Related papers: Thermodynamically Stable DNA Code Design using a S…
DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
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…
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…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
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…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
Recently, brain-inspired spiking neural networks (SNNs) have demonstrated promising capabilities in solving pattern recognition tasks. However, these SNNs are grounded on homogeneous neurons that utilize a uniform neural coding for…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
DNA has the potential to realize a controllable liquid-liquid phase separation (LLPS) system, because the design of its base sequences results in programmable interactions. Here, we have developed a novel DNA-based LLPS system which enables…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
One of the basic tasks in bioinformatics is localizing a short subsequence $S$, read while sequencing, in a long reference sequence $R$, like the human geneome. A natural rapid approach would be finding a hash value for $S$ and compare it…
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…