Computation in Living Cells
Gene Assembly in Ciliates
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61 Result(s)
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Article
Solutions to computational problems through gene assembly
Gene assembly in stichotrichous ciliates is an impressive computational process. They have a unique way of storing their genetic information in two fundamentally different forms within their two types of nucle...
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Article
Parallel complexity of signed graphs for gene assembly in ciliates
We consider a graph-based model for the study of parallelism in ciliate gene assembly, where a signed graph is associated to each micronuclear gene and the gene assembly is modeled as a graph rewriting process...
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Chapter and Conference Paper
Summary of the Workshop on Natural Computing and Graph Transformations
Natural Computing is a research area concerned with computing taking place in nature and with human-designed computing inspired by nature. It is a fast growing, genuinely interdisciplinary field involving, amo...
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Chapter and Conference Paper
Solutions to Computational Problems Through Gene Assembly
Gene assembly in ciliates is an impressive computational process. Ciliates have a unique way of storing their genetic information in two fundamentally different forms within their two types of nuclei. Micronuc...
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Chapter and Conference Paper
A String-Based Model for Simple Gene Assembly
The simple intramolecular model for gene assembly in ciliates is particularly interesting because it can predict the correct assembly of all available experimental data, although it is not universal. The simpl...
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Chapter and Conference Paper
Computing Through Gene Assembly
The intramolecular gene assembly model, [1], uses three molecular recombination operations ld, dlad, and hi. A computing model with two contextual recombination operations del and trl, which are based on ld and d...
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Chapter and Conference Paper
Complexity Measures for Gene Assembly
The process of gene assembly in ciliates is a fascinating example of programmed DNA manipulations in living cells. Macronuclear genes are split into coding blocks (called MDSs), shuffled and separated by non-c...
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Article
Parallelism in Gene Assembly
The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the computational poin...
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Chapter
Modelling Simple Operations for Gene Assembly
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Chapter and Conference Paper
Simple Operations for Gene Assembly
The intramolecular model for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurre...
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Article
Commutation with Ternary Sets of Words
We prove that for any nonperiodic set of words F \subseteq Σ+ with at most three elements, the centralizer of F, i.e., the largest set commuting with F, is F*. Moreover, any set X commuting with F is of the for...
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Chapter and Conference Paper
Parallelism in Gene Assembly
The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the computational poin...
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Book
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Chapter
Graph Pointer Reduction System
In Chap. 10 we represented MDS structure of micronuclear and intermediate genes as graphs. In this chapter we continue this line of formalization by representing the gene assembly process in the framework of g...
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Chapter
Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs
Gene assembly in ciliates is a life process fascinating from both the biological and the computational points of view. Several formal models of this process have been formulated and investigated, among them a ...
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Chapter
An Overview of the Cell
All organisms are composed of cells. Some organisms, like an amoeba or a bacterium, consist of a single cell (unicellular organisms). Plants and animals consist of a few hundred to many trillions of cells (mul...
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Chapter
Intermolecular Model
In this chapter, we consider the intermolecular model for gene assembly in ciliates proposed by Landweber and Kari. However, we present this model in terms of pointer reductions, similarly as done in the rest of ...
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Chapter
Molecular Operations for Gene Assembly
We can only speculate about the significance of the extraordinary modifications in the structure of micronuclear genes in stichotrichous ciliates that have occurred during evolution. However, it is clear the p...
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Chapter
Mathematical Preliminaries
In the chapters to follow we shall consider gene assembly from a more formal point of view through operations on strings and graphs. In this chapter we introduce the basic notions and notations concerning stri...
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Chapter
MDS Descriptor Pointer Reduction System
In Chap. 6 we formalized the MDS structure of micronuclear and intermediate genes through NIDS arrangements and MDS descriptors. In this chapter we shall continue to consider the framework of MDS descriptors. ...
