Inge Jonassen's picture
Inge
Jonassen
Professor
Visit Address: 
HIB - Thormøhlensgt. 55
5020 Bergen
Postal Address: 
Postboks 7803
5020 Bergen
Phone: 
+47 55 58 47 13
+47 905 24 316
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Books
  • 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.
  • Jonassen, Inge; Kim, Junhyong. 2004. Algorithms in Bioinformatics, proceeings of 4th international workshop WABI 2004. Springer. 476 pages. ISBN: 3-540-23018-1.
Journal articles
  • 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; Hovland, Runar; 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 Science 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 Science 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.
  • 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.
  • 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.
  • 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; 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; 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; Ukkonen, Esko. 1998. Predicting Gene Regulatory Elements in Silico on a Genomic Scale. Genome Research. 8: 1202-1215.
  • Jonassen, Inge. 1997. Efficient discovery of conserved patterns using a pattern graph. Computer Applications in the Biosciences. 13: 509-522.
  • 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.
Reports and theses
  • Brazma, Alvis; Jonassen, Inge. 1998. Tutorial: Sequence Pattern Discovery Methods. ISMB'98. 69 pages.
  • 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; 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. 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.
Book sections
  • 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.

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