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+ 1997

Some relevant poster presentations at the Fifth International Conference on Intelligen Systems for Molecular Biology (ISMB97) (Halkidiki, Greece, June 21-25, 1997)

Some relevant presentations at the Ninth International Genome Sequencing and Analysis Conference (GSAC97) (Hilton Head, SC, Sept 13-16, 1997)

Georgia Tech International Conference on Bioinformatics: Gene Discovery in silico: talks and posters (Atlanta, GA, Nov 6-9, 1997)

  1. S. Audic, J.-M. Claverie (1997)
    "Detection of eukaryotic promoters using Markov transition matrices",
    Computer & Chemistry, 21(4): 223-227.
    [ Medline entry ] [ PDF ]

  2. M.A. Basrai, P. Hieter, J.D. Boeke (1997).
    "Small open reading frames: beautiful needle in the haystack",
    Genome Research, 7(8): 768-772.
    [ PDF]

  3. A Brazma, J Vilo, E Ukkonen, K Valtonen (1997),
    "Data mining for regulatory elements in yeast genome",
    ISMB97,65-74.
    [ Medline entry]

  4. C. Burge (1997),
    Identification of genes in human genomic DNA
    (Ph. D thesis, Stanford University, Stanford, CA).
    [ PDF]

  5. C. Burge, S. Karlin (1997),
    "Prediction of complete gene structures in human genomic DNA",
    Journal of Molecular Biology , 268: 78-94.
    [abstract] [ Medline entry ] [ PDF]

    [ GENSCAN is at: http://genes.mit.edu/GENSCAN.html ]

  6. Q.K. Chen, G.Z. Hertz, G.D. Stormo (1997),
    "PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices",
    Computer Applications in Biosciences, 13: 29-35.
    [abstract]

  7. J.-M. Claverie (1997)
    "Computational methods for the identification of genes in vertebrate genomic sequences",
    Human Molecular Genetics, 6(10)(review issue): 1735-1744.
    [abstract] [ html ] [ PDF]

  8. J.-M. Claverie (1997)
    "Exon detection by similarity searches",
    Methods in Molecular Biology, 68: 283-313.

  9. J.-M. Claverie, O. Poirot, F. Lopez (1997),
    "The difficulty of identifying genes in anonymous vertebrate sequences ",
    Computer & Chemistry, 21(4): 203-214.
    [ Medline entry ] [ PDF ]

  10. E.M. Crowley, K. Roeder, M. Bina (1997),
    "A statistical model for locating regulatory regions in genomic DNA",
    Journal of Molecular Biology , 268: 8-14.
    [abstract] [ PDF]

  11. M.E. Dalphin, C.M. Brown, P.A. Stockwell, W.P. Tate (1997),
    "The translational signal database, TransTerm: more organisms, complete genome",
    Nucleic Acids Research, 25(1): 246-247.
    [abstract]

    [ TransTerm is at: http://biochem.otago.ac.nz:800/Transterm/homepage.html ]

  12. SJ de Souza, M Long, L Schoenbach, SW Roy, W Gilbert (1997),
    "The correlation between introns and the three-dimensional structure of proteins",
    [ Medline entry]

  13. L. Duret, P. Bucher (1997),
    "Searching for regulatory elements in human noncoding sequences",
    Current Opinions in Structural Biology, 7: 399-406.
    [abstract]

  14. J.W. Fickett and A. G. Hatzigeorgiou (1997),
    "Eukaryotic promoter recognition",
    Genome Research, 7(9): 861-878.
    [ PDF]

  15. K. Frech, K. Quandt, T. Werner (1997),
    "Software for the analysis of DNA sequence elements of transcription",
    Computer Applications in Biosciences, 13: 89-97.

  16. K. Frech, K. Quandt, T. Werner (1997),
    "Finding protein-binding sites in DNA sequences: the next generation",
    Trends in Biochemical Sciences, 22: 103-104.

  17. W Fujibuchi, M Kanehisa (1997),
    "Prediction of gene expression specificity by promoter sequence patterns",
    DNA Research, 4:81-90.

  18. W Gilbert, SJ de Souza, M Long (1997),
    "Origin of genes",
    Proceedings of the National Academy of Sciences, 94:7698-7703.
    [ Medline entry]

  19. P Guerdoux-Jamet, A Henaut, P Nitschke, JL Risler (1997),
    "Using codon usage to predict genes origin: is the Escherichia coli outer membrane a patchwork of products from different genomes?",
    DNA Research, 4(4):257-265.
    [ Medline entry ]

  20. R. Guigo (1997),
    "Computational gene identification: an open problem",
    Computer & Chemistry, 21(4): 215-222.
    [abstract] [ Medline entry] [ PDF]

  21. J. Henderson, S Salzberg, and K. Fasman (1997),
    "Finding genes in human DNA with a hidden Markov model",
    Journal of Computational Biology, 4(2): 119-126.

    [abstract] [ preprint (postscript) ]

  22. M Hirosawa, T Sazuka, T Yada (1997),
    "Prediction of translation initiation sites on the genome of Synechocystis sp. strain PCC6803 by Hidden Markov model",
    DNA Research, 4(3):179-184.
    [ Medline entry]

  23. X. Huang, M.D. Adams, H. Zhou, A.R. Kerlavage (1997),
    "A tool for analyzing and annotating genomic sequences",
    submitted.

    [ AAT (analysis and annotation tool) is at http://genome.cs.mtu.edu/aat.html ]

  24. A.L. Hughes, M. Yeager (1997)
    "Comparative evolutionary rates of introns and exons in murine rodents",
    Journal of Molecular Evolution, 45: 125-130.
    [abstract]

  25. Anders Krogh (1997),
    "Two methods for improving performace of a HMM and their application for gene finding",
    in ISMB97, 179-186.
    [ Medline entry]

  26. D.J. Lipman (1997),
    "Making (anti)sense of non-coding sequence conservation",
    Nucleic Acids Research, 25(18): 3580-3583.
    [abstract]

  27. M Long, SJ de Souza, W Gilbert (1997),
    "The yeast splice site revisited: new exon consensus from genomic analysis",
    Cell, 91(6):739-740.

  28. H Nielsen, J Engelbrecht, S Brunak, G von Heijne (1997),
    "A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites",
    International Journal of Neural Systems, 8(5-6):581-599.

  29. O. N. Ozoline, A. A. Deev and M. V. Arkhipova (1997),
    "Non-canonical sequence elements in the promoter structure. Cluster analysis of promoters recognized by Escherichia coli RNA polymerase",
    Nucleic Acids Research, 25(23): 4703-4709.
    [abstract]

  30. Anders Gorm Pedersen and Henrik Nielsen (1997),
    "Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis",
    in ISMB97, 226-233.
    [ Medline entry]

  31. Francine B. Perter, Gary J. Olson, Eric Adam (1997),
    "Compilation and analysis of intein sequences",
    Nucleic Acids Research, 25(6): 1087-1093 .
    [ abstract]

  32. G. Pesole, S. Liuni, G. Grillo, C. Saccone (1997),
    "Structural and compositional features of untranslated regions of eukaryotic mRNAs",
    Gene, 205: 95-102.

  33. Christopher J Rawlings, David Searls (1997),
    "Computational gene discovery and human disease",
    Current Opinion in Genetics & Development, 7(3):416-423.

  34. M.G. Reese, F.H. Eeckman, D. Kulp, D. Haussler (1997)
    "Improved Splice Site Detection in Genie",
    Journal of Computational Biology, 4(3): 311-324.

  35. I.B. Rogozin, L. Milanesi (1997)
    "Analysis of donor splice sites in different eukaryotic organisms",
    Journal of Molecular Evolution, 45: 50-59.
    [abstract]

  36. M.A. Roytberg, T.V. Astahova, M.S. Gelfand (1997)
    "Combinatorial approaches to gene recognition",
    Computer & Chemistry, 21(4): 229-235.
    [ Medline entry ]

  37. AA Salamov, VV Solovyev (1997),
    "Recognition of 3'-processing sites of human mRNA precursors",
    Computer Applications in Biosciences, 13(1):23-28.
    [ Medline entry]

  38. S. Salzberg (1997),
    "A method for identifying splice sites and translational start sites in eukaryotic mRNA",
    Computer Applications in Biosciences, 13(4): 365-376.
    [abstract]

    [ VEIL (the Viterbi Exon-Intron Locator) is at http://www.cs.jhu.edu/labs/compbio/veil.html ]

  39. S. Salzberg, A. Delcher, K. Fasman, and J. Henderson (1997)
    "A decision tree system for finding genes in DNA",
    Technical Report 1997-03, Department of Computer Science, Johns Hopkins University.

    [ MORGAN is at http://www.cs.jhu.edu/labs/compbio/morgan.html ]

  40. S Salzberg, A Delcher, S Kasif, O White (1997),
    "Microbial gene identification using interpolated Markov models",
    submitted.

    [ GLIMMER is at http://www.cs.jhu.edu/labs/compbio/glimmer.html]

  41. J Schug, GC Overton (1997),
    "Modeling transcription factor binding sites with Gibbs Sampling and Minimum Description Length encoding",
    ISMB97 , 268-271.
    [ Medline entry]

  42. Victor Solovyev and Asaf Salamov (1997),
    "The gene-finder computer tools for analysis of human and model organisms genome sequences",
    in ISMB97, 294-302.
    [ Medline entry]

  43. S.H. Sze and P.A. Pevzner (1997)
    "Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment",
    Journal of Computational Biology, 4(3): 297-310.
    [abstract]

  44. S. Tiwari, S. Ramachandran, A. Bhattacharya, S. Bhattacharya, R. Ramaswamy (1997),
    "Prediction of probable genes by Fourier analysis of genomic sequences",
    Computer Applications in Biosciences, 13(3): 263-270.
    [abstract]

  45. A. Wagner (1997)
    "A computational genomics approach to the identification of gene networks",
    Nucleic Acids Research, 25(1): 3594-3604.
    [ abstract] [ Medline entry]

  46. E. Wingender. A.E. Kel, O.V. Kel, H. Karas, T. Heinemeyer, P.Dietze, R. Knuppel, A.G. Romaschenko, N.A. Kolchanov (1997),
    "TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation",
    Nucleic Acids Research, 25(1): 265-268.
    [abstract]

    [for TRANSFAC database, see http://transfac.gbf-braunschweig.de]

  47. C.H. Wu (1997),
    "Artificial neural networks for molecular sequence analysis",
    Computer & Chemistry, 21(4): 237-256.
    [ abstract]

  48. Ying Xu, Richard J. Mural, and Edward C. Uberbacher (1997),
    "Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags",
    in ISMB97, 344-353.
    [ Medline entry]

  49. Y. Xu, E.C. Uberbacher (1997)
    "Automated Gene Identification in Large-Scale Genomic Sequences",
    Journal of Computational Biology, 4(3): 325-338.

  50. T Yada (1997),
    ["Gene identification in prokaryotic genomes using hidden Markov model"] (in Japanese),
    Tanpakushitsu Kakusan Koso, 42(17 Suppl):2993-3000.

  51. T Yada, T sazuka, M Hirosawa (1997),
    "Analysis of sequence patterns surrounding the translation initiation sites on Cyanobacterium genome using the hidden Markov model",
    DNA Research, 4(1):1-7.
    [ Medline entry]

  52. T Yada, Y Totoki, T Ishii, K Nakai (1997),
    "Functional prediction of B. subtilis genes from their regulatory sequences",
    ISMB97, 354-357.
    [ Medline entry]

  53. MQ Zhang (1997),
    "Identification of protein coding regions in the human genome based on quadratic discriminant analysis",
    Proceedings of the National Academy of Sciences (USA), 94: 559-564.
    [abstract] [ Medline entry] [ html ] [ PDF ]

    [the MZEF program can be found at http://www.cshl.org/genefinder]