Related papers: Error-correcting Codes for Short Tandem Duplicatio…
Despite their significant advantages over competing technologies, nanopore sequencers are plagued by high error rates, due to physical characteristics of the nanopore and inherent noise in the biological processes. It is thus paramount not…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
We consider the problem of correcting mass readout errors in information encoded in binary polymer strings. Our work builds on results for string reconstruction problems using composition multisets [Acharya et al., 2015] and the unique…
Three-dimensional (3D) printing's accessibility enables rapid manufacturing but also poses security risks, such as the unauthorized production of untraceable firearms and prohibited items. To ensure traceability and accountability,…
The Swap-Insert Correction distance from a string $S$ of length $n$ to another string $L$ of length $m\geq n$ on the alphabet $[1..d]$ is the minimum number of insertions, and swaps of pairs of adjacent symbols, converting $S$ into $L$.…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
We derive the coding capacity for duplication-correcting codes capable of correcting any number of duplications. We do so both for reverse-complement duplications, as well as palindromic (reverse) duplications. We show that except for…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
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…
In this paper, we investigate binary reconstruction codes capable of correcting one deletion and one substitution. We define the \emph{single-deletion single-substitution ball} function $ \mathcal{B} $ as a mapping from a sequence to 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…
The problem of designing codes for deletion-correction and synchronization has received renewed interest due to applications in DNA-based data storage systems that use nanopore sequencers as readout platforms. In almost all instances,…
We study data structures in the presence of adversarial noise. We want to encode a given object in a succinct data structure that enables us to efficiently answer specific queries about the object, even if the data structure has been…
We present a finite blocklength performance bound for a DNA storage channel with insertions, deletions, and substitutions. The considered bound -- the dependency testing (DT) bound, introduced by Polyanskiy et al. in 2010 -- provides an…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
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.…
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…
This paper provides a new instance of quantum deletion error-correcting codes. This code can correct any single quantum deletion error, while our code is only of length 4. This paper also provides an example of an encoding quantum circuit…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…