相关论文: Deciding the Confusability of Words under Tandem R…

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…

A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…

The set of all $ q $-ary strings that do not contain repeated substrings of length $ \leqslant\! 3 $ (i.e., that do not contain substrings of the form $ a a $, $ a b a b $, and $ a b c a b c $) constitutes a code correcting an arbitrary…

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…

Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…

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…

A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…

In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…

Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…

Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…

In this work, we propose constructions that correct duplications of multiple consecutive symbols. These errors are known as tandem duplications, where a sequence of symbols is repeated; respectively as palindromic duplications, where a…

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…

We propose a list-decoding scheme for reconstruction codes in the context of uniform-tandem-duplication noise, which can be viewed as an application of the associative memory model to this setting. We find the uncertainty associated with…

Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…

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…

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…

Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of…

Twins in a finite word are formed by a pair of identical subwords placed at disjoint sets of positions. We investigate the maximum length of twins in a random word over a $k$-letter alphabet. The obtained lower bounds for small values of…

DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…

We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…