Abstract
This paper presents an overview of computational biology approaches and surveys some of the natural computing models using, in both cases, a formal language-based approach.
Full Text
The Full Text of this article is available as a PDF (77.3 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Brendel V., Beckmann J. S., Trifonov E. N. Linguistics of nucleotide sequences: morphology and comparison of vocabularies. J Biomol Struct Dyn. 1986 Aug;4(1):11–21. doi: 10.1080/07391102.1986.10507643. [DOI] [PubMed] [Google Scholar]
- Brendel V., Busse H. G. Genome structure described by formal languages. Nucleic Acids Res. 1984 Mar 12;12(5):2561–2568. doi: 10.1093/nar/12.5.2561. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Collado-Vides J. A transformational-grammar approach to the study of the regulation of gene expression. J Theor Biol. 1989 Feb 22;136(4):403–425. doi: 10.1016/s0022-5193(89)80156-0. [DOI] [PubMed] [Google Scholar]
- Collado-Vides J. Grammatical model of the regulation of gene expression. Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9405–9409. doi: 10.1073/pnas.89.20.9405. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Collado-Vides J., Gutièrrez-Ríos R. M., Bel-Enguix G. Networks of transcriptional regulation encoded in a grammatical model. Biosystems. 1998 Jun-Jul;47(1-2):103–118. doi: 10.1016/s0303-2647(98)00016-1. [DOI] [PubMed] [Google Scholar]
- Dassow J., Mitrana V. On some operations suggested by genome evolution. Pac Symp Biocomput. 1997:97–108. [PubMed] [Google Scholar]
- Dassow J., Mitrana V., Salomaa A. Context-free evolutionary grammars and the structural language of nucleic acids. Biosystems. 1997;43(3):169–177. doi: 10.1016/s0303-2647(97)00036-1. [DOI] [PubMed] [Google Scholar]
- Dong S., Searls D. B. Gene structure prediction by linguistic methods. Genomics. 1994 Oct;23(3):540–551. doi: 10.1006/geno.1994.1541. [DOI] [PubMed] [Google Scholar]
- Head T. Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. Bull Math Biol. 1987;49(6):737–759. doi: 10.1007/BF02481771. [DOI] [PubMed] [Google Scholar]
- Lindenmayer A. Mathematical models for cellular interactions in development. I. Filaments with one-sided inputs. J Theor Biol. 1968 Mar;18(3):280–299. doi: 10.1016/0022-5193(68)90079-9. [DOI] [PubMed] [Google Scholar]
- Pevzner P. A., Borodovsky MYu, Mironov A. A. Linguistics of nucleotide sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words. J Biomol Struct Dyn. 1989 Apr;6(5):1013–1026. doi: 10.1080/07391102.1989.10506528. [DOI] [PubMed] [Google Scholar]
- Sakakibara Y., Brown M., Hughey R., Mian I. S., Sjölander K., Underwood R. C., Haussler D. Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res. 1994 Nov 25;22(23):5112–5120. doi: 10.1093/nar/22.23.5112. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Searls D. B. Linguistic approaches to biological sequences. Comput Appl Biosci. 1997 Aug;13(4):333–344. doi: 10.1093/bioinformatics/13.4.333. [DOI] [PubMed] [Google Scholar]
- Searls David B. The language of genes. Nature. 2002 Nov 14;420(6912):211–217. doi: 10.1038/nature01255. [DOI] [PubMed] [Google Scholar]
- WATSON J. D., CRICK F. H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953 Apr 25;171(4356):737–738. doi: 10.1038/171737a0. [DOI] [PubMed] [Google Scholar]
