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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 consider the outer channel for DNA-based data storage. When transmitting over the outer channel, each DNA string is treated as a unit/symbol that would be either correctly received, or erased, or corrupted by uniformly…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
DNA-based data storage has been attracting significant attention due to its extremely high data storage density, low power consumption, and long duration compared to conventional data storage media. Despite the recent advancements in DNA…
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…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
DNA-based storage is an emerging storage technology that provides high information density and long duration. Due to the physical constraints in the reading and writing processes, error correction in DNA storage poses several interesting…
We present many new results related to reliable (interactive) communication over insertion-deletion channels. Synchronization errors, such as insertions and deletions, strictly generalize the usual symbol corruption errors and are much…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
Motivated by communication channels in which the transmitted sequences are subject to random permutations, as well as by certain DNA storage systems, we study the error control problem in settings where the information is stored/transmitted…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
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…
This paper is concerned with the problem of error-free communication over the i.i.d. duplication channel which acts on a transmitted sequence $ x_1 \cdots x_n $ by inserting a random number of copies of each symbol $ x_i $ next to the…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
Channels with synchronization errors, such as deletion and insertion errors, are crucial in DNA storage, data reconstruction, and other applications. These errors introduce memory to the channel, complicating its capacity analysis. This…
DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…
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…