相关论文: The genetic code multiplet structure, in one numbe…
Algorithms to generate various combinatorial structures find tremendous importance in computer science. In this paper, we begin by reviewing an algorithm proposed by Rohl that generates all unique permutations of a list of elements which…
In the present work, 16 genetic code doublets and their cognate amino acids in the genetic code are fitted into a polyhedron model. Based on the structural regularity in nucleobases, and by using a series of common-sense topological…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I…
In this dissertation, we explore the structure of inversion graphs of permutations--a class of graphs that naturally arises by representing each permutation as a graph, where vertices correspond to entries and edges encode inversions.…
In the context of the genome rearrangement problem, we analyze two well known models, namely the reversal and the prefix reversal models, by exploiting the connection with the notion of permutation pattern. More specifically, for any $k$,…
We study the problem of building generative models of natural source code (NSC); that is, source code written and understood by humans. Our primary contribution is to describe a family of generative models for NSC that have three key…
In this paper, we start by giving the definitions and basic facts about hyperoctahedral number system. There is a natural correspondence between the integers expressed in the latter and the elements of the hyperoctahedral group when we use…
The matrix form of the presentation of the genetic code is described as the cognitive form to analyze structures of the genetic code. A similar matrix form is utilized in the theory of signal processing. The Kronecker family of the genetic…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
Possible explanation of the 64/20 redundancy of the triplet genetic code based on the assumption of quantum nature of genetic information is proposed.
In this paper we continue the study of permutations avoiding the vincular pattern $1-32-4$ by constructing a generating tree with a single label for these permutations. This construction finally provides a clearer explanation of why a…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
We present a unique decoding algorithm of algebraic geometry codes on plane curves, Hermitian codes in particular, from an interpolation point of view. The algorithm successfully corrects errors of weight up to half of the order bound on…
A permutation code is a nonlinear code whose codewords are permutation of a set of symbols. We consider the use of permutation code in the deletion channel, and consider the symbol-invariant error model, meaning that the values of the…
We survey the known results about simple permutations. In particular, we present a number of recent enumerative and structural results pertaining to simple permutations, and show how simple permutations play an important role in the study…
We study a construction, which produces surfaces $Y \subset P_3$ with cusps. For example we obtain surfaces of degree six with 18, 24 or 27 three-divisible cusps. For sextic surfaces in a particular family of up to 30 cusps the codes of…
We consider compositions of natural numbers when there are different types of each natural number. Several recursions as well as some closed formulas for the number of compositions is derived. We also find its relationships with some known…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
Information is often encoded as an aperiodic chain of building blocks. Modern digital computers use bits as the building blocks, but in general the choice of building blocks depends on the nature of the information to be encoded. What are…