Related papers: DNA Storage Error Simulator: A Tool for Simulating…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
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…
How can an author store digital information so that it will be reliably useful, even years later when he is no longer available to answer questions? Methods that might work are not good enough; what is preserved today should be reliably…
The object of this article is to review the development of ultrahigh-density, nanoscale data storage, i.e., nanostorage. As a fundamentally new type of storage system, the recording mechanisms of nanostorage may be completely different to…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
SIMD||DNA is a model of DNA strand displacement allowing parallel in-memory computation on DNA storage. We show how to simulate an arbitrary 3-symbol space-bounded Turing machine with a SIMD||DNA program, giving a more direct and efficient…
Emerging DNA storage technologies use composite DNA letters, where information is represented by a probability vector, leading to higher information density and lower synthesis costs. However, it faces the problem of information leakage in…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic…
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…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…
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…
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
Recently, DNA data storage systems have attracted many researchers worldwide. Motivated by the success stories of such systems, in this work we propose a software called BacSoft to clone the data in a bacterial plasmid by using the concept…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
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…
DNA storage has matured from concept to practical stage, yet its integration with neural compression pipelines remains inefficient. Early DNA encoders applied redundancy-heavy constraint layers atop raw binary data - workable but primitive.…