computational gene recognition

[front page] [about] [programs] [databases] [complete genomes] [dna correlations] [mirror]
2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 |
1990 | 1989 | 1988 | 1987 | 1986 | 1985 | 1984 | 1983 | 1982 | 1981 | 1980 | pre-1980 |

+ 1994

  1. D Barrick, K Villanueba, J Childs, R Kalil, TD Schneider, CE Lawrence, L Gold, and GD Stormo, (1994), "Quantitative analysis of ribosome binding sites in E. coli", Nucleic Acids Research, 22, 1287-1295.

  2. MS Boguski, CM Tolstoshev, DE Bassett Jr. (1994), "Gene discovery in dbEST", Science, 265, 1993
    [supplement material: http://www.ncbi.nlm.nih.gov/dbEST/ (dbEST) ].

  3. M Borodovsky, EV Koonin, KE Rudd (1994), "New genes in old sequence: a strategy for finding genes in the bacterial genome", Trends in Biochemical Sciences 19, 309-313.

  4. M Borodovsky, KE Rudd, EV Koonin (1994), "Intrinsic and extrinsic approaches for detecting genes in a bacterial genome", Nucleic Acids Research, 22, 4756-4767.
    [ abstract] [abstract]

  5. DM Church, CJ Stotler, JL Rutter, JR Murrell, JA Trofatter, AJ Buckler (1994), "Isolation of genes from complex sources of mammalian genomic DNA using exon amplification", Nature Genetics, 6: 98-105.

  6. JM Claverie (1994), "Some useful statistical properties of position-weight matrices", Computers & Chemistry, 18(3):287-294
    [ abstract]

  7. JM Claverie (1994) , "Large scale sequence analysis", in Automated DNA Sequencing and Analysis , eds. MD Adams, C Fields, and JC Venter, pp. 267-279 (Academic Press, San Diego, CA).

  8. JM Claverie (1994), "A streamlined random sequencing strategy for finding coding exons", Genomics, 23: 575-581.
    [abstract]

  9. S Dong, DB Searls (1994), "Gene structure prediction by linguistic methods", Genomics, 23, 540-551.
    [abstract]
    [supplement material: http://cbil.humgen.upenn.edu/~sdong/genlang_home.html (GenLang)]

  10. JW Fickett (1994), "Inferring genes from open reading frames", Computers & Chemistry, 18(3): 203-205.
    [ abstract] [ abstract] [ Medline entry]

  11. CA Fields (1994), "Integrating computational and experimental methods for gene discovery", in Automated DNA Sequencing and Analysis eds. MD Adams, C Fields, and JC Venter, pp. 321-325, (Academic Press, San Diego, CA).

  12. promoter/TF
    C Fondat, A Kalogeropoulos (1994), "Approaching the function of new genes by the detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III", Current Genetics, 25, 396-406.

  13. P Green (1994), "Ancient conserved regions in gene sequences", Current Opinion in Structural Biology, 4:404-412.

  14. A Griffin, HG Griffin (1994), Computer Analysis of Sequence Data (2 vol) (Humana Press. Totwa, NJ).

  15. similarity
    S Henikoff (1994), "Comparative sequence analysis: finding genes", in Biocomputing: Informatics and Genome Projects ed. DW Smith (Academic Press)

  16. promoter/TF
    R Knueppel, P Dietze, W Lehnberg, K Frech, E Wingender (1994), "TRANSFAC retrieval program: A network model database of eukaryotic transcription regulating sequences and proteins", Journal of Computational Biology, 1, 191-198.

  17. promoter/TF
    Y Kondrakhin, V Shamir, N Kolchanov (1994) "Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3' terminal processing sites", Computer Applications in Biosciences, 10, 597-603.

  18. AK Konopka (1994), "Sequences and codes: fundamentals of biomolecular cryptography", in Biocomputing: Informatics and Genome Projects , ed. DW Smith (Academic Press)

  19. A Krogh, IS Mian, D Haussler (1994), "A hidden Markov model that finds genes in E. coli DNA", Nucleic Acids Research, 22, 4768-4778. (and in a slightly expanded version: UCSC Report CRL-93-33.)

  20. R Lopez, F Larsen, H Prydz (1994), "Evaluation of the exon predictions of the GRAIL software", Genomics, 24, 133-136.

  21. promoter/TF
    H Mizushima, K Hayashi (1994), "Establishment of transcription factor database and human mutation database", in Proceedings of Genome Informatics Workshop 1994 , eds. Miyano, S., Akutsu, T., Imai, H., Gotoh, O., Takagi, T. (Universal Academy Press, Tokyo).

  22. SM Ossadnik, SV Buldyrev, AL Goldberger, S Havlin, RN Mantegna, VK Peng, M Simons, HE Stanley (1994), "Correlation approach to identify coding regions in DNA sequences", Biophysical Journal, 67, 64-70.

  23. JJ Puthukattukaran, S Chalasani and P Senapathy (1994), "Serial and parallel algorithms for gene finding", in Proceedings of the Third International Symposium on High Performance Distributed Computing, pp. 186-193 (San Francisco, CA)

  24. similarity
    K Robison, W Gilbert, GM Church (1994), "Large scale bacterial gene discovery by similarity search", Nature Genetics, 7: 205-214.

  25. P Senapathy (1994), Independent Birth of Organisms , (Genome Press, Madison, WI).

  26. JW Shavlik (1994), "Finding frameshift errors in anonymous DNA", in Automated DNA Sequencing and Analysis eds. MD Adams, C Fields, and JC Venter, eds. pp. 280-288, (Academic Press, San Diego, CA).

  27. GB Singh, SA Krawetz (1994), "Computer based exon detection: an evaluation metric for comparison", International Journal of Genome Research, 1:321-338.

  28. VV Solovyev, AA Salamov, CB Lawrence (1994), "The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames", Proceedings of the second international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.354-362.
    [ Medline entry]
    [supplement material: http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html (Genefinder)]

  29. VV Solovyev, AA Salamov, CB Lawrence (1994) "Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames", Nucleic Acids Research, 22:5156-5163.
    [ abstract] [ Medline entry]

  30. alternative-splicing
    S Stamm, MQ Zhang, TG Marr, DM Helfman (1994), "A sequence compilation and comparison of exons that are alternatively spliced in neurons", Nucleic Acids Research, 22(9):1515-1526.
    [ Medline entry]

  31. similarity
    DJ States, W Gish (1994), "Combined use of sequence similarity and codon bias for coding region identification", Journal of Computational Biology, 1:39-50.

  32. GD Stormo, D Haussler (1994), "Optimally parsing a sequence into different classes based on multiple types of evidence", Proceedings of the second international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp. 369-375.

  33. A Thomas, MH Skolnick (1994), "A probabilistic model for detecting coding regions in DNA sequences", IMA Journal of Mathematics Applied in Medicine and Biology, 11:149-160.

  34. promoter/TF
    PH von Hippel (1994), "Protein-DNA recognition: new perspectives and underlying themes", Science, 263, 769-770.

  35. Y Xu, RJ Mural, EC Uberbaker (1994), "Constructing gene models from accurately predicted exons: an application of dynamic programming", Computer Applications in Biosciences, 10:613-623.
    [ abstract]

  36. Y Xu, JR Einstein, RJ Mural, M Shah, EC Uberbacher (1994), "An improved system for exon recognition and gene modeling in human DNA sequences", Proceedings of the second international conference on Intelligent Systems for Molecular Biology (AAAI Press), pp.376-383.

  37. translation
    T Yada, M Ishikawa, Y Totoki, K Okubo (1994) , "Statistical analysis of human DNA sequences in the vicinity of poly(A) signal", Institute for New Generation Computer Technology, Technical Report TR-876.

  38. MQ Zhang, TG Marr (1994), "Fission yeast gene structure and recognition", Nucleic Acids Research, 22(9):1750-1759.
    [ Medline entry]