相关论文: On DNA Codes Over the Non-Chain Ring $\mathbb{Z}_4…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…
We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…
To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
In this paper we study two dimensional minimal linear code over the ring $\mathbb{Z}_{p^n}$(where $p$ is prime). We show that if the generator matrix $G$ of the two dimensional linear code $M$ contains $p^n+p^{n-1}$ column vector of the…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Linear codes over finite rings become one of hot topics in coding theory after Hommons et al.([4], 1994) discovered that several remarkable nonlinear binary codes with some linear-like properties are the images of Gray map of linear codes…
Recursive decoding techniques are considered for Reed-Muller (RM) codes of growing length $n$ and fixed order $r.$ An algorithm is designed that has complexity of order $n\log n$ and corrects most error patterns of weight up to…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
By using the notion of $d$-embedding $\Gamma$ of a (canonical) subgeometry $\Sigma$ and of exterior set with respect to the $h$-secant variety $\Omega_{h}(\mathcal{A})$ of a subset $\mathcal{A}$, $ 0 \leq h \leq n-1$, in the finite…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and tradeoffs of DNA-based storage systems under a simple model, motivated by current…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
A linear code with parameters $[n, k, n-k+1]$ is called a maximum distance separable (MDS for short) code. A linear code with parameters $[n, k, n-k]$ is said to be almost maximum distance separable (AMDS for short). A linear code is said…
DNA Polymerase is an enzyme that participates in the process of DNA replication. In general, forward DNA polymerase moves along the template strand in a 3'-5' direction, and the daughter strand is formed in a 5'-3' direction. This paper…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
It is an important task to construct quantum maximum-distance-separable (MDS) codes with good parameters. In the present paper, we provide six new classes of q-ary quantum MDS codes by using generalized Reed-Solomon (GRS) codes and…
Early hardware limitations of GPU (lack of synchronization primitives and limited memory caching mechanisms) can make GPU-based computation inefficient. Now Bio-technologies bring more chances to Bioinformatics and Biological Engineering.…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Generalized quasi-cyclic (GQC) codes with arbitrary lengths over the ring $\mathbb{F}_{q}+u\mathbb{F}_{q}$, where $u^2=0$, $q=p^n$, $n$ a positive integer and $p$ a prime number, are investigated. By the Chinese Remainder Theorem,…