Gene assembly in ciliates: Molecular operations (bibtex)
by Harju, Tero, Petre, Ion and Rozenberg, Grzegorz
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 (see Prescott et al. citePr71) - the review of subsequent biological studies of this process can be found in Prescott citePr25,Pr2000 and Prescott and Rozenberg citePR2. The computational nature of gene assembly was first pointed out by Kari and Landweber citeLaKa1, citeLaKa2 - 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 citeAdleman94. 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 in citeEPR2, and studied in more details in the articles citeEHPPR2-citeHR, citeEPRtemp-citePR2. 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 citeciliate_book provides a broad and in-depth treatment of both the biological and the formal aspects of gene assembly.
Reference:
Gene assembly in ciliates: Molecular operations (Harju, Tero, Petre, Ion and Rozenberg, Grzegorz), In Bulletin of EATCS, 2003.
Bibtex Entry:
@Article{j2,
  author   = {Harju, Tero AND Petre, Ion AND Rozenberg, Grzegorz},
  title    = {Gene assembly in ciliates: Molecular operations},
  journal  = {Bulletin of EATCS},
  year     = {2003},
  number   = {81},
  pages    = {236-249},
  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 (see Prescott et al.~cite{Pr71})~-~the review of subsequent biological studies of this process can be found in Prescott~cite{Pr25,Pr2000} and Prescott and Rozenberg~cite{PR2}. The computational nature of gene assembly was first pointed out by Kari and Landweber~cite{LaKa1}, cite{LaKa2} - 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~cite{Adleman94}. 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 in~cite{EPR2}, and studied in more details in the articles~cite{EHPPR2}-cite{HR}, cite{EPRtemp}-cite{PR2}. 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~cite{ciliate_book} provides a broad and in-depth treatment of both the biological and the formal aspects of gene assembly. },
  file     = {HPR2004a.pdf:pdfs/HPR2004a.pdf:PDF},
}
Powered by bibtexbrowser