Some publications in bioinformatics - I. Jonassen:

  1. Methods for finding motifs in sets of related biosequences
    Inge Jonassen.
    Dr. scient thesis, 1996, Dept. of Informatics, Univ. of Bergen.
    More information about the thesis is available, and the introductory part is available in postscript format.
    The thesis also contains the papers 2-6 below:
  2. Approaches to the automatic discovery of patterns in biosequences.
    Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David Gilbert.
    Journal of Computational Biology 5, 279-305 (1998)
    Earlier (and longer) version:
    Dept. of Informatics, Univ. of Bergen, Reports in Informatics no 113, Dec. 1995.
    Postscript paper.
  3. Finding flexible patterns in unaligned protein sequences.
    Inge Jonassen, John F. Collins, Desmond Higgins.
    Protein Science 1995;4(8):1587-1595.
    Abstract
  4. Efficient discovery of conserved patterns using a pattern graph.
    Inge Jonassen.
    CABIOS 13, 509-522 (1997)
    Longer version: Dept. of Informatics, Univ. of Bergen, Reports in Informatics no 118, March 1996.
    Postscript paper, PROSITE test cases.
  5. Scoring function for pattern discovery programs taking into account sequence diversity.
    Inge Jonassen, Carsten Helgesen, Desmond Higgins.
    Dept. of Informatics, Univ. of Bergen, Reports in Informatics no 116, Febr. 1996.
    Postscript paper, Test cases.
  6. Discovering patterns and subfamilies in biosequences
    Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo
    in Proceedings of the Fourth International Conference on Intellignent Systems for Molecular Biology (ISMB-96), AAAI Press 1996, p 34-43.
    More information.
  7. A Constraint Based Structure Description Language for Biosequence
    Ingvar Eidhammer, David Gilbert, Inge Jonassen, Madu Ratnayake
    Dept. of Informatics, Univ. of Bergen, Reports in Informatics no 133, May 1997, also Report 1997/04 from Dept. of Computer Science, City University, London, UK.
    More information, Postscript paper.
  8. StructWeb: Bioseequence structure searching on the Web using clp(FD)
    David Gilbert, Ingvar Eidhammer, Inge Jonassen
    Presented at the CP'97 workshop on Constraint Reasoning on the Internet.
    Also report 1997/05 from Dept. of Computer Science, City University, London, UK.
    More information, postscript paper, Web server
  9. CBSDL: a constraint based structure description language for biosequences
    David Gilbert, Ingvar Eidhammer, Inge Jonassen
    Presented at the Constraints and Bioinformatics/Biocomputing workshop at CP'97
    More information.
  10. Relation patterns and their automatic discovery in biosequences
    Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, Esko Ukkonen
    Dept. of Informatics, Univ. of Bergen, Reports in Informatics no 135, June 1997.
    More information, Postscript paper.
  11. Structure Prediction of the Zinc-finger protein family by the use of a parallel genetic algorithm
    Kjell Petersen, Ingvar Eidhammer, Rein Aasland, Inge Jonassen
    Proceedings of NIK97 (Norwegian Informatics Conference), p 57-68, Tapir 1997.
  12. Sequence Pattern Discovery
    Alvis Brazma, Inge Jonassen
    Tutorial given at ISMB-98
  13. Pattern discovery in biosequences
    Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen
    Lecture Notes in Artificial Intelligence, Vol. 1433, Springer, 1998, p. 255-270.
  14. Discovery of Local Packing Motifs in Protein Structures
    Inge Jonassen, Ingvar Eidhammer, William R. Taylor
    Proteins: Structure, Function, and Genetics 34, 206-219 (1999).
  15. Prediction of Regulatory Elements in Silico on a Genomic Scale
    Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen
    Genome Research 8, 1202-1215 (1998)
    Suppportive WWW site
  16. Discovering patterns conserved in sets of unaligned protein sequences
    Inge Jonassen
    Chapter 3 in Predicting Protein Structure edited by D.M.Webster, Methods in Molecular Biology series, Humana Press, 2000.
  17. Structure Comparison and Structure Patterns
    Ingvar Eidhammer, Inge Jonassen, William R. Taylor
    Journal of Computational Biology 7, 685-716 (2000).
    Earlier version:
    Dept. of Informatics, Univ. of Bergen, Reports in Informatics no 174, July 1999.
    Postscript paper
  18. InterPro - An integrated documentation resource for protein families, domains and functional sites
    R.Apweiler, T.K.Attwood, A.Bairoch, A.Bateman, E.Birney, P.Bucher, J-J.Codani, F.Corpet, M.D.R.Croning, R.Durbin, T.Etzold, W.Fleischmann, J.Gouzy, H.Hermjakob, I.Jonassen, D.Kahn, A.Kanapin, R.Schneider, F.Servant, E.Zdobnov
    CCP11 Newsletter Issue 10 - 1 March 2000
  19. Searching the Protein Structure Databank with Weak Sequence Patterns and Structural Constraints
    Inge Jonassen, Ingvar Eidhammer, Svenn Grindhaug, William R. Taylor
    Journal of Molecular Biology, 304 (4), 597-617 (2000).
    Supportive web site
  20. Structure Motif Discovery and Mining the PDB
    Inge Jonassen, Ingvar Eidhammer, Darrell Conklin, William R. Taylor
    German Conference on Bioinformatics 2000
    pdf file
  21. Methods for discovering conserved patterns in protein sequences and structures
    Inge Jonassen
    Chapter 7 in Bioinformatics: Sequence Structure and Databanks edited by Des Higgins and Willie Taylor, Practical Approach Series, Oxford University Press 2000.
  22. Mining for putative regulatory elements in the yeast genome using gene expression data
    Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan Robinson, Esko Ukkonen
    Proceedings of the eighth internaional conference on intelligent systems for molecular biology, ISMB2000, AAAI Press, 384-394.
  23. J-Express: exploring gene expression data using Java
    Bjarte Dysvik and Inge Jonassen
    Bioinformatics 17 (4), 369-370.
  24. New feature subset selection procedures for classification of expression profiles
    Trond H. BÝ and Inge Jonassen
    Genome Biology 3 (4), 0017.1-0017.11
  • This list is not updated - see more references google scholar or pubmed
  • See also Inge Jonassen's presentations page.

    Inge Jonassen's Home page.