Related papers: A Characterization of the DNA Data Storage Channel
We consider error-correcting coding for DNA-based storage. We model the DNA storage channel as a multi-draw IDS channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel…
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…
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…
Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…
We investigate the capacity of noisy frequency-based channels, motivated by DNA data storage in the short-molecule regime, where information is encoded in the frequency of items types rather than their order. The channel output is a…
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…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…
This work presents a theoretical analysis of the probability of successfully retrieving data encoded with MDS codes (e.g., Reed-Solomon codes) in DNA storage systems. We study this probability under independent and identically distributed…
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…
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…
Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data.…
In this paper, we study how often unique decoding from $t$ insertions or $t$ deletions occurs for error correcting codes. Insertions and deletions frequently occur in synchronization problems and DNA, a medium which is beginning to be used…
RNA can be used as a high-density medium for data storage and transmission; however, an important RNA process -- replication -- is noisy. This paper presents an error analysis for RNA as a data transmission medium, analyzing how deletion…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing…
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…
A number of methods have been proposed over the last decade for encoding information using deoxyribonucleic acid (DNA), giving rise to the emerging area of DNA data embedding. Since a DNA sequence is conceptually equivalent to a sequence of…