Related papers: Constrained Error-Correcting Codes for Efficient D…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
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…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
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…
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…
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…
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…
Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash,…
We study the theoretical problem of synthesizing multiple DNA strands under spatial constraints, motivated by large-scale DNA synthesis technologies. In this setting, strands are arranged in an array and synthesized according to a fixed…
We investigate weakly constrained codes, in which specific patterns occur with prescribed frequencies rather than being strictly forbidden as in conventional constrained coding. We propose a capacity-achieving construction of a weakly…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
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…
In the recent years, DNA has emerged as a potentially viable storage technology. DNA synthesis, which refers to the task of writing the data into DNA, is perhaps the most costly part of existing storage systems. Accordingly, this high cost…
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…