Related papers: Two-Insertion/Deletion/Substitution Correcting Cod…
This paper studies the problem of constructing codes correcting deletions in arrays. Under this model, it is assumed that an $n\times n$ array can experience deletions of rows and columns. These deletion errors are referred to as…
This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes.…
Motivated by applications in DNA-based storage and communication systems, we study deletion and insertion errors simultaneously in a burst. In particular, we study a type of error named $t$-deletion-$s$-insertion-burst ($(t,s)$-burst for…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
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…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
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 consider the problem of constructing binary codes to recover from $k$-bit deletions with efficient encoding/decoding, for a fixed $k$. The single deletion case is well understood, with the Varshamov-Tenengolts-Levenshtein code from 1965…
We improve Levenshtein's upper bound for the cardinality of a code of length four that is capable of correcting single deletions over an alphabet of even size. We also illustrate that the new upper bound is sharp. Furthermore we construct…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
We improve the upper bound of Levenshtein for the cardinality of a code of length 4 capable of correcting single deletions over an alphabet of even size. We also illustrate that the new upper bound is sharp. Furthermore we will construct an…
Codes for correcting sticky insertions/deletions and limited-magnitude errors have attracted significant attention due to their applications of flash memories, racetrack memories, and DNA data storage systems. In this paper, we first…
An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…
Codes correcting bursts of deletions and localized deletions have garnered significant research interest in recent years. One of the primary objectives is to construct codes with minimal redundancy. Currently, the best known constructions…
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…
We introduce a general class of codes which includes several well-known classes of deletion/insertion correcting codes as special cases. For example, the Helberg code, the Levenshtein code, the Varshamov--Tenengolts code, and most variants…
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…
Motivated by applications in DNA-based storage, we introduce the new problem of code design in the Damerau metric. The Damerau metric is a generalization of the Levenshtein distance which, in addition to deletions, insertions and…
This paper investigates linear-time decoding algorithms for two classes of error-correcting codes. One of the classes is monotone codes which are known as single deletion codes. The other is azinv codes which are known as single balanced…
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…