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Gene assembly in ciliates: formal frameworks

Tero Harju, Ion Petre, Grzegorz Rozenberg, Gene assembly in ciliates: formal frameworks. Bulletin of the European Association of Theoretical Computer Science 82, 227–241, 2004.

Abstract:

Natural Computing is concerned with computing taking place in nature and with human-designed computing inspired by nature. It is an interdisciplinary research area that has already had a significant effect on the development of computer science:
human-designed computing inspired by nature includes areas such as neural computing, evolutionary algorithms, DNA computing and
quantum computing.

Also, there is a growing research trend spread throughout the disciplines of bioinformatics, computational biology and DNA computing (among others) that investigates computational nature of complex biological phenomena. As a matter of fact, part of this research considers some of the basic life processes as computations. One of such processes that has recently attracted the attention is gene assembly in ciliates (single-celled eukaryotic organisms).

The study of this process was initiated in 1971.

The computational nature of gene assembly was first pointed out by Kari and Landweber - they noticed that the process of assembling genes resembles the structure of the molecular solution of the directed hamiltonian path problem proposed by Adleman in his seminal paper (1994). Kari and Landweber have proposed a model based on intermolecular interactions, and subsequently they have investigated the
computational power of this model in the sense of computation theory. Another model of gene assembly, based on intramolecular interactions (different parts of the same molecule interacting with each other) was introduced Ehrenfeucht, Prescott and Rozenberg. This research concentrates on the (formal and biological) properties of the process of gene assembly itself.

This paper surveys the latter line of research (hopefully) making it accessible to a broader audience. It consists of two parts. The
current Part~I provides the basic biological background and introduces molecular operations involved in the process of gene assembly. Part~II reviews theoretical properties of models based on these operations.

A recent monograph by Ehrenfeucht, Harju, Petre, Prescott, Rozenberg provides a broad and in-depth treatment of both the biological and the formal aspects of gene assembly.

BibTeX entry:

@ARTICLE{jHaPeRo04a,
  title = {Gene assembly in ciliates: formal frameworks},
  author = {Harju, Tero and Petre, Ion and Rozenberg, Grzegorz},
  journal = {Bulletin of the European Association of Theoretical Computer Science},
  volume = {82},
  pages = {227–241},
  year = {2004},
}

Belongs to TUCS Research Unit(s): FUNDIM, Fundamentals of Computing and Discrete Mathematics, Computational Biomodeling Laboratory (Combio Lab)

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