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Algebraic decoding algorithms are commonly applied for the decoding of Reed-Solomon codes. Their main advantages are low computational complexity and predictable decoding capabilities. Many algorithms can be extended for correction of both…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
Erasure codes provide a storage efficient alternative to replication based redundancy in (networked) storage systems. They however entail high communication overhead for maintenance, when some of the encoded fragments are lost and need to…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
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.…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
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…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Due to the sequential nature of the successive-cancellation (SC) algorithm, the decoding of polar codes suffers from significant decoding latencies. Fast SC decoding is able to speed up the SC decoding process, by implementing parallel…
We consider zero-delay single-user and multi-user source coding with average distortion constraint and decoder side information. The zero-delay constraint translates into causal (sequential) encoder and decoder pairs as well as the use of…
We consider the problem of constructing codes that can correct $\delta$ deletions occurring in an arbitrary binary string of length $n$ bits. Varshamov-Tenengolts (VT) codes can correct all possible single deletions $(\delta=1)$ with an…
This paper studies optimization of zero-delay source-channel codes, and specifically the problem of obtaining globally optimal transformations that map between the source space and the channel space, under a given transmission power…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
In coding theory, handling errors that occur when symbols are inserted or deleted from a transmitted message is a long-standing challenge. Optimising redundancy for insertion and deletion channels remains a key open problem with significant…
Biomolecular computation has emerged as an important area of computer science research due to its high information density, immense parallelism opportunity along with potential applications in cryptography, genetic engineering and…