Related papers: An End-to-End Coding Scheme for DNA-Based Data Sto…
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…
Since the birth of computer and networks, fuelled by pervasive computing and ubiquitous connectivity, the amount of data stored and transmitted has exponentially grown through the years. Due to this demand, new solutions for storing data…
A network coding-based scheme is proposed to improve the energy efficiency of distributed storage systems in WSNs (wireless sensor networks), which mainly focuses on two problems: firstly, consideration is given to effective distributed…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate…
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…
Large-scale distributed storage systems typically use erasure codes to provide durability of data in the face of failures. A set of $k$ blocks to be stored is encoded using an $[n, k]$ code to generate $n$ blocks that are then stored on…
We study the following semi-deterministic setting of the joint source-channel coding problem: a deterministic source sequence (a.k.a. individual sequence) is transmitted via a memoryless channel, using delay-limited encoder and decoder,…
"Independent and identically distributed" errors do not accurately capture the noisy behavior of real-world data storage and information transmission technologies. Motivated by this, we study channels with input-correlated synchronization…
The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the…
The accelerating growth of global data generation demands data storage platforms that offer high capacity, long lifespan, and low energy consumption beyond the limits of electronic memory technologies. Optical storage provides an attractive…
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 problem of lossless fixed-rate streaming coding of discrete memoryless sources with side information at the decoder is studied. A random time-varying tree-code is used to sequentially bin strings and a Stack Algorithm with a variable…
High-throughput solid-state nanopore experiments generate continuous MHz-rate data streams in which only a small fraction of data contains informative molecular information. This creates storage and processing bottlenecks that limit…
The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
In this paper, we study how often unique decoding from $t$ insertions or $t$ deletions occurs for error correcting codes. Insertions and deletions frequently occur in synchronization problems and DNA, a medium which is beginning to be used…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…
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…