相关论文: On DNA Codes Over the Non-Chain Ring $\mathbb{Z}_4…
Codes over Galois rings have been studied extensively during the last three decades. Negacyclic codes over $GR(2^a,m)$ of length $2^s$ have been characterized: the ring $\mathcal{R}_2(a,m,-1)= \frac{GR(2^a,m)[x]}{\langle x^{2^s}+1\rangle}$…
A linear code of length $n$ over a finite chain ring $R$ with residue field $\F_q$ is a $R$-submodule of $R^n$. A $R$-linear code is a code over $\F_q$ (not necessarily linear) which is the generalized Gray map image of a linear code over…
In this paper, we develop the theory of convolutional codes over finite commutative chain rings. In particular, we focus on maximum distance profile (MDP) convolutional codes and we provide a characterization of these codes, generalizing…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash,…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
Using data from contact maps of the DNA-polymer of $E. Coli$ (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain.…
In 2011 the DNA seesaw gate motif was introduced. It is a powerful feed-forward DNA nanodevice that can perform digital logic computations. The landmark of that work managed to evaluate moderately large Boolean circuits by cascading…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
Enzymatic DNA labeling is a powerful tool with applications in biochemistry, molecular biology, biotechnology, medical science, and genomic research. This paper contributes to the evolving field of DNA-based data storage by presenting a…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
In this paper, we give a new method for constructing LCD codes. We employ group rings and a well known map that sends group ring elements to a subring of the $n \times n$ matrices to obtain LCD codes. Our construction method guarantees that…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
Long length-scale structural deformations of DNA play a central role in many biological processes including gene expression. The elastic rod model, which uses a continuum approximation, has emerged as a viable tool to model deformations of…
DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…
Block codes are considered for improving the reliability of messages stored in a computer memory with both stuck-at defects and random errors. It is assumed that the side information about the state of the defects is available to the…
A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a…