Related papers: On the Design of Codes for DNA Computing: Secondar…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
Weak superimposed codes are combinatorial structures related closely to generalized cover-free families, superimposed codes, and disjunct matrices in that they are only required to satisfy similar but less stringent conditions. This class…
Messenger RNA (mRNA) vaccines are being used for COVID-19, but still suffer from the critical issue of mRNA instability and degradation, which is a major obstacle in the storage, distribution, and efficacy of the vaccine. Previous work…
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…
This paper proposes a polar code construction scheme that reduces constituent-code supplemented decoding latency. Constituent codes are the sub-codewords with specific patterns. They are used to accelerate the successive cancellation…
Recent developments in storage -- especially in the area of resistive random access memory (ReRAM) -- are attempting to scale the storage density by regarding the information data as two-dimensional (2D), instead of one-dimensional (1D).…
Locally Decodable Codes (LDCs) are error-correcting codes $C:\Sigma^n\rightarrow \Sigma^m$ with super-fast decoding algorithms. They are important mathematical objects in many areas of theoretical computer science, yet the best…
We examined what determines the designability of 2-letter codes (H and P) lattice proteins from three points of view. First, whether the native structure is searched within all possible structures or within maximally compact structures.…
Designing channel codes under low-latency constraints is one of the most demanding requirements in 5G standards. However, a sharp characterization of the performance of traditional codes is available only in the large block-length limit.…
We propose a list-decoding scheme for reconstruction codes in the context of uniform-tandem-duplication noise, which can be viewed as an application of the associative memory model to this setting. We find the uncertainty associated with…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
We consider the problem of constructing binary codes to recover from $k$-bit deletions with efficient encoding/decoding, for a fixed $k$. The single deletion case is well understood, with the Varshamov-Tenengolts-Levenshtein code from 1965…
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency,…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
The present paper is devoted to the study of the combinatorics of 216 maximal $C^3$ circular codes --- a particular type of structure arising in the analysis of genomic sequences. Their circularity property is believed to be intimately…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
This paper presents an optimal construction of $N$-bit-delay almost instantaneous fixed-to-variable-length (AIFV) codes, the general form of binary codes we can make when finite bits of decoding delay are allowed. The presented method…
In this paper, we describe a new type of DNA codes over two noncommutative rings $E$ and $F$ of order four with characteristic 2. Our DNA codes are based on quasi self-dual codes over $E$ and $F$. Using quasi self-duality, we can describe…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
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…