Related papers: On Duplication-Free Codes for Disjoint or Equal-Le…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
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…
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…
Symmetric fix-free codes are prefix condition codes in which each codeword is required to be a palindrome. Their study is motivated by the topic of joint source-channel coding. Although they have been considered by a few communities they…
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…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
In 1969 J. Verhoeff provided the first examples of a decimal error detecting code using a single check digit to provide protection against all single, transposition, and adjacent twin errors. The three codes he presented are length 3-digit…
This paper presents conditions for constructing permutation-invariant quantum codes for deletion errors and provides a method for constructing them. Our codes give the first example of quantum codes that can correct two or more deletion…
Rate-compatible error-correcting codes (ECCs), which consist of a set of extended codes, are of practical interest in both wireless communications and data storage. In this work, we first study the lower bounds for rate-compatible ECCs,…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
The majority of the human genome consists of repeated sequences. An important type of repeated sequences common in the human genome are tandem repeats, where identical copies appear next to each other. For example, in the sequence…
In this paper, we study achievable rates of concatenated coding schemes over a deoxyribonucleic acid (DNA) storage channel. Our channel model incorporates the main features of DNA-based data storage. First, information is stored on many,…
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…
In 1969 J. Verhoeff provided the first examples of a decimal error detecting code using a single check digit to provide protection against all single, transposition and adjacent twin errors. The three versions of such a code that he…
We describe a generalization of the group testing problem termed symmetric group testing. Unlike in classical binary group testing, the roles played by the input symbols zero and one are "symmetric" while the outputs are drawn from a…
Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problems asks, given two strings, to split both strings into an identical set of blocks. We consider an extension of this problem to unbalanced…
Distributed storage systems that deploy erasure codes can provide better features such as lower storage overhead and higher data reliability. In this paper, we focus on fractional repetition (FR) codes, which are a class of storage codes…