Related papers: Properties and constructions of constrained codes …
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
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…
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…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
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 strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
Motivated by applications in DNA-based storage, we study explicit encoding and decoding schemes of binary strings satisfying locally balanced constraints, where the $(\ell,\delta)$-locally balanced constraint requires that the weight of any…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…