Related papers: Low-redundancy codes for correcting multiple short…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
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…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
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…
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…
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…
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 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,…
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…
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…
In this work, we investigate the problem of constructing codes capable of correcting two deletions. In particular, we construct a code that requires redundancy approximately 8 log n + O(log log n) bits of redundancy, where n is the length…
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…
Tandem duplication in DNA 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 {\em et al.} (2016) proposed the study of codes that…
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…
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…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
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…
Recent work by Smagloy et al. (ISIT 2020) shows that the redundancy of a single-deletion $s$-substitution correcting code is asymptotically at least $(s+1)\log n+o(\log n)$, where $n$ is the length of the codes. They also provide a…
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…