computational gene recognition

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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. promoter/TF
    S Audic, JM Claverie (1997) "Detection of eukaryotic promoters using Markov transition matrices", Computers & Chemistry, 21(4): 223-227.
    [ abstract] [ Medline entry ] [ PDF ]

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

  3. promoter/TF
    A Brazma, J Vilo, E Ukkonen, K Valtonen (1997), "Data mining for regulatory elements in yeast genome", Proceedings of the fifth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.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]
    [supplement material: http://genes.mit.edu/GENSCAN.html (GENSCAN) ]

  6. promoter/TF
    QK Chen, GZ Hertz, GD 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. JM Claverie (1997) "Computational methods for the identification of genes in vertebrate genomic sequences", Human Molecular Genetics, 6(10)(review issue): 1735-1744.
    [abstract] [abstract] [ html ] [ PDF]

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

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

  10. promoter/TF
    EM 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. translation
    ME Dalphin, CM Brown, PA Stockwell, WP Tate (1997), "The translational signal database, TransTerm: more organisms, complete genome", Nucleic Acids Research, 25(1): 246-247.
    [abstract]
    [supplement material: http://biochem.otago.ac.nz:800/Transterm/homepage.html (TransTerm)]

  12. splicing
    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. promoter/TF
    L Duret, P Bucher (1997), "Searching for regulatory elements in human noncoding sequences", Current Opinion in Structural Biology, 7: 399-406.
    [abstract]

  14. promoter/TF
    JW Fickett, AG Hatzigeorgiou (1997), "Eukaryotic promoter recognition", Genome Research, 7(9): 861-878.
    [ PDF]

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

  18. splicing
    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", Journal of Molecular Medicine, 75:389-393.

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

  22. annotation
    Nomi L Harris (1997), "Genotator: a workbench for sequence annotation", Genome Research, 7(7):754-762.
    [abstract]

  23. J Henderson, S Salzberg, K Fasman (1997), "Finding genes in human DNA with a hidden Markov model", Journal of Computational Biology, 4(2): 119-126.
    [abstract] [ preprint (postscript) ] [supplement material: http://www.tigr.org/~salzberg/veil.html (vail)]

  24. translation
    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]

  25. similarity
    X Huang, MD Adams, H Zhou, AR Kerlavage (1997), "A tool for analyzing and annotating genomic sequences", Genomics, 46:37-45.

    [supplement material: http://genome.cs.mtu.edu/aat.html (AAT)]

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

  27. Marilyn Kozak (1997), "Recognition of AUG and alternative initiator codons is augmented by G in position +4 but is not generally affected by the nucleotides in positions +5 and +6", EMBO Journal, 16:2482-2492.

  28. Anders Krogh (1997), "Two methods for improving performace of a HMM and their application for gene finding", Proceedings of the fifth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.179-186.
    [ Medline entry]

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

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

  31. 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.

  32. promoter/TF
    ON Ozoline, AA Deev, MV 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]

  33. translation
    Anders Gorm Pedersen and Henrik Nielsen (1997), "Neural network prediction of translation initiation sites in eukaryotes: perspectives for EST and genome analysis", Proceedings of the fifth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.226-233.
    [ Medline entry]

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

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

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

  37. splicing
    MG Reese, FH Eeckman, D Kulp, D Haussler (1997) "Improved splice site detection in genie", Journal of Computational Biology, 4(3): 311-324.

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

  39. MA Roytberg, TV Astahova, MS Gelfand (1997) "Combinatorial approaches to gene recognition", Computers & Chemistry, 21(4): 229-235.
    [ Medline entry ]

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

  41. splicing
    translation
    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]

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

    [supplement material: http://www.tigr.org/~salzberg/morgan.html (MORGAN)]

  43. S Salzberg, A Delcher, S Kasif, O White (1997), "Microbial gene identification using interpolated Markov models", Nucleic Acids Research, 26(2):544-548.
    [supplement material: http://www.tigr.org/~salzberg/glimmer.html (GLIMMER)]

  44. promoter/TF
    J Schug, GC Overton (1997), "Modeling transcription factor binding sites with Gibbs sampling and minimum description length encoding", Proceedings of the fifth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.268-271.
    [ Medline entry]

  45. Victor Solovyev, Asaf Salamov (1997), "The gene-finder computer tools for analysis of human and model organisms genome sequences", Proceedings of the fifth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.294-302.
    [ Medline entry]

  46. similarity
    SH Sze, PA Pevzner (1997), "Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment", Journal of Computational Biology, 4(3): 297-310.
    [abstract]

  47. 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]

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

  49. promoter/TF
    E Wingender. AE Kel, OV Kel, H Karas, T Heinemeyer, P Dietze, R Knuppel, AG Romaschenko, NA Kolchanov (1997), "TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation", Nucleic Acids Research, 25(1): 265-268.
    [abstract]
    [supplement mateiral: http://transfac.gbf-braunschweig.de (TRANSFAC)]

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

  51. Ying Xu, Richard J Mural, and Edward C Uberbacher (1997), "Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags", Proceedings of the fifth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.344-353.
    [ Medline entry]

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

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

  54. translation
    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] [PDF]

  55. promoter/TF
    T Yada, Y Totoki, T Ishii, K Nakai (1997), "Functional prediction of B. subtilis genes from their regulatory sequences", Proceedings of the fifth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.354-357.
    [ Medline entry]

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

    [supplement material: http://argon.cshl.org/genefinder (MZEF)]