相关论文: DNA Codes that Avoid Secondary Structures

The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…

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…

This paper is dealing with DNA cyclic codes which play an important role in DNA computing and have attracted a particular attention in the literature. Firstly, we introduce a new family of DNA cyclic codes over the ring…

The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…

DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…

Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…

Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…

Several technological limitations of traditional silicon based computing are leading towards the paradigm shift, from silicon to carbon, in computational world. Among the unconventional modes of computing evolved in past several decades,…

An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the…

A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…

Cryptography is the science that secures data and communication over the network by applying mathematics and logic to design strong encryption methods. In the modern era of e-business and e-commerce the protection of confidentiality,…

In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…

In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly…

RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…

Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…

As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…

The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…

The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…

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…