Related papers: Modular non-repeating codes for DNA storage
We consider the problem of designing low-redundancy codes in settings where one must correct deletions in conjunction with substitutions or adjacent transpositions; a combination of errors that is usually observed in DNA-based data storage.…
Classical erasure codes, e.g. Reed-Solomon codes, have been acknowledged as an efficient alternative to plain replication to reduce the storage overhead in reliable distributed storage systems. Yet, such codes experience high overhead…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters,…
DNA-Encoded Library (DEL) has proven to be a powerful tool that utilizes combinatorially constructed small molecules to facilitate highly-efficient screening assays. These selection experiments, involving multiple stages of washing,…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
The surge in demand for cost-effective, durable long-term archival media, coupled with density limitations of contemporary magnetic media, has resulted in synthetic DNA emerging as a promising new alternative. Despite its benefits, storing…
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme…
DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Distributed storage systems with replication are well known for storing large amount of data. A large number of replication is done in order to provide reliability. This makes the system expensive. Various methods have been proposed over…
Regenerating codes provide an efficient way to recover data at failed nodes in distributed storage systems. It has been shown that regenerating codes can be designed to minimize the per-node storage (called MSR) or minimize the…
Peer-to-peer distributed storage systems provide reliable access to data through redundancy spread over nodes across the Internet. A key goal is to minimize the amount of bandwidth used to maintain that redundancy. Storing a file using an…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
Recent advances in next-generation sequencing technologies have facilitated the use of deoxyribonucleic acid (DNA) as a novel covert channels in steganography. There are various methods that exist in other domains to detect hidden messages…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…