Inge
Jonassen
Professor
Visit Address:
HIB - Thormøhlensgt. 55
Postal Address:
Postboks 7803
5020 Bergen
Phone:
+47 55 58 47 13
+47 905 24 316
E-mail:
Books
- 2004. PROTEIN BIOINFORMATICS An Algorithmic Approach to Sequence and Structure Analysis. 355 pages. ISBN: 0-470-84839-1.
- 2004. Algorithms in Bioinformatics, proceeings of 4th international workshop WABI 2004. Springer. 476 pages. ISBN: 3-540-23018-1.
Journal articles
- 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 (Print). 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 Genetics. 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 (Print). 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 Genetics. 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. 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. 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 Genetics. 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. 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 Genetics.
- 1998. Approaches to the automatic discovery of patterns in biosequences. Journal of Computational Biology. 5: 277-304.
- 1998. Predicting Gene Regulatory Elements in Silico on a Genomic Scale. Genome Research. 8: 1202-1215.
- 1997. Efficient discovery of conserved patterns using a pattern graph. Computer Applications in the Biosciences. 13: 509-522.
- 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.
Reports and theses
- 1998. Tutorial: Sequence Pattern Discovery Methods. ISMB'98. 69 pages.
- 1998. Workshop: Sequence Pattern Discovery Methods (or Data Mining in Biosequences). EMBL-EBI. 60 pages.
- 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.
- 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.
Book sections
- 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. 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.
More information in national current research information system (CRIStin)