Related papers: On the combinatorics of circular codes
A covering code is a set of codewords with the property that the union of balls, suitably defined, around these codewords covers an entire space. Generally, the goal is to find the covering code with the minimum size codebook. While most…
In this work, we study cyclic codes that have generators as Fibonacci polynomials over finite fields. We show that these cyclic codes in most cases produce families of maximum distance separable and optimal codes with interesting…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Code loops are certain Moufang $2$-loops constructed from doubly even binary codes that play an important role in the construction of local subgroups of sporadic groups. More precisely, code loops are central extensions of the group of…
The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…
In this thesis, we introduced and carried out a combinatorial study of permutations that avoid one or two patterns of length 3 according to the statistic number of crossings. For this purpose, we manipulated a bijection of Elizalde and Pak…
This paper considers cyclic DNA codes of arbitrary length over the ring $R=\F_2[u]/u^4-1$. A mapping is given between the elements of $R$ and the alphabet $\{A,C,G,T\}$ which allows the additive stem distance to be extended to this ring.…
In this note, an intrinsic description of some families of linear codes with symmetries is given, showing that they can be described more generally as quasi group codes, that is, as linear codes allowing a group of permutation automorphisms…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
We investigate the combinatorics and geometry of permutation polytopes associated to cyclic permutation groups, i.e., the convex hulls of cyclic groups of permutation matrices. We give formulas for their dimension and vertex degree. In the…
In this paper upper and lower bounds on the probability of decoding failure under maximum likelihood decoding are derived for different (nonbinary) Raptor code constructions. In particular four different constructions are considered; (i)…
LDPC codes constructed from permutation matrices have recently attracted the interest of many researchers. A crucial point when dealing with such codes is trying to avoid cycles of short length in the associated Tanner graph, i.e. obtaining…
In this paper, we will investigate a harmonic cycle (discrete harmonic form). With a CW-complex, we can construct the combinatorial Laplacian operator. The kernel of the operator is the harmonic space, the set of harmonic cycles, and is…
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Pattern avoidance for permutations has been extensively studied, and has been generalized to vincular patterns, where certain elements can be required to be adjacent. In addition, cyclic permutations, i.e., permutations written in a circle…
Circuit codes are constructed from induced cycles in the graph of the $n$ dimensional hypercube. They are both theoretically and practically important, as circuit codes can be used as error correcting codes. When constructing circuit codes,…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
Two new constructions are presented for coils and snakes in the hypercube. Improvements are made on the best known results for snake-in-the-box coils of dimensions 9, 10 and 11, and for some other circuit codes of dimensions between 8 and…