Computational Nature of Gene Assembly in Ciliates

Brijder, Robert; Daley, Mark; Harju, Tero; Jonoska, Nataša; Petre, Ion; Rozenberg, Grzegorz

doi:10.1007/978-3-540-92910-9_37

Cited by 8 publications

(6 citation statements)

References 72 publications

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“…These are: theoretical computing models (in info), descriptions, and experimental observations and simulations. Several examples in the literature about biological computation include bacteria colonies [32,33]; gene assembly in ciliates [34][35][36]; biochemical reactions [37,38]; gene networks, proteinprotein interaction networks, and transport networks [39,40]; cells [41]; information diffusion in the endocrine system; defense adaptation and coordination in the immune system [42,43]; information processing in swarm insects [44]; plants [45]; and evolution as computation [46,47]. A large part of the examples just mentioned assume implicitly or explicitly the TM as a final and complete model of computation [48] and, therefore, take the CTt as the upper bound of what can be computed.…”

Section: Biological Hypercomputationmentioning

confidence: 99%

Biological hypercomputation: A new research problem in complexity theory

Maldonado

Cruz

2014

Complexity

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This article discusses the meaning and scope of biological hypercomputation (BH) that is to be considered as new research problem within the sciences of complexity. The framework here is computational, setting out that life is not a standard Turing Machine. Living systems, we claim, hypercompute, and we aim at understanding life not by what it is, but rather by what it does. The distinction is made between classical and nonclassical hypercomputation. We argue that living processes are nonclassical hypercomputation. BH implies then new computational models. Finally, we sketch out the possibilities, stances, and reach of BH.

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Section: Biological Hypercomputationmentioning

confidence: 99%

Biological hypercomputation: A new research problem in complexity theory

Maldonado

Cruz

2014

Complexity

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“…This transformation of single genes from their MIC form to their MAC form is formally modelled in a series of papers by Ehrenfeucht et al (see, e.g., [10,5,7,8]), culminating in a book [6]. See [2] for a more recent overview of the "computational" aspects of gene assembly.…”

Section: Gene Assembly In Ciliates and Schur Complementationmentioning

confidence: 99%

Binary Symmetric Matrix Inversion Through Local Complementation

Brijder

Hoogeboom

2012

Fundamenta Informaticae

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We consider the Schur complement operation for symmetric matrices over GF(2), which we identify with graphs through the adjacency matrix representation. It is known that Schur complementation for such a matrix (i.e., for a graph) can be decomposed into a sequence of two types of elementary Schur complement operations: (1) local complementation on a looped vertex followed by deletion of that vertex and (2) edge complementation on an edge without looped vertices followed by deletion of that edge. We characterize the symmetric matrices over GF(2) that can be transformed into the empty matrix using only operations of (1). As a consequence, we find that these matrices can be inverted using local complementation. The result is applied to the theory of gene assembly in ciliates.

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“…Works dealing with (real) genome recombinations and reconstructions often assume to start with a set of substrings for which multiplicity is not known, as it is the case for ciliates rearrangements [9,10]. On the other hand, current methods for DNA assembling which belong to "next-generation" (of second, third, and fourth generation) sequencing (NGS) allow us to have several duplicates of given k-mers.…”

Section: Introductionmentioning

confidence: 99%

Spectral concepts in genome informational analysis

Bonnici¹,

Franco²,

Manca³

2021

Preprint

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The concept of k-spectrum for genomes is here investigated as a basic tool to analyze genomes. Related spectral notions based on k-mers are introduced with some related mathematical properties which are relevant for informational analysis of genomes. Procedures to generate spectral segmentations of genomes are provided and are tested (under several values of length k for k-mers) on cases of real genomes, such as some human chromosomes and Saccharomyces cervisiae.

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Computational Nature of Gene Assembly in Ciliates

Cited by 8 publications

References 72 publications

Biological hypercomputation: A new research problem in complexity theory

Biological hypercomputation: A new research problem in complexity theory

Binary Symmetric Matrix Inversion Through Local Complementation

Spectral concepts in genome informational analysis

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