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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,…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
Steganography is the process of embedding secret data into another message or data, in such a way that it is not easily noticeable. With the advancement of deep learning, Deep Neural Networks (DNNs) have recently been utilized in…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
The Internet is a ubiquitous and affordable communications network suited for e-commerce and medical image communications. Security has become a major issue as data communication channels can be intruded by intruders during transmission.…
Distributed systems, such as biological and artificial neural networks, process information via complex interactions engaging multiple subsystems, resulting in high-order patterns with distinct properties across scales. Investigating how…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
Whereas cryptography easily arouses attacks by means of encrypting a secret message into a suspicious form, steganography is advantageous for its resilience to attacks by concealing the message in an innocent-looking cover signal. Minimal…
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…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Optical phase-modulated fringe-patterns are usually digitized with XxY pixels and 8 bits/pixel (or higher) gray-levels. The digitized 8 bits/pixel are raw-data bits, not Shannon information bits. Here we show that noisy fringe-patterns…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
It is not obvious how to extend Shannon's original information entropy to higher dimensions, and many different approaches have been tried. We replace the English text symbol sequence originally used to illustrate the theory by a discrete,…
Semantic communication (SemCom) is accelerating its momentum to catch up with the massive increase in users' demands in both quantity and quality, with the assistance of advanced deep learning (DL) techniques. Specifically, SemCom can…
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…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
The shotgun sequencing process involves fragmenting a long DNA sequence (input string) into numerous shorter, unordered, and overlapping segments (referred to as \emph{reads}). The reads are sequenced, and later aligned to reconstruct the…
Strong influence of water molecules on the transport and magnetic properties of DNA, observed in this study, opens up real opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…