Related papers: DNA-Correcting Codes: End-to-end Correction in DNA…

In order to achieve fault tolerance, highly reliable system often require the ability to detect errors as soon as they occur and prevent the speared of erroneous information throughout the system. Thus, the need for codes capable of…

This paper presents a novel coding scheme for distributed storage systems containing nodes with adversarial errors. The key challenge in such systems is the propagation of erroneous data from a single corrupted node to the rest of the…

The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…

In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…

DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…

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…

At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…

The exponentially increasing demand for data storage has been facing more and more challenges during the past years. The energy costs that it represents are also increasing, and the availability of the storage hardware is not able to follow…

DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…

The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the…

DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…

Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…

A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…

Data storage is one of the main computing issues of this century. Not only storage devices are converging to strict physical limits, but also the amount of data generated by users is growing at an unbelievable rate. To face these…

Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…

A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…

DNA-based storage has emerged as a promising alternative to traditional data storage methods, offering unmatched advantages in data density, longevity, and sustainability. Two main approaches have developed: in-vitro storage, where…

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…

Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…

This paper investigates the use of redundancy and self repairing against node failures in distributed storage systems, using various strategies. In replication method, access to one replication node is sufficient to reconstruct a lost node,…