Related papers: On reversible and reversible-complementary DNA cod…
The program Reverse Mathematics (RM for short) seeks to identify the axioms necessary to prove theorems of ordinary mathematics, usually working in the language of second-order arithmetic $L_{2}$. A major theme in RM is therefore the study…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
In 2021, Augot, Couvreur, Lavauzelle and Neri introduced a new class of rank metric codes which can be regarded as rank metric counterparts of Reed-Muller codes. Given a finite Galois extension $\mathbb{L} / \mathbb{K}$, these codes are…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
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…
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…
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…
For a linear code $C$ of length $n$ with dimension $k$ and minimum distance $d$, it is desirable that the quantity $kd/n$ is large. Given an arbitrary field $\mathbb{F}$, we introduce a novel, but elementary, construction that produces a…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Provably correct software is one of the key challenges in our softwaredriven society. While formal verification establishes the correctness of a given program, the result of program synthesis is a program which is correct by construction.…
A locally recoverable code of locality $r$ over $\mathbb{F}_{q}$ is a code where every coordinate of a codeword can be recovered using the values of at most $r$ other coordinates of that codeword. Locally recoverable codes are efficient at…
In this paper, we construct linear codes over $\mathbb{Z}_4$ with bounded $GC$-content. The codes are obtained using a greedy algorithm over $\mathbb{Z}_4$. Further, upper and lower bounds are derived for the maximum size of DNA codes of…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
This paper investigates fundamental properties of nonlinear binary codes by looking at the codebook matrix not row-wise (codewords), but column-wise. The family of weak flip codes is presented and shown to contain many beautiful properties.…
We complete the building-up construction for self-dual codes by resolving the open cases over $GF(q)$ with $q \equiv 3 \pmod 4$, and over $\Z_{p^m}$ and Galois rings $\GR(p^m,r)$ with an odd prime $p$ satisfying $p \equiv 3 \pmod 4$ with…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…
In a DNA sequence, we have the celebrated Watson-Crick complement $\overline{T}=A$, $\overline{A}=T$, $\overline{C}=G$, and $\overline{G}=C$. Given an integer $m\ge 2$, a secondary structure in a DNA sequence refers to the existence of two…
Turing's famous 'machine' framework provides an intuitively clear conception of 'computing with real numbers'. A recursive counterexample to a theorem shows that the theorem does not hold when restricted to computable objects. These…