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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…
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,…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
Process monitoring based on neural networks is getting more and more attention. Compared with classical neural networks, high-order neural networks have natural advantages in dealing with heteroscedastic data. However, high-order neural…
With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…
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…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
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…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
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…
In this paper, we consider pattern avoidance in a subset of words on $\{1,1,2,2,\dots,n,n\}$ called reverse double lists. In particular a reverse double list is a word formed by concatenating a permutation with its reversal. We enumerate…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
As transistor dimensions continue to shrink, binary devices are rapidly approaching their fundamental limits in power density. In response, multi-valued systems have attracted significant attention due to their enhanced information density.…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data.…
We give recurrence relations for the enumeration of symmetric elements within four classes of arc diagrams corresponding to certain involutions and set partitions whose blocks contain no consecutive integers. These arc diagrams are…