Related papers: Half-Marker Codes for Deletion Channels with Appli…
We present a finite blocklength performance bound for a DNA storage channel with insertions, deletions, and substitutions. The considered bound -- the dependency testing (DT) bound, introduced by Polyanskiy et al. in 2010 -- provides an…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
We investigate the problem of maintaining an encoded distributed storage system when some nodes contain adversarial errors. Using the error-correction capabilities that are built into the existing redundancy of the system, we propose a…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
Data synchronization is a fundamental problem with applications in diverse fields such as cloud storage, genomics, and distributed systems. This paper addresses the challenge of synchronizing two files, one of which is a subsequence of the…
Distributed storage systems often introduce redundancy to increase reliability. When coding is used, the repair problem arises: if a node storing encoded information fails, in order to maintain the same level of reliability we need to…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to…
This paper presents a coding scheme for an insertion deletion substitution channel. We extend a previous scheme for the deletion channel where polar codes are modified by adding "guard bands" between segments. In the new scheme, each guard…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…