Related papers: The DNA Storage Channel: Capacity and Error Probab…
In distributed communication, each transmitter prepares an ensemble of channel codes. To encode a message, a transmitter chooses a channel code individually without sharing the coding choice with other transmitters or with the receiver.…
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…
Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of…
We derive a new upper bound on the reliability function for channel coding over discrete memoryless channels. Our bounding technique relies on two main elements: (i) adding an auxiliary genie-receiver that reveals to the original receiver a…
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 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…
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…
This paper tackles two problems that fall under the study of coding for insertions and deletions. These problems are motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm,…
We consider a generalization of the discrete memoryless channel, in which the channel probability distribution is replaced by a uniform distribution over clouds of channel output sequences. For a random ensemble of such channels, we derive…
Deoxyribonucleic acid (DNA) has emerged as a promising building block for next-generation ultra-high density storage devices. Although DNA has high durability and extremely high density in nature, its potential as the basis of storage…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
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,…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
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…
We consider the maximum coding rate achievable by uniformly-random codes for the deletion channel. We prove an upper bound that's within 0.1 of the best known lower bounds for all values of the deletion probability $d,$ and much closer for…
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.…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
"Independent and identically distributed" errors do not accurately capture the noisy behavior of real-world data storage and information transmission technologies. Motivated by this, we study channels with input-correlated synchronization…