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Locally Decodable Codes (LDCs) are error-correcting codes $C:\Sigma^n\rightarrow \Sigma^m$ with super-fast decoding algorithms. They are important mathematical objects in many areas of theoretical computer science, yet the best…
Line codes make it possible to mitigate interference, to prevent short pulses, and to generate streams of bipolar signals with no direct-current (DC) power content through balancing. They find application in magnetic recording (MR) devices,…
Regenerating code is a class of code very suitable for distributed storage systems, which can maintain optimal bandwidth and storage space. Two types of important regenerating code have been constructed: the minimum storage regeneration…
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…
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…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Intracellular positive ions neutralise negative charges on the phosphates of a DNA strand conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
We analyze security aspects of the SecureDNA system regarding its system design, engineering, and implementation. This system enables DNA synthesizers to screen order requests against a database of hazards. By applying novel cryptography,…
In this paper, we focus on the design of binary constant weight codes that admit low-complexity encoding and decoding algorithms, and that have a size $M=2^k$. For every integer $\ell \geq 3$, we construct a $(n=2^\ell, M=2^{k_{\ell}},…
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…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…
Motivated by DNA-based data storage, we investigate a system where digital information is stored in an unordered set of several vectors over a finite alphabet. Each vector begins with a unique index that represents its position in the whole…
DNA-based storage has emerged as a promising alternative to traditional data storage methods, offering unmatched advantages in data density, longevity, and sustainability. Two main approaches have developed: in-vitro storage, where…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
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…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…