Related papers: On Algebraic Approaches for DNA Codes with Multipl…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
This paper considers cyclic DNA codes of arbitrary length over the ring $R=\F_2[u]/u^4-1$. A mapping is given between the elements of $R$ and the alphabet $\{A,C,G,T\}$ which allows the additive stem distance to be extended to this ring.…
In this paper, we discuss DNA codes that are cyclic or quasi-cyclic over $\Z_{4}+\omega \Z_{4}$, where $\omega^{2}=2+2\omega$ along with methods to construct these with combinatorial constraints. We also generalize results obtained for the…
Motivated by applications in DNA-based storage, we study explicit encoding and decoding schemes of binary strings satisfying locally balanced constraints, where the $(\ell,\delta)$-locally balanced constraint requires that the weight of any…
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…
In an interesting paper Professor Cunsheng Ding provided three constructions of cyclic codes of length being a product of two primes. Numerical data shows that many codes from these constructions are best cyclic codes of the same length and…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
A two-dimensional string is simply a two-dimensional array. We continue the study of the combinatorial properties of repetitions in such strings over the binary alphabet, namely the number of distinct tandems, distinct quartics, and runs.…
Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the…
In this paper, we construct new families of convolutional codes. Such codes are obtained by means of algebraic geometry codes. Additionally, more families of convolutional codes are constructed by means of puncturing, extending, expanding…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
Ultrametric approach to the genetic code and the genome is considered and developed. $p$-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be…
We introduce a logical foundation to reason on tree structures with constraints on the number of node occurrences. Related formalisms are limited to express occurrence constraints on particular tree regions, as for instance the children of…
Some recent studies have suggested using GANs for numeric data generation such as to generate data for completing the imbalanced numeric data. Considering the significant difference between the dimensions of the numeric data and images, as…
We study the locally recoverable codes on algebraic curves. In the first part of this article, we provide a bound of generalized Hamming weight of these codes. Whereas in the second part, we propose a new family of algebraic geometric LRC…
Constacyclic codes contain cyclic codes as a subclass and have nice algebraic structures. Constacyclic codes have theoretical importance, as they are connected to a number of areas of mathematics and outperform cyclic codes in several…