Related papers: On reversible and reversible-complementary DNA cod…
Reverse Mathematics (RM for short) is a program in the foundations of mathematics with the aim of finding the minimal axioms required for proving theorems about countable and separable objects. RM usually takes place in second-order…
In this work, we study linear error-correcting codes against adversarial insertion-deletion (indel) errors. While most constructions for the indel model are nonlinear, linear codes offer compact representations, efficient encoding, and…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
Currently known secondary construction techniques for linear codes mainly include puncturing, shortening, and extending. In this paper, we propose a novel method for the secondary construction of linear codes based on their weight…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
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…
We introduce alphabet-permutation (AP) codes, a new family of error-correcting codes defined by iteratively applying random coordinate-wise permutations to a fixed initial word. A special case recovers random additive codes and random…
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
We consider the design of regenerating codes for distributed storage systems at the minimum bandwidth regeneration (MBR) point. The codes allow for a repair process that is exact and uncoded, but table-based. These codes were introduced in…
We provide a comprehensive overview of the fundamental structural properties of weighted projective Reed-Muller codes. We give a recursive construction for these codes, under some conditions for the weights, and we use it to derive bounds…
We construct a family of linear maximally recoverable codes with locality $r$ and dimension $r+1.$ For codes of length $n$ with $r\approx n^\alpha, 0\le\alpha\le 1$ the code alphabet is of the order $n^{1+3\alpha},$ which improves upon the…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
Counting distinct permutations with replacement, especially when involving multiple subwords, is a longstanding challenge in combinatorial analysis, with critical applications in cryptography, bioinformatics, and statistical modeling. This…
This paper describes new, simple, recursive methods of construction for orientable sequences, i.e. periodic binary sequences in which any n-tuple occurs at most once in a period in either direction. As has been previously described, such…
Let $p$ be an odd prime number, $\mathbb{F}_{p^m}$ be a finite field of cardinality $p^m$ and $s$ a positive integer. Using some combinatorial identities, we obtain certain properties for Kronecker product of matrices over $\mathbb{F}_p$…
A composition of a nonnegative integer (n) is a sequence of positive integers whose sum is (n). A composition is palindromic if it is unchanged when its terms are read in reverse order. We provide a generating function for the number of…
Cantor's diagonal method is traditionally used to prove the uncountability of the set of all infinite binary sequences. This paper analyzes the expressive limits of this method. It is shown that under any constructive application --…
In this paper, we study three applications of recursion to problems in coding and random permutations. First, we consider locally recoverable codes with partial locality and use recursion to estimate the minimum distance of such codes. Next…
Constrained coding is a fundamental field in coding theory that tackles efficient communication through constrained channels. While channels with fixed constraints have a general optimal solution, there is increasing demand for parametric…
A covering code is a set of codewords with the property that the union of balls, suitably defined, around these codewords covers an entire space. Generally, the goal is to find the covering code with the minimum size codebook. While most…