Related papers: Improved Rank-Modulation Codes for DNA Storage wit…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and tradeoffs of DNA-based storage systems under a simple model, motivated by current…
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 DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an…
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…
The problem of storing permutations in a distributed manner arises in several common scenarios, such as efficient updates of a large, encrypted, or compressed data set. This problem may be addressed in either a combinatorial or a coding…
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…
In this paper, we study error exponents for a concatataned coding based class of DNA storage codes in which the number of reads performed can be variable. That is, the decoder can sequentially perform reads and choose whether to output the…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
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…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
The rank modulation scheme has been proposed for efficient writing and storing data in non-volatile memory storage. Error-correction in the rank modulation scheme is done by considering permutation codes. In this paper we consider codes in…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…