immune system.
  • Jørgensen, Marte Holten; Lagesen, Karin; Mable, Barbara & Brysting, Anne Krag (2011). A time and economically effecient protocol using high throughput sequencing to create large sequence datasets for population genetics.
  • Lagesen, Karin; Ussery, David Wayne & Wassenaar, TM (2010). Genome update: the 1000th genome - a cautionary tale. Microbiology.  ISSN 1350-0872.  156, s 603- 608 . doi: 10.1099/mic.0.038257-0
  • Lagesen, Karin & Rognes, Torbjørn (2008). Computational characterization of ribosomal RNAs in prokaryotes .
  • Davidsen, Tonje; Rødland, Einar Andreas; Lagesen, Karin; Frye, Stephan Alfons; Ambur, Ole Herman; Rognes, Torbjørn; Tønjum, Tone & Seeberg, Erling Christen (2003). Biased distribution of bacterial DNA uptake sequences towards genome maintenance genes.
  • Davidsen, Tonje; Rødland, Einar Andreas; Lagesen, Karin; Seeberg, Erling Christen; Rognes, Torbjørn & Tønjum, Tone (2003). Biased distribution of bacterial DNA uptake sequences.
  • Davidsen, L.; Lagesen, Karin; Rødland, A. E.; Rognes, Torbjørn & Tønjum, Tone (2003). Biased distribution of bacterial DNA uptake sequences.
  • Davidsen, Tonje; Rødland, Einar Andreas; Lagesen, Karin; Frye, Stephan Alfons; Ambur, Ole Herman; Rognes, Torbjørn & Tonjum, Tone (2003). Biased distribution of bacterial DNA uptake sequences towards genome maintenance genes.

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Published Aug. 8, 2013 3:17 PM - Last modified Nov. 4, 2016 8:01 AM