Computational Nature of Gene assembly in ciliates (bibtex)
by Brijder, Robert, Harju, Tero, Jonoska, Natasha, Petre, Ion and Rozenberg, Grzegorz
Abstract:
The mathematical study of gene assembly in ciliates was initiated in [58] and in [59], where it was noted that the DNA rearrangements performed by ciliates have a strong computational appeal. The first results dealt with the computational capabilities of suitably defined models for gene assembly, using classical approaches from theoretical computer science, especially based on formal languages and computability theory. Shortly afterwards, a parallel line of research was initiated in [33] and in [75], where the focus was to study various properties of the gene assembly process itself, understood as an information processing process that transforms one genetic structure into another. This research area has witnessed an explosive development, with a large number of results and approaches currently available. Some of them belong to computer science: models based on rewriting systems, permutations, strings, graphs, and formal languages, invariants results, computability results, etc., see, e.g., [29], while others, such as template-based DNA recombination, belong to theoretical and experimental biology, see, e.g., [34] and [5]. In this chapter we review several approaches and results in the computational study of gene assembly. In Section 2 we introduce the basic biological details of the gene assembly process as currently understood and experimentally observed. After mathematical preliminaries in Section 3, we introduce two of the mostly studied molecular models for gene assembly (intermolecular and intramolecular) in Sections 4 and 5. We also discuss several mathematical approaches used in studying these models. In Section 6 we discuss some properties of the gene assembly process, called invariants, that hold independently of molecular model and assembly strategy. In Section 7 we present models for template-based DNA recombination as a possible molecular implementation of the gene assembly process. We conclude the chapter with a brief discussion in Section 8.
Reference:
Computational Nature of Gene assembly in ciliates (Brijder, Robert, Harju, Tero, Jonoska, Natasha, Petre, Ion and Rozenberg, Grzegorz), Chapter in (G. Rozenberg, T.H.W. Back, J.N. Kok, ed.), Springer, volume 2 (Molecular Computation), 2012.
Bibtex Entry:
@InBook{c197,
  pages     = {1233-1280},
  title     = {Computational Nature of Gene assembly in ciliates},
  publisher = {Springer},
  year      = {2012},
  author    = {Brijder, Robert AND Harju, Tero AND Jonoska, Natasha AND Petre, Ion AND Rozenberg, Grzegorz},
  editor    = {G. Rozenberg, T.H.W. Back, J.N. Kok},
  volume    = {2 (Molecular Computation)},
  abstract  = {The mathematical study of gene assembly in ciliates was initiated in [58] and in [59], where it was noted that the DNA rearrangements performed by ciliates have a strong computational appeal. The first results dealt with the computational capabilities of suitably defined models for gene assembly, using classical approaches from theoretical computer science, especially based on formal languages and computability theory. Shortly afterwards, a parallel line of research was initiated in [33] and in [75], where the focus was to study various properties of the gene assembly process itself, understood as an information processing process that transforms one genetic structure into another. This research area has witnessed an explosive development, with a large number of results and approaches currently available. Some of them belong to computer science: models based on rewriting systems, permutations, strings, graphs, and formal languages, invariants results, computability results, etc., see, e.g., [29], while others, such as template-based DNA recombination, belong to theoretical and experimental biology, see, e.g., [34] and [5]. In this chapter we review several approaches and results in the computational study of gene assembly. In Section 2 we introduce the basic biological details of the gene assembly process as currently understood and experimentally observed. After mathematical preliminaries in Section 3, we introduce two of the mostly studied molecular models for gene assembly (intermolecular and intramolecular) in Sections 4 and 5. We also discuss several mathematical approaches used in studying these models. In Section 6 we discuss some properties of the gene assembly process, called invariants, that hold independently of molecular model and assembly strategy. In Section 7 we present models for template-based DNA recombination as a possible molecular implementation of the gene assembly process. We conclude the chapter with a brief discussion in Section 8.},
  booktitle = {Handbook of Natural Computing},
  file      = {Ciliate_chapter_2012-09-13-15-18.pdf:pdfs/Ciliate_chapter_2012-09-13-15-18.pdf:PDF},
}
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