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Generating protein sequences conditioned on protein structures is an impactful technique for protein engineering. When synthesizing engineered proteins, they are commonly translated into DNA and expressed in an organism such as yeast. One…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
Lifted Reed-Solomon and multiplicity codes are classes of codes, constructed from specific sets of $m$-variate polynomials. These codes allow for the design of high-rate codes that can recover every codeword or information symbol from many…
Quasi-polycyclic (QP for short) codes over a finite chain ring $R$ are a generalization of quasi-cyclic codes, and these codes can be viewed as an $R[x]$-submodule of $\mathcal{R}_m^{\ell}$, where $\mathcal{R}_m:= R[x]/\langle f\rangle$,…
In this paper, we obtain several new classes of irreducible polynomials having integer coefficients whose zeros lie inside an open disk around the origin or outside a closed annular region in the complex plane. Such irreducible polynomials…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Goppa codes are particularly appealing for cryptographic applications. Every improvement of our knowledge of Goppa codes is of particular interest. In this paper, we present a sufficient and necessary condition for an irreducible monic…
There has been much research on codes over $\mathbb{Z}_4$, sometimes called quaternary codes, for over a decade. Yet, no database is available for best known quaternary codes. This work introduces a new database for quaternary codes. It…
In this paper, we study skew cyclic codes with arbitrary length over the ring $R=\mathbb{F}_{p}+u\mathbb{F}_{p}$ where $p$ is an odd prime and $% u^{2}=0$. We characterize all skew cyclic codes of length $n$ as left $% R[x;\theta…
In this paper we study the structure of $\theta$-cyclic codes over the ring $B_k$ including its connection to quasi-$\tilde{\theta}$-cyclic codes over finite field $\mathbb{F}_{p^r}$ and skew polynomial rings over $B_k.$ We also…
Let $S$ be a domain and $R=S[t;\sigma,\delta]$ a skew polynomial ring, where $\sigma$ is an injective endomorphism of $S$ and $\delta$ a left $\sigma$ -derivation. We give criteria for skew polynomials $f\in R$ of degree less or equal to…
We describe families of nonassociative finite unital rings that occur as quotients of natural nonassociative orders in generalized nonassociative cyclic division algebras over number fields. These natural orders have already been used to…
Let $(K,v)$ be a discrete valued field with valuation ring $\oo$, and let $\oo_v$ be the completion of $\oo$ with respect to the $v$-adic topology. In this paper we discuss the advantages of manipulating polynomials in $\oo_v[x]$ in a…
Quadratic permutation polynomial interleavers over integer rings have recently received attention in practical turbo coding systems from deep space applications to mobile communications. In this correspondence, a necessary and sufficient…
The classical Reed-Muller codes over a finite field $\mathbb{F}_q$ are based on evaluations of $m$-variate polynomials of degree at most $d$ over a product set $U^m$, for some $d$ less than $|U|$. Because of their good distance properties,…
Let $S \subset R$ be an arbitrary subset of a unique factorization domain $R$ and $\K$ be the field of fractions of $R$. The ring of integer-valued polynomials over $S$ is the set $\mathrm{Int}(S,R)= \{ f \in \mathbb{K}[x]: f(a) \in R\…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…
We present new constructions of binary quantum codes from quaternary linear Hermitian self-dual codes. Our main ingredients for these constructions are nearly self-orthogonal cyclic or duadic codes over F_4. An infinite family of…
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…