Related papers: DNA Codes that Avoid Secondary Structures
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
Generating protein sequences conditioned on protein structures is an impactful technique for protein engineering. When synthesizing engineered proteins, they are commonly translated into DNA and expressed in an organism such as yeast. One…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
The aim of this work is to study the structure and properties of the binary LCD codes having an automorphisms of odd prime order and to present a method for their construction.
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
We initiate the study of DNA-based distributed storage systems, where information is encoded across multiple DNA data storage containers to achieve robustness against container failures. In this setting, data are distributed over $M$…
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…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA…
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…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
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…
Codes have been used for centuries to convey secret information.To a cryptanalyst, the interception of a code is only the first step in recovering a secret message.Deoxyribonucleic acid (DNA) is a biological and molecular code.Through the…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
In this paper, we consider the outer channel for DNA-based data storage. When transmitting over the outer channel, each DNA string is treated as a unit/symbol that would be either correctly received, or erased, or corrupted by uniformly…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…