Related papers: The DNA Storage Channel: Capacity and Error Probab…

This paper studies the impact of a transmitter's molecule generation process on the capacity of a concentration based Molecular Communication (MC) system. Constraints caused by the molecule generation process affect the availability of the…

Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…

Channels with synchronization errors, exhibiting deletion and insertion errors, find practical applications in DNA storage, data reconstruction, and various other domains. Presence of insertions and deletions render the channel with memory,…

We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…

The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…

The reliability function of memoryless channels with noiseless feedback and variable-length coding has been found to be a linear function of the average rate in the classic work of Burnashev. In this work we consider unifilar channels with…

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…

This paper presents an achievability bound that evaluates the exact probability of error of an ensemble of random codes that are decoded by a minimum distance decoder. Compared to the state-of-the-art which demands exponential computation…

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…

As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…

Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…

Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…

DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…

The past decade has seen notable advances in our understanding of structured error-correcting codes, particularly binary Reed--Muller (RM) codes. While initial breakthroughs were for erasure channels based on symmetry, extending these…

The one-bit deletion and duplication channel is investigated. An input to this channel consists of a block of bits which experiences either a deletion, or a duplication, or remains unchanged. For this channel a capacity expression is…

Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…

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…

We study the stability of low-density parity-check (LDPC) codes under blockwise or bitwise maximum $\textit{a posteriori}$ (MAP) decoding, where transmission takes place over a binary-input memoryless output-symmetric channel. Our study…

We consider three capacity definitions for general channels with channel side information at the receiver, where the channel is modeled as a sequence of finite dimensional conditional distributions not necessarily stationary, ergodic, or…

Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…