Related papers: Error-correcting Codes for Short Tandem Duplicatio…
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…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
DNA strands serve as a storage medium for $4$-ary data over the alphabet $\{A,T,G,C\}$. DNA data storage promises formidable information density, long-term durability, and ease of replicability. However, information in this intriguing…
In this paper we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where a data set is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
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…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
DNA is an attractive candidate for data storage. Its millennial durability and nanometer scale offer exceptional data density and longevity. Its relevance to medical applications also drives advances in DNA-related biotechnology. To protect…
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…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
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…
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…
DNA data storage offers a high-density, long-term alternative to traditional storage systems, addressing the exponential growth of digital data. Composite DNA extends this paradigm by leveraging mixtures of nucleotides to increase storage…
In recent years, the emergence of DNA storage systems has led to a widespread focus on the research of codes correcting insertions, deletions, and classic substitutions. During the initial investigation, Levenshtein discovered the VT codes…
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…
Recently, DNA storage has surfaced as a promising alternative for data storage, presenting notable benefits in terms of storage capacity, cost-effectiveness in maintenance, and the capability for parallel replication. Mathematically, the…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…