Related papers: DNA-Based Data Storage Systems: A Review of Implem…
Distributed storage systems often introduce redundancy to increase reliability. When coding is used, the repair problem arises: if a node storing encoded information fails, in order to maintain the same level of reliability we need to…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
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…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…
The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction,…
The term Big Data is usually used to describe huge amount of data that is generated by humans from digital media such as cameras, internet, phones, sensors etc. By building advanced analytics on the top of big data, one can predict many…
Regenerating codes are a class of codes proposed for providing reliability of data and efficient repair of failed nodes in distributed storage systems. In this paper, we address the fundamental problem of handling errors and erasures during…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
We present a theoretical discussion of a self-assembly scheme which makes it possible to use DNA to uniquely encode the composition and structure of micro- and nanoparticle clusters. These anisotropic DNA-decorated clusters can be further…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
Neural networks based on soft and biological matter constitute an interesting potential alternative to traditional implementations based on electric circuits. DNA is a particularly promising system in this context due its natural ability to…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
This article proposes a blockchain-based file storage system that utilizes DNA encryption for enhanced security. The system utilizes blockchain technology to provide decentralized and tamper-proof file storage, while DNA encryption is…
The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k-mers, which are short fixed-length strings present in a…