- E-mailInge.Jonassen@uib.no
- Phone+47 55 58 47 13+47 905 24 316
- Visitor AddressHIB - Thormøhlensgt. 55
- Postal AddressPostboks 78035020 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.
- 2019. Bacterial and archaeal metagenome-assembled genome sequences from Svalbard permafrost. Microbiology Resource Announcements (MRA). 8:e00516-19: 1-3. doi: 10.1128/MRA.00516-19
- 2018. Deblender: A semi-/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples. BMC Bioinformatics. 19: 1-17. doi: 10.1186/s12859-018-2442-5
- 2018. Mathematical modelling of nitric oxide/cyclic GMP/cyclic AMP signalling in platelets. International Journal of Molecular Sciences. 19: 1-21. doi: 10.3390/ijms19020612
- 2018. Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer. PLOS ONE. 13:e0206665: 1-21. doi: 10.1371/journal.pone.0206665
- 2018. Development and testing of an 18S rRNA phylogenetic microarray for marine sediments. Journal of Microbiological Methods. 154: 95-106. doi: 10.1016/j.mimet.2018.10.007
- 2018. Norwegian e-Infrastructure for Life Sciences (NeLS). F1000 Research. 7:968. 15 pages. doi: 10.5256/f1000research.16472.r35600
- 2018. RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol. Aquatic Toxicology. 201: 174-186. doi: 10.1016/j.aquatox.2018.06.003
- 2017. Protected sampling is preferable in bronchoscopic studies of the airway microbiome. ERJ Open Research. 3. doi: 10.1183/23120541.00019-2017
- 2017. GBA2 mutations cause a Marinesco-Sjogren-like syndrome: Genetic and biochemical studies. PLOS ONE. 12:e0169309: 1-10. doi: 10.1371/journal.pone.0169309
- 2017. Expression of Nestin associates with BRCA1 mutations, a basal-like phenotype and aggressive breast cancer. Scientific Reports. 7:1089: 1-12. doi: 10.1038/s41598-017-00862-w
- 2017. DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments. PLOS ONE. 12:e0179443: 1-18. doi: 10.1371/journal.pone.0179443
- 2017. Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts. BMC Cancer. 17:108: 1-13. doi: 10.1186/s12885-017-3109-8
- 2017. Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics. 18:76: 1-11. doi: 10.1186/s12864-016-3416-5
- 2016. Novel SLC19A3 promoter deletion and allelic silencing in biotin-thiamine-responsive basal ganglia encephalopathy. PLOS ONE. 11. doi: 10.1371/journal.pone.0149055
- 2016. Disentangling genetic and epigenetic determinants of ultrafast adaptation. Molecular Systems Biology. 12. doi: 10.15252/msb.20166951
- 2016. High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities. Molecular Ecology. 25: 4392-4406. doi: 10.1111/mec.13761
- 2016. The Atlantic salmon genome provides insights into rediploidization. Nature. 533: 200-205. doi: 10.1038/nature17164
- 2016. RareVariantVis: New tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data. Bioinformatics. 32: 3018-3020. doi: 10.1093/bioinformatics/btw359
- 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
- 2015. Distributed and interactive visual analysis of omics data. Journal of Proteomics. 129: 78-82. doi: 10.1016/j.jprot.2015.05.029
- 2014. Characterization of the 18s rRNA gene for designing universal eukaryote specific primers. PLOS ONE. 9. doi: 10.1371/journal.pone.0087624
- 2014. The Norwegian Bioionformatics Platform. NBS-nytt. 2. 32-35.
- 2013. Filtering duplicate reads from 454 pyrosequencing data. Bioinformatics. 29: 830-836. doi: 10.1093/bioinformatics/btt047
- 2013. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics. 29: 1325-1332. doi: 10.1093/bioinformatics/btt113
- 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
- 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
- 2013. How does sequence variability affect de novo assembly quality? Journal of Natural History. 47: 901-910. doi: 10.1080/00222933.2012.738833
- 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
- 2012. Exome sequencing and genetic testing for MODY. PLOS ONE. 7. 8 pages. doi: 10.1371/journal.pone.0038050
- 2012. CREST--classification resources for environmental sequence tags. PLOS ONE. 7. doi: 10.1371/journal.pone.0049334
- 2012. CREST - classification resources for environmental sequence tags. PLOS ONE. 7: e49334-e49334. Published 2012-11-08. doi: 10.1371/journal.pone.0049334
- 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
- 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
- 2011. Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics. 27: I304-I309. doi: 10.1093/bioinformatics/btr251
- 2011. Exploring the limits of fold discrimination by structural alignment: A large scale benchmark using decoys of known fold. Computational biology and chemistry. 35: 174-188. doi: 10.1016/j.compbiolchem.2011.04.008
- 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
- 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
- 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
- 2011. The genome sequence of Atlantic cod reveals a unique immune system. Nature. 477: 207-210. doi: 10.1038/nature10342
- 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
- 2010. Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics. 26: i420-i425. doi: 10.1093/bioinformatics/btq365
- 2010. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biology. 11. 7 pages. doi: 10.1186/gb-2010-11-9-403
- 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
- 2010. BioXSD: the common data-exchange format for everyday bioinformatics web services. Bioinformatics. 26: i540-i546. doi: 10.1093/bioinformatics/btq391
- 2010. The EMBRACE web service collection. Nucleic Acids Research. 38: W683-W688. doi: 10.1093/nar/gkq297
- 2010. Combined epigenetic and signal transduction therapy modulate specific signal transduction patterns in acute myeloid leukemia. Haematologica. 95: 510-510.
- 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
- 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
- 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
- 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
- 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
- 2009. Probing the "Dark Matter" of protein fold space. Structure. 17: 1244-1252. doi: 10.1016/j.str.2009.07.012
- 2009. Probing the "Dark Matter" of protein fold space. Structure. 17: 1244-1252. doi: 10.1016/j.str.2009.07.012
- 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
- 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
- 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
- 2008. The BREW workshop series: a stimulating experience in PhD education. Briefings in Bioinformatics. 9: 250-253. doi: 10.1093/bib/bbn002
- 2008. Structural fragments in protein model refinement. Protein Peptide Letters. 15: 964-971.
- 2008. Repeats and EST analysis for new organisms. BMC Genomics. 9. 7 pages. doi: 10.1186/1471-2164-9-23
- 2008. Genomic Diversity among Beijing and non-Beijing Mycobacterium tuberculosis Isolates from Myanmar. PLOS ONE. 3: e1973. doi: 10.1371/journal.pone.0001973
- 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
- 2008. Prediction of protein structure from ideal forms. Proteins: Structure, Function, and Bioinformatics. 70: 1610-1619. doi: 10.1002/prot.21913
- 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
- 2007. Characterization of early stages of human B cell development by gene expression profiling. Journal of Immunology. 179: 3662-3671.
- 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
- 2007. ERG upregulation and related ETS transcription factors in prostate cancer. International Journal of Oncology. 30: 19-32.
- 2007. TMM@: a web application for the analysis of transmembrane helix mobility. BMC Bioinformatics. 8. 8 pages. doi: 10.1186/1471-2105-8-232
- 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
- 2007. Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users. Oncology Reports. 18: 1061-1075.
- 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
- 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
- 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
- 2006. Protein model refinement using structural fragment tessellation. Computational biology and chemistry. 30: 360-366.
- 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.
- 2006. RBR: library-less repeat detection for ESTs. Bioinformatics. 22: 2232-2236.
- 2006. ERG upregulation in relation to other transcription factors in prostate cancer. NBS-nytt. 1: 72.
- 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
- 2006. Dynamic domain threading. Proteins: Structure, Function, and Bioinformatics. 64: 601-614.
- 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.
- 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.
- 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.
- 2005. Single-minded 2 homolog gene is overexpressed in prostate cancer. Virchows Archiv. 447: 432-432.
- 2005. Gene expression profiles in prostate cancer: Association with patient subgroups and tumour differentiation. International Journal of Oncology. 26: 329-336.
- 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
- 2005. Gene expression profile in oral and head and neck carcinomas between patients from Sudan and Norway. Oral Oncology. 41;1: 157-158.
- 2005. Overexpression of ERG and SIM2 transcription factors in prostate cancer. International Journal of Molecular Medicine. 16: S76-S76.
- 2005. Guest editorial: WABI special section part II. IEEE/ACM Transactions on Computational Biology & Bioinformatics. 2: 1-2. doi: 10.1109/TCBB.2005.11
- 2005. A graph based algorithm for generating EST consensus sequences. Bioinformatics. 21: 1371-1375. Published 2005-04-15.
- 2005. Masking repeats while clustering ESTs. Nucleic Acids Research. 33: 2176-2180.
- 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
- 2004. LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Research. 32: art. no.-e34.
- 2004. Utdanningsmuligheter innen bioinformatikk ved UIB. NBS-nytt. 28: 8.
- 2004. PROTEIN BIOINFORMATICS An Algorithmic Approach to Sequence and Structure Analysis. 355 pages. ISBN: 0-470-84839-1.
- 2004. XHM: a system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 5. doi: 10.1186/1471-2105-5-117
- 2004. XHM: a system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 5. doi: 10.1186/1471-2105-5-117
- 2004. XHM: A system for detection of potential cross hybridizations in DNA microarrays. BMC Bioinformatics. 5: 117.
- 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.
- 2004. Algorithms in Bioinformatics, proceeings of 4th international workshop WABI 2004. Springer. 476 pages. ISBN: 3-540-23018-1.
- 2004. Guest Editorial: WABI Special Section Part 1. IEEE/ACM Transactions on Computational Biology & Bioinformatics. 1: 137-138.
- 2004. A structural pattern-based method for protein fold recognition. Proteins: Structure, Function, and Bioinformatics. 56: 222-234.
- 2004. Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. BMC Bioinformatics. 4: art. no.-60.
- 2004. Genomic insights into methanotrophy: The complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biology. 2: 1616-1628.
- 2003. Fast Sequence Clustering Using a Suffix Array Algorithm. Bioinformatics. 19: 1221-1226.
- 2003. Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. BMC Bioinformatics. 4: 60.
- 2000. Discovering patterns conserved in sets of unaligned protein sequences. 33-52. In:
- 2000. Protein Structure Prediction (volume 143 in the series Methods in Molecular Biology). ISBN: 0-89603-637-5.
- 2000. Methods for discovering conserved patterns in protein sequences and structures. 143-166. In:
- 2000. Bioinformatics. Sequence, structure and databanks. Oxford University Press. ISBN: 0-19-963790-3.
- 2000. Searching the protein structure databank with weak sequence patterns and structural constraints. Journal of Molecular Biology. 304: 599-619.
- 1999. Discovery of Local Packing Motifs in Protein Structures. Proteins: Structure, Function, and Bioinformatics.
- 1998. Tutorial: Sequence Pattern Discovery Methods. ISMB'98. 69 pages.
- 1998. Approaches to the automatic discovery of patterns in biosequences. Journal of Computational Biology. 5: 277-304.
- 1998. Workshop: Sequence Pattern Discovery Methods (or Data Mining in Biosequences). EMBL-EBI. 60 pages.
- 1998. Predicting Gene Regulatory Elements in Silico on a Genomic Scale. Genome Research. 8: 1202-1215.
- 1997. Relation patterns and their automatic discovery in biosequences. Reports in Informatics. 135. Institutt for informatikk. 15 pages.
- 1997. A constraint based structure description language for biosequences. Reports in Informatics. 133. Institutt for Informatikk, UiB. 42 pages.
- 1997. Efficient discovery of conserved patterns using a pattern graph. Computer Applications in the Biosciences. 13: 509-522.
- 1996. Efficient discovery of conserved patterns using a pattern graph. Reports in Informatics. 118. Inst. for Informatikk, UiB. 27 pages.
- 1996. Methods for fiding motifs in sets of related biosequences. Inst. for informatikk, UiB, Bergen. 145 pages.
- 1996. Scoring function for pattern discovery programs taking into account sequence diversity. Reports in Informatics. 116. Institutt for Informatikk, UiB. 18 pages.
- 1995. Approaches to the automatic discovery of patterns in biosequences. Reports in Informatics. 113. Institutt for Informatikk, UiB. 42 pages.
- 1995. Finding flexible patterns in unaligned protein sequences. Protein Science. 4: 1587-1595.
- 1995. Finding flexible patterns in unaligned protein sequences. Protein Science. 4: 1587-1595.
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