Related papers: On the Design of Codes for DNA Computing: Secondar…
In this article, we study the algebraic structure of double cyclic codes of length $(m, n)$ over $\mathbb{F}_4$ and we give a necessary and sufficient condition for a double cyclic code over $\mathbb{F}_4$ to be reversible. Also, we…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
We study the theoretical problem of synthesizing multiple DNA strands under spatial constraints, motivated by large-scale DNA synthesis technologies. In this setting, strands are arranged in an array and synthesized according to a fixed…
Biomolecular computation has emerged as an important area of computer science research due to its high information density, immense parallelism opportunity along with potential applications in cryptography, genetic engineering and…
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…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…
Block codes are considered for improving the reliability of messages stored in a computer memory with both stuck-at defects and random errors. It is assumed that the side information about the state of the defects is available to the…
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…
In this paper, we develop the theory for constructing DNA cyclic codes of odd length over $R=\Z_4[u]/\langle u^2-1 \rangle$ based on the deletion distance. Firstly, we relate DNA pairs with a special 16 elements of ring $R$. Cyclic codes of…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The…
In this paper, we study the static cell probe complexity of non-adaptive data structures that maintain a subset of $n$ points from a universe consisting of $m=n^{1+\Omega(1)}$ points. A data structure is defined to be non-adaptive when the…
In this paper, we study the theory for constructing DNA cyclic codes of odd length over $\Z_4[u]/\langle u^2 \rangle$ which play an important role in DNA computing. Cyclic codes of odd length over $\Z_4 + u \Z_4$ satisfy the reverse…
Complex orthogonal designs (CODs) are used to construct space-time block codes. COD $\mathcal{O}_z$ with parameter $[p, n, k]$ is a $p \times n$ matrix, where nonzero entries are filled by $\pm z_i$ or $\pm z^*_i$, $i = 1, 2,..., k$, such…
Code generation maps a program description to executable source code in a programming language. Existing approaches mainly rely on a recurrent neural network (RNN) as the decoder. However, we find that a program contains significantly more…
Secure codes are widely-studied combinatorial structures which were introduced for traitor tracing in broadcast encryption. To determine the maximum size of such structures is the main research objective. In this paper, we investigate the…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…