Related papers: On reversible and reversible-complementary DNA cod…
The additive codes may have better parameters than linear codes. However, it is still a challenging problem to efficiently construct additive codes that outperform linear codes, especially those with greater distances than linear codes of…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
Maximum-distance separable (MDS) convolutional codes are characterized by the property that their free distance reaches the generalized Singleton bound. In this paper, new criteria to construct MDS convolutional codes are presented.…
Recursive list decoding of Reed-Muller (RM) codes, with moderate list size, is known to approach maximum-likelihood (ML) performance of short length $(\leq 256)$ RM codes. Recursive decoding employs the Plotkin construction to split the…
Rewriting is a formalism widely used in computer science and mathematical logic. The classical formalism has been extended, in the context of functional languages, with an order over the rules and, in the context of rewrite based languages,…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…
RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of…
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets…
We consider recursive decoding for Reed-Muller (RM) codes and their subcodes. Two new recursive techniques are described. We analyze asymptotic properties of these algorithms and show that they substantially outperform other decoding…
In this work, we give three new techniques for constructing Hermitian self-dual codes over commutative Frobenius rings with a non-trivial involutory automorphism using $\lambda$-circulant matrices. The new constructions are derived as…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Let $A$ be a finite or countable alphabet and let $\theta$ be literal (anti)morphism onto $A^*$ (by definition, such a correspondence is determinated by a permutation of the alphabet). This paper deals with sets which are invariant under…
In this work, we study linear error-correcting codes against adversarial insertion-deletion (insdel) errors, a topic that has recently gained a lot of attention. We construct linear codes over $\mathbb{F}_q$, for…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
We extend the notion of locality from the Hamming metric to the rank and subspace metrics. Our main contribution is to construct a class of array codes with locality constraints in the rank metric. Our motivation for constructing such codes…
Cyclic codes over finite fields are widely implemented in data storage systems, communication systems, and consumer electronics, as they have very efficient encoding and decoding algorithms. They are also important in theory, as they are…
Let $F$ be a field and let $F^{r\times s}$ denote the space of $r\times s$ matrices over $F$. Given equinumerous subsets $\mathcal{A}=\{A_i\mid i \in I\}\subseteq F^{r\times r}$ and $\mathcal{B}=\{B_i\mid i\in I\}\subseteq F^{s\times s}$ we…
We investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…
We give a polynomial representation for additive cyclic codes over $\mathbb{F}_{p^2}$. This representation will be applied to uniquely present each additive cyclic code by at most two generator polynomials. We determine the generator…