Related papers: On the Design of Codes for DNA Computing: Secondar…
Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash,…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…
We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…
We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
We derive theoretical upper and lower bounds on the maximum size of DNA codes of length n with constant GC-content w and minimum Hamming distance d, both with and without the additional constraint that the minimum Hamming distance between…
The structures of cyclic DNA codes of odd length over the finite rings R=Z_{4}+wZ_{4}, w^{2}=2 and S=Z_{4}+wZ_{4}+vZ_{4}+wvZ_{4},w^{2}=2,v^{2}=v,wv=vw are studied. The links between the elements of the rings R, S and 16 and 256 codons are…
We introduce a new family of binary linear codes suitable for steganographic matrix embedding. The main characteristic of the codes is the staircase random block structure of the generator matrix. We propose an efficient list decoding…
In this paper we propose a simple method for generating short-length rate-compatible codes over $\mathbb{Z}_M$ that are robust to non-coherent detection for $M$-PSK constellations. First, a greedy algorithm is used to construct a family of…
The study of constant-weight codes in $\ell_1$-metric was motivated by the duplication-correcting problem for data storage in live DNA. It is interesting to determine the maximum size of a code given the length $n$, weight $w$, minimum…
Let $p$ be an odd prime and $r,s,m$ be positive integers. In this study, we initiate our exploration by delving into the intricate structure of all repeated-root cyclic codes and their duals with a length of $2^rp^s$ over the finite field…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
The problem of correcting deletions and insertions has recently received significantly increased attention due to the DNA-based data storage technology, which suffers from deletions and insertions with extremely high probability. In this…
DNA strand displacement systems have proven themselves to be fertile substrates for the design of programmable molecular machinery and circuitry. Domain-level reaction enumerators provide the foundations for molecular programming languages…
The genetic code is the function from the set of codons to the set of amino acids by which a DNA sequence encodes proteins. Since the codons also influence the shape of the DNA molecule itself, the same sequence that encodes a protein also…
Designing DNA and protein sequences with improved function has the potential to greatly accelerate synthetic biology. Machine learning models that accurately predict biological fitness from sequence are becoming a powerful tool for…
In this work, we study two types of constraints on two-dimensional binary arrays. In particular, given $p,\epsilon>0$, we study (i) The $p$-bounded constraint: a binary vector of size $m$ is said to be $p$-bounded if its weight is at most…
We propose a new deterministic methodology to predict RNA sequence and protein folding. Is stem enough for structure prediction? The main idea is to consider all possible stem formation in the given sequence. With the stem loop energy and…
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…