Related papers: Geno-Weaving: Low-Complexity Capacity-Achieving DN…

Since the birth of computer and networks, fuelled by pervasive computing and ubiquitous connectivity, the amount of data stored and transmitted has exponentially grown through the years. Due to this demand, new solutions for storing data…

This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…

The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…

Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…

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…

Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…

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…

Nucleic acid sensing is crucial for advancing diagnostics, therapeutic monitoring and molecu-lar biology research, by enabling the precise identification of DNA and RNA interactions. Here, we present an innovative sensing platform based on…

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…

DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…

Storing data in DNA is being explored as an efficient solution for archiving and in-object storage. Synthesis time and cost remain challenging, significantly limiting some applications at this stage. In this paper we investigate efficient…

We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…

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…

Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…

Encoding digital information into DNA sequences offers an attractive potential solution for storing rapidly growing data under the information age and the rise of artificial intelligence. However, practical implementations of DNA storage…

Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…

In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…

We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…

To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…

Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…