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1996

Some relevant poster presentations at the Intelligen Systems for Molecular Biology'96 (St. Louis, June 12-15, 1996)

1. Pierre Baldi, Soren Brunak, Yves Chauvin, Anders Krogh (1996), "Naturally occurring nucleosome positioning signals in human exons and introns", Journal of Molecular Biology, 263: 503-510. [abstract] [ PDF]

2. C Barry, G Fichant, A Kalogeropoulos, Y Quentin (1996), "A computer filtering method to drive out tiny genes from the yeast genome", Yeast, 12(11):1163-1178. [ Medline entry]

3. promoter/TF

   Craig J Benham (1996), "Computation of DNA structural variability - a new predictor of DNA regulatory regions", Computer Applications in Biosciences, 12(5): 375-381.
   [ abstract]

4. promoter/TF

   P Bucher, JW Fickett, A Hatzigeorgiou (1996), "Computational analysis of transcriptional regulatory elements: a field in flux", Computer Applications in Biosciences, 12(5): 361-362.

5. M Burset, R Guigo (1996), "Evaluation of gene structure prediction programs", Genomics, 34(3): 353-367.
   [ Medline entry ] [ PDF]

   [the data can be found at http://www.imim.es/GeneIdentification/Evaluation/Index.html ; the following programs are evaluated:GeneID, GeneID+, SORFIND, GParser2, GParser3, GRAIL II, GAP, GenLang, FgeneH, XPound.]

6. JM Claverie, S Audic (1996) "The statistical significance of nucleotide position-weight matrix matches", Computer Applications in Biosciences, 12: 431-439. [abstract]

7. SJ de Souza, M Long, L Schoenbach, SW Roy, W Gilbert (1996), "Intron positions correlate with module boundaries in ancient proteins", Proceedings of the National Academy of Sciences, 93:14632-14636.
   [ Medline entry]

8. JW Fickett (1996), "Quantitative discrimination of MEF2 sites", Molecular and Cellular Biology, 16(1): 437-441.
   [abstract]

9. JW Fickett (1996), "Coordinate positioning of MEF2 and myogenin binding sites", Gene, 172(1): GC19-32.

10. JW Fickett (1996), "The gene identification problem: an overview for developers", Computers & Chemistry, 20: 103-118
    [ abstract] [ PDF ]

11. JW Fickett (1996), "Finding genes by computer: the state of the art", Trends in Genetics, 12(8): 316-320.
    [ abstract]

12. annotation

    T Gaasterland, CW Sensen (1996), "Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture", Biochimie, 78:302-310.

13. similarity

    Mikhail S Gelfand, Andrey A Mironov, Pavel A Pevzner (1996): "Gene recognition via spliced sequence alignment", Proceedings of the National Academy of Sciences, 93(17): 9061-9066.
    [ abstract] [ Medline entry]
    [supplement material: http://hto-13.usc.edu/software/procrustes/index.html (PROCRUSTES)]

14. MS Gelfand, LI Podolsky, TV Astakhova, MA Roytberg (1996), "Recognition of Genes in Human DNA Sequences", Journal of Computational Biology: 3(2):223-234.
    [ abstract] [ Medline entry]

15. Robert Giegerich, Folker Meyer, and Chris Schleiermacher (1996) "GeneFisher - Software support for the detection of postulated genes" Proceedings of the fourth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.68-77.

16. splicing

    SM Hebsgaard, PG Korning, N Tolskup, J Engelbrecht, P Rouzé S Brunak (1996), "Splice site prediction in Arabidopsis theliana pre-mRNA by combining local and global sequence information", Nucleic Acids Research, 24(17): 3439-3452. [abstract] [ PDF ]

    [supplement material: http://www.cbs.dtu.dk/services/NetPGene/ (NetPlantGene)]

17. promoter/TF

    GB Hutchinson (1996), "The prediction of vertebrate promoter regions using differential hexamer frequency analysis", Computer Applications in Biosciences, 12(5): 391-398.
    [abstract]
    [supplement material: http://www.rabbithutch.com/ (PROMFIND) ]

18. promoter/TF

    H Karas, R Knuppel, W Schulz, H Sklenar, E Wingender (1996), "Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements", Computer Applications in Biosciences, 12(5): 441-446 (1996).
    [ abstract]

19. translation

    Marilyn Kozak (1996), "Interpreting cDNA sequences: some insights from studies on translation", Mammalian Genome, 7:563-574.

20. David Kulp, target=_> David Haussler, Martin G Reese, and Frank H Eeckman (1996), "A generalized hidden Markov model for the recognition of human genes in DNA", Proceedings of the fourth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.134-142.
    [abstract] [ Medline entry]
    [supplement material: http://www.fruitfly.org/seq_tools/genie.html (genie)]

21. JD McIninch, WS Hayes, M Borodovsky (1996), "Applications of GeneMark in Multispecies Environments", Proceedings of the fourth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.166-175. [ Medline entry ]

22. promoter/TF

    S Matis, Y Xu, M Shah, X Guan, JR Einstein, R Mural, E Uberbacher (1996) "Detection of RNA polymerase II promoters and polyadenylation sites in human DNA", Computers & Chemistry, 20: 135-140.

23. promoter/TF

    L Milanesi, M Muselli, P Arrigo (1996), "Hamming Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes", Computer Applications in Biosciences, 12(5): 399-404.
    [ abstract]

24. JL Oliver, A Marin (1996), "A relationship between GC content and coding-sequence length", Journal of Molecular Evolution, 43: 216-223.
    [abstract]

25. promoter/TF

    Anders Gorm Pedersen, Pierre Baldi, Søren Brunak, Yves Chauvan (1996), "Characterization of prokaryotic and eukaryotic promoters using hidden Markov models", Proceedings of the fourth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 182-191.
    [ abstract] [ Medline entry] [ PDF ]

26. translation

    G Pesole, G Grillo, S Liuni (1996), "Databases of mRNA untranslated regions for metazoa", Computers & Chemistry, 20(1):141-144.
    [ Medline entry ]

27. Graziano Pesole, Marcella Attimonelli, Cecilia Saccone (1996), "Linguistic analysis of nucleotide sequences: algorithms for pattern recognition and analysis of codon strategy", Methods in Enzymology, 266: 281-294 .

28. translation

    I Ponte, C Monsalves, M Cabanas, P Martinez, P Suau (1996), "Sequence simplicity and evolution of the 3' untranslated region of the histone H1^o gene", Journal of Molecular Evolution, 43: 125-134.
    [abstract]

29. promoter/TF

    DS Prestridge (1996), "SIGNAL SCAN 4.0: additional databases and sequence formats", Computer Applications in Biosciences, 12(2):157-160.
    [ Medline entry]

30. similarity

    IB Rogozin, L Milanesi, NA Kolchanov (1996), "Gene structure prediction using information on homologous protein sequence", Computer Applications in Biosciences, 12(3): 161-170.
    [abstract]
    [supplement material: at http://www.itba.mi.cnr.it/webgene (WebGene)]

31. promoter/TF

    DA Rosenblueth, D Thieffry, AM Huerta, H Salgado, J Collado-Vides (1996), "Syntactic recognition of regulatory regions in Escherichia coli", Computer Applications in Biosciences, 12(5): 415-422 (1996)
    [abstract]

32. Steven Salzberg, Xin Chen, John Henderson, and Kenneth Fasman (1996), "Finding genes in DNA using decision trees and dynamic programming", Proceedings of the fourth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.201-210.
    [ abstract] [ Medline entry]

33. translation

    T Sazuka, O Ohara (1996), "Sequence features surrounding the translation initiation sites assigned on the genome sequence of Synechocystis sp. strain PCC6803 by amino-terminal protein sequencing", DNA Research, 3:225-232.
    [PDF]

34. PM Sharp, MC Smith (1996), "Identifying bacterial genes--a cautionary tale", Microbiology, 142(4):717-718.

35. M Termier, A Kalogeropoulos (1996), "Discrimination between fortuitous and biologically constrained open reading frames in DNA sequences of Saccharomyces cerevisiae", Yeast, 12(4):369-384.

36. promoter/TF

    EN Trifonov (1996), "Interfering contexts of regulatory sequence elements", Computer Applications in Biosciences, 12(5): 423-429.
    [ abstract]

37. Edward C Uberbacher, Ying Xu, Richard J Mural (1996), "Discovering and understanding genes in human DNA sequence using GRAIL", Methods in Enzymology, 266: 259-281 .

38. TD Wu (1996) "A segment-based dynamic programming algorithm for predicting gene", Journal of Computational Biology, 3: 375-394.
    [abstract]

39. similarity

    Ying Xu, Edward C Uberbacher (1996), "Gene prediction by pattern recognition and homology search", Proceedings of the fourth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 241-251.
    [abstract] [ Medline entry]

40. T Yada, M Hirosawa (1996), "Detection of short protein coding regions within the cyanobacterium genome: Application of the Hidden Markov Model", DNA Research, 3:355-361. [ Medline entry]

41. Tetsushi Yada and Makoto Hirosawa (1996), "Gene recognition in Cyanobacterium genomic sequence data using the midden Markov model", Proceedings of the fourth international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 252-260.
    [ Medline entry]

42. T Yada, M Ishikawa, H Tanaka, K Asai (1996), "Extraction of hidden Markov model representations of signal patterns in DNA sequences", Pacific Symposium on Biocomputing, 1:686-696.