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Computation in Living Cell: Gene Assembly in Ciliates

Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescot, Grzegorz Rozenberg, Computation in Living Cell: Gene Assembly in Ciliates. Natural Computing, Springer, 2004.


Natural Computing is concerned with computation that is taking place in Nature. The investigation of computations in living cells is one of the central and fastest growing areas of research in this field. Gene assembly in ciliates (unicellular organisms) is a splendid example of such computations, and it is fascinating from both the biological and the computational viewpoints. As a matter of fact, both biology and the science of computation have benefited from this interdiscplinary research on computational nature of gene assembly - this work has helped to clarify important biological aspects of gene assembly, yielded novel insights into the nature of computation, and broadened our understanding of what computation is about.

This monograph gives a self-contained and accessible account of both the biology and the formal analysis of the gene assembly process. It is organized as follows.

Part I provides the biological background, which is presented in a tutorial way and directed towards computer scientists. First, it gives an overview of the structures common to cells and molecular principles on which cells operate. Then it introduces the basic biology of ciliates concentrating on these features that make ciliates uniquely useful for the study of natural computing - in particular, the process of gene assembly, the main topic of this book, is extensively discussed.

Part II introduces formal models for studying gene assembly. It begins with a chapter on the process of model forming that leads to the formulation of these models - this chapter is an informal introduction to the formal framework of this book and it lays a foundation for biologists to acquire intuitive insights and understanding about the formal chapters of Part II. The mathematical framework for the formal models considered here is based on string and graph rewriting.

The three chapters of Part III provide three examples of research topics concerned with gene assembly. The first chapter considers properties of gene assembly that are independent of the choice of gene assembly strategy. The second chapter analyses the influence of molecular operations on the form of the gene assembly as a process of dynamically changing decomposition of a graph representing a gene.

Finally, Part IV, which is an epilogue, provides a perspective on the research presented in this book, and in particular it outlines a number of possible future lines of research.

BibTeX entry:

  title = {Computation in Living Cell: Gene Assembly in Ciliates},
  author = {Ehrenfeucht, Andrzej and Harju, Tero and Petre, Ion and Prescot, David M. and Rozenberg, Grzegorz},
  series = {Natural Computing},
  publisher = {Springer},
  year = {2004},
  ISBN = {3-540-40795-2},

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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