Home
Click
  • E-mailInge.Jonassen@uib.no
  • Phone+47 55 58 47 13+47 905 24 316
  • Visitor Address
    HIB - Thormøhlensgt. 55
  • Postal Address
    Postboks 7803
    5020 Bergen

My field of research is bioinformatics - development and application of informatics methods for the analysis of molecular biology data. My interests include methods for the automatic discovery of patterns, data analysis, algorithms and machine learning applied on molecular biology data. The research in my group includes tight collaboration with experimental groups wihtin different fields of biological and medical research. I work with analysis of different types of data including DNA sequences (including genomes), protein sequences and structures, gene expression data, and data generated usiing high-throughput technologies, e.g., next-generation sequencing. My group is also engaged in development and applicationof methods for integration of data and tools within bioinformatics.

I teach mostly bioinformatics courses, but I have also been teaching user courses in informatics and operating systems.

  • Flønes, Irene Hana; Sztromwasser, Pawel Szymon; Haugarvoll, Kristoffer; Dölle, Christian; Lykouri, Maria; Schwarzlmüller, Thomas; Jonassen, Inge; Miletic, Hrvoje; Johansson, Stefan; Knappskog, Per; Bindoff, Laurence; Tzoulis, Charalampos. 2016. Novel SLC19A3 promoter deletion and allelic silencing in biotin-thiamine-responsive basal ganglia encephalopathy. PLoS ONE. 11. doi: 10.1371/journal.pone.0149055
  • Lien, Sigbjørn; Koop, Ben F; Sandve, Simen Rød; Miller, Jason R.; Kent, Matthew Peter; Nome, Torfinn; Hvidsten, Torgeir Rhoden; Leong, Jong; Minkley, David R.; Zimin, Aleksey; Grammes, Fabian; Grove, Harald; Gjuvsland, Arne Bjørke; Walenz, Brian; Hermansen, Russell A.; von Schalburg, Kristian R.; Rondeau, Eric; Genova, Alex Di; Antony Samy, Jeevan Karloss; Vik, Jon Olav; Vigeland, Magnus Dehli; Caler, Lis; Grimholt, Unni; Jentoft, Sissel; Våge, Dag Inge; de Jong, Pieter J.; Moen, Thomas; Baranski, Matthew; Palti, Yniv; Smith, Douglas W.; Yorke, James A.; Nederbragt, Alexander J.; Tooming-Klunderud, Ave; Jakobsen, Kjetill Sigurd; Jiang, Xuanting; Fan, Dingding; Hu, Yan; Liberles, David A.; Vidal, Rodrigo; Iturra, Patricia; Jones, Steven J.M.; Jonassen, Inge; Maass, Alejandro; Omholt, Stig William; Davidson, William S. 2016. The Atlantic salmon genome provides insights into rediploidization. Nature. 533: 200-205. doi: doi:10.1038/nature17164
  • Bredholt, Geir; Mannelqvist, Monica; Stefansson, Ingunn; Birkeland, Even; Bø, Trond Hellem; Øyan, Anne Margrete; Trovik, Jone; Kalland, Karl-Henning; Jonassen, Inge; Salvesen, Helga; Wik, Elisabeth; Akslen, Lars A. 2015. Tumor necrosis is an important hallmark of aggressive endometrial cancer and associates with hypoxia, angiogenesis and inflammation responses. OncoTarget. 6: 39676-39691. doi: 10.18632/oncotarget.5344
  • Farag, Yehia Mohamed Mokhtar; Berven, Frode; Jonassen, Inge; Petersen, Kjell; Barsnes, Harald. 2015. Distributed and interactive visual analysis of omics data. Journal of Proteomics. 129: 78-82. doi: 10.1016/j.jprot.2015.05.029
  • Hadziavdic, Kenan; Lekang, Katrine; Lanzén, Anders; Jonassen, Inge; Thompson, Eric; Troedsson, Christofer. 2014. Characterization of the 18s rRNA gene for designing universal eukaryote specific primers. PLoS ONE. 9. doi: 10.1371/journal.pone.0087624
  • Nygård, Ståle; Jonassen, Inge. 2014. The Norwegian Bioionformatics Platform. NBS-nytt. 2. 32-35.
  • Balzer, Susanne; Malde, Ketil; Grohme, Markus A.; Jonassen, Inge. 2013. Filtering duplicate reads from 454 pyrosequencing data. Bioinformatics. 29: 830-836. doi: 10.1093/bioinformatics/btt047
  • Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter. 2013. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics. 29: 1325-1332. doi: 10.1093/bioinformatics/btt113
  • Lanzén, Anders; Simachew, Addis; Gessesse, Amare; Chmolowska, Dominika; Jonassen, Inge; Øvreås, Lise. 2013. Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS ONE. 8. 12 pages. doi: 10.1371/journal.pone.0072577
  • Petersen, Kjell; Rajcevic, Uros; Rahim, Siti Aminah Abdul; Jonassen, Inge; Kalland, Karl-Henning; Jimenez, Connie R.; Bjerkvig, Rolf; Niclou, Simone P. 2013. Gene set based integrated data analysis reveals phenotypic differences in a brain cancer model. PLoS ONE. 8. 11 pages. doi: 10.1371/journal.pone.0068288
  • Skern-Mauritzen, Rasmus; Malde, Ketil; Besnier, Francois; Nilsen, Frank; Jonassen, Inge; Reinhardt, Richard; Koop, Ben F.; Dalvin, Sussie Trine; Mæhle, Stig; Kongshaug, Heidi; Glover, Kevin. 2013. How does sequence variability affect de novo assembly quality? Journal of Natural History. 47: 901-910. doi: 10.1080/00222933.2012.738833
  • Christoforou, Andrea; Dondrup, Michael; Mattingsdal, Morten; Mattheisen, Manuel; Giddaluru, Sudheer; Nöthen, Markus M.; Rietschel, Marcella; Cichon, Sven; Djurovic, Srdjan; Andreassen, Ole Andreas; Jonassen, Inge; Steen, Vidar Martin; Puntervoll, Pål; Le Hellard, Stephanie. 2012. Linkage-disequilibrium-based binning affects the interpretation of GWASs. American Journal of Human Genetics. 90: 727-733. doi: 10.1016/j.ajhg.2012.02.025
  • Johansson, Stefan; Irgens, Henrik Underthun; Chudasama, Kishankumar; Molnes, Janne; Aerts, Jan; Roque, Francisco; Jonassen, Inge; Levy, Shawn; Lima, Kari; Knappskog, Per; Bell, Graeme I.; Molven, Anders; Njølstad, Pål Rasmus. 2012. Exome sequencing and genetic testing for MODY. PLoS ONE. 7. 8 pages. doi: 10.1371/journal.pone.0038050
  • Lanzén, Anders; Huson, Daniel H.; Gorfer, M; Grindhaug, Svenn Helge; Jonassen, Inge; Jonassen, Inge; Øvreås, Lise; Urich, Tim. 2012. CREST--classification resources for environmental sequence tags. PLoS ONE. 7. doi: 10.1371/journal.pone.0049334
  • Lanzén, Anders; Jørgensen, Steffen Leth; Huson, Daniel H.; Gorfer, Markus; Grindhaug, Svenn Helge; Jonassen, Inge; Øvreås, Lise; Urich, Tim. 2012. CREST - classification resources for environmental sequence tags. PLoS ONE. 7: e49334-e49334. Published 2012-11-08. doi: 10.1371/journal.pone.0049334
  • Sridhar, Settu; Sharma, Animesh; Kongshaug, Heidi; Nilsen, Frank; Jonassen, Inge. 2012. Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity. BMC Genomics. 13. doi: 10.1186/1471-2164-13-598
  • Stavrum, Ruth; Valvatne, Håvard; Stavrum, Anne-Kristin; Riley, Lee W.; Ulvestad, Elling; Jonassen, Inge; Doherty, Timothy Mark; Grewal, Harleen. 2012. Mycobacterium tuberculosis Mcel protein complex initiates rapid induction of transcription of genes involved in substrate trafficking. Genes and Immunity. 13: 496-502. doi: 10.1038/gene.2012.24
  • Balzer, Susanne; Malde, Ketil; Jonassen, Inge. 2011. Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics. 27: I304-I309. doi: 10.1093/bioinformatics/btr251
  • Hollup, Siv Midtun; Sadowski, Michael I; Jonassen, Inge; Taylor, William R. 2011. Exploring the limits of fold discrimination by structural alignment: A large scale benchmark using decoys of known fold. Computational biology and chemistry (Print). 35: 174-188. doi: 10.1016/j.compbiolchem.2011.04.008
  • Lanzén, Anders; Jørgensen, Steffen Leth; Bengtsson, Mia M. B.; Jonassen, Inge; Øvreås, Lise; Urich, Tim. 2011. Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiology Ecology. 77: 577-589. doi: 10.1111/j.1574-6941.2011.01138.x
  • Mannelqvist, Monica; Stefansson, Ingunn Marie; Bredholt, Geir; Bø, Trond Hellem; Øyan, Anne Margrete; Jonassen, Inge; Kalland, Karl-Henning; Salvesen, Helga Birgitte; Akslen, Lars A. 2011. Gene Expression Patterns Related to Vascular Invasion and Aggressive Features in Endometrial Cancer. American Journal of Pathology. 178: 861-871. doi: 10.1016/j.ajpath.2010.10.040
  • Skavland, Jørn; Jørgensen, Katarina Mariann; Hadziavdic, Kenan; Hovland, Randi; Jonassen, Inge; Bruserud, Øystein; Gjertsen, Bjørn Tore. 2011. Specific cellular signal-transduction responses to in vivo combination therapy with ATRA, valproic acid and theophylline in acute myeloid leukemia. Blood Cancer Journal. 1. doi: 10.1038/bcj.2011.2
  • 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. 477: 207-210. doi: 10.1038/nature10342
  • Stavrum, Ruth; Stavrum, Anne-Kristin; Valvatne, Håvard; Riley, Lee W.; Ulvestad, Elling; Jonassen, Inge; Assmus, Jørg; Doherty, T. Mark; Grewal, Harleen. 2011. Modulation of transcriptional and inflammatory responses in murine macrophages by the mycobacterium tuberculosis mammalian cell entry (Mce) 1 complex. PLoS ONE. 6. 11 pages. doi: 10.1371/journal.pone.0026295
  • Balzer, Susanne; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge. 2010. Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics. 26: i420-i425. doi: 10.1093/bioinformatics/btq365
  • Davidson, William S; Koop, Ben F; Jones, Steven JM; Vidal, Rodrigo; Iturra, Patricia; Maass, Alejandro; Jonassen, Inge; Lien, Sigbjørn; Omholt, Stig W. 2010. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biology. 11. 7 pages. doi: 10.1186/gb-2010-11-9-403
  • Drabløs, Finn; Petersen, Kjell; Johansen, Jostein; Nygård, Ståle; Ahmad, Rafi; Smalås, Arne; Hovig, Eivind; Jonassen, Inge. 2010. The FUGE Bioinformatics platform: a central platform in the FUGE2 period. MITAT. Minimally invasive therapy & allied technologies. 19: 70-71. doi: 10.3109/13645706.2010.500867
  • Kalas, Matus; Puntervoll, Pål; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge. 2010. BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics. 26: i540-i546. doi: 10.1093/bioinformatics/btq391
  • Pettifer, Steve; Ison, Jon; Kalaš, Matúš; Thorne, David; McDermott, Philip; Jonassen, Inge; Ali, Liaquat; Fernandez, Jose M; Rodriguez, Jose M; Pisano, David G; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B; Bongcam-Rudloff, Eric; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K; Cameron, Graham; Vriend, Gert. 2010. The EMBRACE web service collection. Nucleic Acids Research. 38: W683-W688. doi: 10.1093/nar/gkq297
  • Skavland, Jørn; Hadziavdic, Kenan; Jonassen, Inge; Bruserud, Øystein; Gjertsen, Bjørn Tore. 2010. Combined epigenetic and signal transduction therapy modulate specific signal transduction patterns in acute myeloid leukemia. Haematologica. 95: 510-510.
  • Ke, Xisong; Qu, Yi; Rostad, Kari; Li, Wen-Cheng; Lin, Biaoyang; Halvorsen, Ole Johan; Haukaas, Svein Andreas; Jonassen, Inge; Petersen, Kjell; Goldfinger, Naomi; Rotter, Varda; Akslen, Lars A.; Øyan, Anne Margrete; Kalland, Karl-Henning. 2009. Genome-wide profiling of histone H3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis. PLoS ONE. 4. 14 pages. doi: 10.1371/journal.pone0004687
  • Leversen, Nils Anders; De Souza, Gustavo; Målen, Hiwa; Prasad, Swati; Jonassen, Inge; Wiker, Harald G. 2009. Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods. Microbiology. 155: 2375-2383. doi: 10.1099/mic.0.025270-0
  • Pendino, Frederic; Nguyen, Eric; Jonassen, Inge; Dysvik, Bjarte; Azouz, Abdulkader; Lanotte, Michel; Ségal-Bendirdjian, Evelyne; Lillehaug, Johan. 2009. Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis. Blood. 113: 3172-3181. doi: 10.1182/blood-2008-07-170035
  • Salvesen, Helga Birgitte; Carter, Scott L.; Mannelqvist, Monica; Dutt, Amit; Getz, Gad; Stefansson, Ingunn Marie; Ræder, Maria Therese Barøy; Sos, Martin L.; Engelsen, Ingeborg Bøe; Trovik, Jone; Wik, Elisabeth; Greulich, Heidi; Bø, Trond Hellem; Jonassen, Inge; Thomas, Roman K.; Zander, Tim; Garraway, Levi A.; Øyan, Anne Margrete; Sellers, William R.; Kalland, Karl-Henning; Meyerson, Matthew; Akslen, Lars A.; Beroukhim, Rameen. 2009. Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation. Proceedings of the National Academy of Sciences of the United States of America. 106: 4834-4839. doi: 10.1073/pnas.0806514106
  • Sælensminde, Gisle; Halskau jr, Øyvind; Jonassen, Inge. 2009. Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role. Extremophiles. 13: 11-20. doi: 10.1007/s00792-008-0192-4
  • Taylor, William R.; Chelliah, Vijayalakshmi; Hollup, Siv Midtun; MacDonald, James D.; Jonassen, Inge. 2009. Probing the "Dark Matter" of protein fold space. Structure. 17: 1244-1252. doi: 10.1016/j.str.2009.07.012
  • Taylor, William R.; Chelliah, Vijayalakshmi; Hollup, Siv Midtun; MacDonald, James T.; Jonassen, Inge. 2009. Probing the "Dark Matter" of protein fold space. Structure. 17: 1244-1252. doi: 10.1016/j.str.2009.07.012
  • Øyan, Anne Margrete; Ånensen, Nina; Bø, Trond Hellem; Stordrange, Laila; Jonassen, Inge; Bruserud, Øystein; Kalland, Karl-Henning; Gjertsen, Bjørn Tore. 2009. Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia. BMC Cancer. 9. doi: 10.1186/1471-2407-9-77
  • De Souza, Gustavo Antonio; Målen, Hiwa; Søfteland, Tina; Sælensminde, Gisle; Prasad, Swati; Jonassen, Inge; Wiker, Harald G. 2008. High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example. BMC Genomics. 9. 13 pages. Published 2008-07-02. doi: 10.1186/1471-2164-9-316
  • Eichner, Christiane; Frost, Petter; Dysvik, Bjarte; Jonassen, Inge; Kristiansen, Bjørn; Nilsen, Frank. 2008. Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis. BMC Genomics. 9. 15 pages. doi: 10.1186/1471-2164-9-126
  • Giegerich, Robert; Brazma, Alvis; Jonassen, Inge; Ukkonen, Esko; Vingron, Martin. 2008. The BREW workshop series: a stimulating experience in PhD education. Briefings in Bioinformatics. 9: 250-253. doi: 10.1093/bib/bbn002
  • Hollup, Siv Midtun; Taylor, William R.; Jonassen, Inge. 2008. Structural fragments in protein model refinement. Protein peptide letters. 15: 964-971.
  • Malde, Ketil; Jonassen, Inge. 2008. Repeats and EST analysis for new organisms. BMC Genomics. 9. 7 pages. doi: 10.1186/1471-2164-9-23
  • Stavrum, Ruth M Støbakk; Valvatne, Håvard; Bø, Trond Hellem; Jonassen, Inge; Hinds, Jason; Butcher, Philip; Grewal, Harleen. 2008. Genomic Diversity among Beijing and non-Beijing Mycobacterium tuberculosis Isolates from Myanmar. PLoS ONE. 3: e1973. doi: 10.1371/journal.pone.0001973
  • Sælensminde, Gisle; Halskau jr, Øyvind; Jonassen, Inge. 2008. Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role. Extremophiles. doi: 10.1007/s00792-008-0192-4
  • Taylor, William R.; Bartlett, Gail J.; Chefliah, Vijayalakshmi; Klose, Daniel; Lin, Kuang; Sheldon, Tom; Jonassen, Inge. 2008. Prediction of protein structure from ideal forms. Proteins: Structure, Function, and Genetics. 70: 1610-1619. doi: 10.1002/prot.21913
  • Halvorsen, Ole Johan; Rostad, Kari; Øyan, Anne Margrete; Puntervoll, Hanne Eknes; Bø, Trond Hellem; Stordrange, Laila; Olsen, Sue; Haukaas, Svein Andreas; Hood, Leroy; Jonassen, Inge; Kalland, Karl-Henning; Akslen, Lars A. 2007. Increased expression of sim2-s protein is a novel marker of aggressive prostate cancer. Clinical Cancer Research. 13: 892-897. doi: 10.1158/1078-0432.CCR-06-1207
  • Hystad, ME; Myklebust, JH; Bø, Trond Hellem; Bo, TH; Sivertsen, EA; Rian, E; Forfang, L; Munthe, E; Rosenwald, A; Chiorazzi, M; Jonassen, Inge; Staudt, LM; Smeland, E.B. 2007. Characterization of early stages of human B cell development by gene expression profiling. Journal of Immunology. 179: 3662-3671.
  • Petersen, Kjell; Øyan, Anne Margrete; Rostad, Kari; Olsen, Sue; Bø, Trond Hellem; Salvesen, Helga; Gjertsen, Bjørn Tore; Bruserud, Øystein; Halvorsen, Ole Johan; Akslen, Lars A.; Steen, Vidar Martin; Jonassen, Inge; Kalland, Karl-Henning. 2007. Comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization. Analytical Biochemistry. 366: 46-58. doi: 10.1016/j.ab.2007.03.013
  • Rostad, Kari; Mannelqvist, Monica; Halvorsen, Ole Johan; Øyan, Anne Margrete; Bø, Trond Hellem; Stordrange, Laila; Olsen, Sue; Haukaas, Svein Andreas; Lin, Biaoyang; Hood, Leroy; Jonassen, Inge; Akslen, Lars A.; Kalland, Karl-Henning. 2007. ERG upregulation and related ETS transcription factors in prostate cancer. International Journal of Oncology. 30: 19-32.
  • Skjærven, Lars; Jonassen, Inge; Reuter, Nathalie. 2007. TMM@: a web application for the analysis of transmembrane helix mobility. BMC Bioinformatics. 8. 8 pages. doi: 10.1186/1471-2105-8-232
  • Stansberg, Christine; Vik-Mo, Audun Osland; Holdhus, Rita; Breilid, Harald; Srebro, Boleslaw; Petersen, Kjell; Jørgensen, Hugo Arild; Jonassen, Inge; Steen, Vidar Martin. 2007. Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation. BMC Genomics. 8. doi: 10.1186/1471-2164-8-94
  • Suhr, Mai Lill; Dysvik, Bjarte; Bruland, Ove; Warnakulasauriya, Saman; Amaratunga, Asoka N.; Jonassen, Inge; Vasstrand, Endre N.; Ibrahim, Salah Osman. 2007. Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users. Oncology Reports. 18: 1061-1075.
  • Sælensminde, Gisle; Saelensminde, G; Halskau, Øyvind; Halskau, O; Helland, Ronny; Willassen, Nils Peder; Jonassen, I. 2007. Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins. Extremophiles. 11: 585-596. doi: 10.1007/s00792-007-0072-3
  • Øyan, Anne Margrete; Bø, Trond Hellem; Jonassen, Inge; Ulvestad, Elling; Gjertsen, Bjørn Tore; Bruserud, Øystein; Kalland, Karl-Henning. 2007. Global gene expression in classification, pathogenetic understanding and identification of therapeutic targets in Acute Myeloid Leukemia. Current Pharmaceutical Biotechnology. 8: 344-354. doi: 10.2174/138920107783018435
  • Dysvik, Bjarte; Vasstrand, Endre N.; Løvlie, Roger; Osman, A-Aziz Elgindi; Kross, Kenneth Wilfred; Aarstad, Hans J.; Johannessen, Anne Chr.; Ibrahim, Salah Osman; Jonassen, Inge. 2006. Gene Expression Profiles of Head and Neck Carcinomas from Sudanese and Norwegian Patients Reveal Common Biological Pathways Regardless of Race and Lifestyle. Clinical Cancer Research. 12: 1109-1120. doi: 10.1158/1078-0432.CCR-05-0115
  • Jonassen, Inge; Klose, Daniel; Taylor, William R. 2006. Protein model refinement using structural fragment tessellation. Computational biology and chemistry (Print). 30: 360-366.
  • Kalland, Karl-Henning; Rostad, Kari; Mannelqvist, Monica; Halvorsen, Ole Johan; Øyan, Anne Margrete; Bø, Trond Hellem; Olsen, Sue; Haukaas, Svein Andreas; Lin, Biaoyang; Hood, Leroy; Jonassen, Inge; Akslen, Lars A. 2006. Global gene expression analysis of transcription factors in prostate cancer and cell lines. International Journal of Molecular Medicine. 18: S27. Published 2006-10-14.
  • Malde, Ketil; Schneeberger, Korbinian; Coward, Eivind; Jonassen, Inge. 2006. RBR: library-less repeat detection for ESTs. Bioinformatics. 22: 2232-2236.
  • Rostad, Kari; Mannelqvist, Monica; Halvorsen, Ole Johan; Øyan, Anne Margrete; Bø, Trond Hellem; Ulvestad, Elling; Olsen, Sue; Haukaas, Svein Andreas; Hood, Leroy; Jonassen, Inge; Akslen, Lars A.; Kalland, Karl-Henning. 2006. ERG upregulation in relation to other transcription factors in prostate cancer. NBS-nytt. 1: 72.
  • Sakariassen, Per Øystein; Prestegarden, Lars; Wang, Jian; Skaftnesmo, Kai Ove; Mahesparan, Rupavathana; Molthoff, Carla; Sminia, Peter; Sundlisæter, Eirik; Misra, Anjan; Tysnes, Berit Bølge; Chekenya, Martha; Peters, Hans; Lende, Gabriel; Kalland, Karl-Henning; Øyan, Anne Margrete; Petersen, Kjell; Jonassen, Inge; van der Kogel, Albert; Feuerstein, Burt G.; Terzis, A. Jorge A.; Bjerkvig, Rolf; Enger, Per Øyvind. 2006. Angiogenesis-independent tumor growth mediated by stem-like cancer cells. Proceedings of the National Academy of Sciences of the United States of America. 103: 16466-16471. doi: 10.1073/pnas.0607668103
  • Taylor, William R.; Lin, KA; Klose, D; Fraternali, F; Jonassen, Inge. 2006. Dynamic domain threading. Proteins: Structure, Function, and Genetics. 64: 601-614.
  • Øyan, Anne Margrete; Bø, Trond Hellem; Jonassen, Inge; Gjertsen, Bjørn Tore; Bruserud, Øystein; Kalland, Karl-Henning. 2006. cDNA microarray analysis of non-selected cases of acute myeloid leukemia demonstrates distinct clustering independent of cytogenetic aberrations and consistent with morphological signs of differentiation. International Journal of Oncology. 28: 1065-1080.
  • Øyan, Anne Margrete; Bø, Trond Hellem; Jonassen, Inge; Gjertsen, Bjørn Tore; Bruserud, Øystein; Kalland, Karl-Henning. 2006. cDNA microarray analysis of non-selected cases of acute myeloid leukemia demonstrates distinct clustering independent of cytogenetic aberrations and consistent with morphological signs of differentiation. NBS-nytt. 1: 106.
  • Øyan, Anne Margrete; Ånensen, Nina; Bø, Trond Hellem; Stordrange, Laila; Jonassen, Inge; Bruserud, Øystein; Kalland, Karl-Henning; Gjertsen, Bjørn Tore. 2006. The early gene expression signature of acute myeloid leukemia (AML) blasts during in vivo chemotherapy. International Journal of Molecular Medicine. 18: S65. Published 2006-10-13.
  • Halvorsen, Ole Johan; Rostad, Kari; Øyan, Anne Margrete; Bø, Trond Hellem; Stordrange, Laila; Olsen, Sue; Haukaas, Svein Andreas; Hood, Leroy; Jonassen, Inge; Kalland, Karl-Henning; Akslen, Lars A. 2005. Single-minded 2 homolog gene is overexpressed in prostate cancer. Virchows Archiv. 447: 432-432.
  • Halvorsen, Ole Johan; Øyan, Anne Margrete; Bø, Trond Hellem; Olsen, Sue; Rostad, Kari; Haukaas, Svein Andreas; Bakke, August; Marzolf, Bruz; Dimitrov, Krassen; Stordrange, Laila; Lin, Biaoyang; Jonassen, Inge; Hood, Leroy; Akslen, Lars A.; Kalland, Karl-Henning. 2005. Gene expression profiles in prostate cancer: Association with patient subgroups and tumour differentiation. International Journal of Oncology. 26: 329-336.
  • Hjelmervik, Trond Ove; Petersen, Kjell; Jonassen, Inge; Jonsson, Roland; Bolstad, Anne Isine. 2005. Gene expression profiling of minor salivary glands clearly distinguishes primary Sjögren's syndrome patients from healthy control subjects. Arthritis and Rheumatism. 52: 1534-1544. doi: 10.1002/art.21006
  • Ibrahim, Salah Osman; Dysvik, Bjarte; Vasstrand, Endre N.; Løvlie, Roger; Elgindi, O. A-Aziz; Kross, Kenneth Wilfried; Aarstad, Hans Jørgen; Johannessen, Anne Chr.; Jonassen, Inge. 2005. Gene expression profile in oral and head and neck carcinomas between patients from Sudan and Norway. Oral Oncology. 41;1: 157-158.
  • Kalland, Karl-Henning; Halvorsen, Ole Johan; Rostad, Kari; Mannelqvist, Monica; Øyan, Anne Margrete; Bø, Trond Hellem; Stordrange, Laila; Olsen, Sue; Haukaas, Svein Andreas; Hood, Leroy; Jonassen, Inge; Akslen, Lars A. 2005. Overexpression of ERG and SIM2 transcription factors in prostate cancer. International Journal of Molecular Medicine. 16: S76-S76.
  • Kim, Junhyong; Jonassen, Inge. 2005. Guest editorial: WABI special section part II. IEEE/ACM Transactions on Computational Biology & Bioinformatics. 2: 1-2. doi: 10.1109/TCBB.2005.11
  • Malde, Ketil; Coward, Eivind; Jonassen, Inge. 2005. A graph based algorithm for generating EST consensus sequences. Bioinformatics. 21: 1371-1375. Published 2005-04-15.
  • Schneeberger, Korbinian; Malde, Ketil; Coward, Eivind; Jonassen, Inge. 2005. Masking repeats while clustering ESTs. Nucleic Acids Research. 33: 2176-2180.
  • Øyan, Anne Margrete; Bø, Trond Hellem; Jonassen, Inge; Ulvestad, Elling; Gjertsen, Bjørn Tore; Kalland, Karl-Henning; Bruserud, Øystein. 2005. CD34 expression in native human acute myelogenous leukemia blasts: Differences in CD34 membrane molecule expression are associated with different gene expression profiles. Cytometry. 64B: 18-27. doi: 10.1002/cyto.b.20044
  • Bø, Trond Hellem; Dysvik, Bjarte; Jonassen, Inge. 2004. LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Research. 32: art. no.-e34.
  • Eidhammer, Ingvar; Aasland, Rein; Coward, Eivind; Jonassen, Inge. 2004. Utdanningsmuligheter innen bioinformatikk ved UIB. NBS-nytt. 28: 8.
  • Eidhammer, Ingvar; Jonassen, Inge; Taylor, William R. 2004. PROTEIN BIOINFORMATICS An Algorithmic Approach to Sequence and Structure Analysis. 355 pages. ISBN: 0-470-84839-1.
  • Flikka, Kristian; Yadetie, Fekadu; Lægreid, Astrid; Jonassen, Inge. 2004. XHM: A system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 5: 117.
  • Flikka, Kristian; Yadetie, Fekadu; Lægreid, Astrid; Jonassen, Inge. 2004. XHM: a system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 5. doi: 10.1186/1471-2105-5-117
  • Flikka, Kristian; Yadetie, Fekadu; Lægreid, Astrid; Jonassen, Inge. 2004. XHM: a system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 5. doi: 10.1186/1471-2105-5-117
  • Hjelmervik, Trond Ove; Petersen, Kjell; Jonassen, Inge; Jonsson, Roland; Bolstad, Anne Isine. 2004. Gene expression profiling of minor salivary glands in primary Sjögren's syndrome clearly groups patients and healthy control indiviluals. Arthritis and Rheumatism. 50: S577-S577.
  • Jonassen, Inge; Kim, Junhyong. 2004. Algorithms in Bioinformatics, proceeings of 4th international workshop WABI 2004. Springer. 476 pages. ISBN: 3-540-23018-1.
  • Kim, Junhyong; Jonassen, Inge. 2004. Guest Editorial: WABI Special Section Part 1. IEEE/ACM Transactions on Computational Biology & Bioinformatics. 1: 137-138.
  • Taylor, William R.; Jonassen, Inge. 2004. A structural pattern-based method for protein fold recognition. Proteins: Structure, Function, and Genetics. 56: 222-234.
  • Wang, Junbai; Bø, Trond Hellem; Bo, TH; Jonassen, Inge; Myklebost, Ola; Hovig, Johannes Eivind; Hovig, Eivind. 2004. Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. BMC Bioinformatics. 4: art. no.-60.
  • Ward, Naomi; Larsen, Øivind; Bruseth, Live J.; Jensen, Harald B; Birkeland, Nils-Kåre; Grindhaug, Svenn Helge; Eidhammer, Ingvar; Jonassen, Inge; Lillehaug, Johan; Eisen, Jonathan. 2004. Genomic insights into methanotrophy: The complete genome sequence of Methylococcus capsulatus (Bath). PLoS biology. 2: 1616-1628.
  • Malde, Ketil; Coward, Eivind; Jonassen, Inge. 2003. Fast Sequence Clustering Using a Suffix Array Algorithm. Bioinformatics. 19: 1221-1226.
  • Wang, Junbai; Bø, Trond; Jonassen, Inge; Myklebost, Ola; Hovig, Eivind. 2003. Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. BMC Bioinformatics. 4: 60.
  • Jonassen, Inge. 2000. Methods for discovering conserved patterns in protein sequences and structures. 143-166. In:
    • Higgins, Des; Taylor, Willie. 2000. Bioinformatics. Sequence, structure and databanks. Oxford University Press. ISBN: 0-19-963790-3.
  • Jonassen, Inge. 2000. Discovering patterns conserved in sets of unaligned protein sequences. 33-52. In:
    • Webster, David M. 2000. Protein Structure Prediction (volume 143 in the series Methods in Molecular Biology). ISBN: 0-89603-637-5.
  • Jonassen, Inge; Eidhammer, Ingvar; Grindhaug, Svenn Helge; Taylor, William R. 2000. Searching the protein structure databank with weak sequence patterns and structural constraints. Journal of Molecular Biology. 304: 599-619.
  • Jonassen, Inge; Eidhammer, Ingvar; Taylor, William R. 1999. Discovery of Local Packing Motifs in Protein Structures. Proteins: Structure, Function, and Genetics.
  • Brazma, Alvis; Jonassen, Inge. 1998. Tutorial: Sequence Pattern Discovery Methods. ISMB'98. 69 pages.
  • Brazma, Alvis; Jonassen, Inge; Eidhammer, Ingvar; Gilbert, David. 1998. Approaches to the automatic discovery of patterns in biosequences. Journal of Computational Biology. 5: 277-304.
  • Brazma, Alvis; Jonassen, Inge; Vilo, Jaak. 1998. Workshop: Sequence Pattern Discovery Methods (or Data Mining in Biosequences). EMBL-EBI. 60 pages.
  • Brazma, Alvis; Jonassen, Inge; Vilo, Jaak; Ukkonen, Esko. 1998. Predicting Gene Regulatory Elements in Silico on a Genomic Scale. Genome Research. 8: 1202-1215.
  • Brazma, Alvis; Jonassen, Inge; Eidhammer, Ingvar; Ukkonen, Esko. 1997. Relation patterns and their automatic discovery in biosequences. Reports in Informatics. 135. Institutt for informatikk. 15 pages.
  • Eidhammer, Ingvar; Gilbert, David; Jonassen, Inge; Ratnayake, Madu. 1997. A constraint based structure description language for biosequences. Reports in Informatics. 133. Institutt for Informatikk, UiB. 42 pages.
  • Jonassen, Inge. 1997. Efficient discovery of conserved patterns using a pattern graph. Computer Applications in the Biosciences. 13: 509-522.
  • Jonassen, Inge. 1996. Efficient discovery of conserved patterns using a pattern graph. Reports in Informatics. 118. Inst. for Informatikk, UiB. 27 pages.
  • Jonassen, Inge. 1996. Methods for fiding motifs in sets of related biosequences. Inst. for informatikk, UiB, Bergen. 145 pages.
  • Jonassen, Inge; Helgesen, Carsten; Higgins, Desmond. 1996. Scoring function for pattern discovery programs taking into account sequence diversity. Reports in Informatics. 116. Institutt for Informatikk, UiB. 18 pages.
  • Brazma, Alvis; Jonassen, Inge; Eidhammer, Ingvar; Gilbert, David. 1995. Approaches to the automatic discovery of patterns in biosequences. Reports in Informatics. 113. Institutt for Informatikk, UiB. 42 pages.
  • Jonassen, Inge; Collins, John F.; Higgins, Desmond G. 1995. Finding flexible patterns in unaligned protein sequences. Protein Science. 4: 1587-1595.
  • Jonassen, Inge; Collins, John F.; Higgins, Desmond G. 1995. Finding flexible patterns in unaligned protein sequences. Protein Science. 4: 1587-1595.

More information in national current research information system (CRIStin)