Related papers: Improved Coding over Sets for DNA-Based Data Stora…
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…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
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…
Erasure codes are an efficient means of storing data across a network in comparison to data replication, as they tend to reduce the amount of data stored in the network and offer increased resilience in the presence of node failures. The…
This paper studies the sequence reconstruction problem for a channel inspired by protein identification. We introduce a coloring channel, where a sequence is transmitted through a channel that deletes all symbols not belonging to a fixed…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
Several recently proposed code-based cryptosystems base their security on a slightly generalized version of the classical (syndrome) decoding problem. Namely, in the so-called restricted (syndrome) decoding problem, the error values stem…
We consider linear network error correction (LNEC) coding when errors may occur on edges of a communication network of which the topology is known. In this paper, we first revisit and explore the framework of LNEC coding, and then unify two…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
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,…
We construct new families of multi-error-correcting quantum codes for the amplitude damping channel. Our key observation is that, with proper encoding, two uses of the amplitude damping channel simulate a quantum erasure channel. This…
The explosion of the amount of data stored in cloud systems calls for more efficient paradigms for redundancy. While replication is widely used to ensure data availability, erasure correcting codes provide a much better trade-off between…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
Distributed storage systems support failures of individual devices by the use of replication or erasure correcting codes. While erasure correcting codes offer a better storage efficiency than replication for similar fault tolerance, they…
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…
Source-channel coding for an energy limited wireless sensor node is investigated. The sensor node observes independent Gaussian source samples with variances changing over time slots and transmits to a destination over a flat fading…
Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…
Regenerating codes provide an efficient way to recover data at failed nodes in distributed storage systems. It has been shown that regenerating codes can be designed to minimize the per-node storage (called MSR) or minimize the…