Related papers: Error Probability Bounds for Coded-Index DNA Stora…
DNA storage has emerged as a promising solution for large-scale and long-term data preservation. Among various error types, insertions are the most frequent errors occurring in DNA sequences, where the inserted symbol is often identical or…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error…
This paper studies the problem of reconstructing a word given several of its noisy copies. This setup is motivated by several applications, among them is reconstructing strands in DNA-based storage systems. Under this paradigm, a word is…
The decoding error probability of codes is studied as a function of their block length. It is shown that the existence of codes with a polynomially small decoding error probability implies the existence of codes with an exponentially small…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
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…
We consider a molecular channel, in which messages are encoded to the frequency of objects (or concentration of molecules) in a pool, and whose output during reading time is a noisy version of the input frequencies, as obtained by sampling…
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…
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…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
This paper studies the concentration properties of random codes. Specifically, we show that, for discrete memoryless channels, the error exponent of a randomly generated code with pairwise-independent codewords converges in probability to…
We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
Constrained sequence codes have been widely used in modern communication and data storage systems. Sequences encoded with constrained sequence codes satisfy constraints imposed by the physical channel, hence enabling efficient and reliable…
Many proofs in discrete mathematics and theoretical computer science are based on the probabilistic method. To prove the existence of a good object, we pick a random object and show that it is bad with low probability. This method is…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
Synchronization errors, such as insertions and deletions, present a fundamental challenge in DNA-based data storage systems, arising from both synthesis and sequencing noise. These channels are often modeled as…
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…
A new class of folded subspace codes for noncoherent network coding is presented. The codes can correct insertions and deletions beyond the unique decoding radius for any code rate $R\in[0,1]$. An efficient interpolation-based decoding…