Related papers: Metrics and Harmonic Analysis on DNA
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…
An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically…
Dielectric spectroscopy is used to investigate fundamental length scales of 146 bp short-fragment (nucleosomal) dilute Na-DNA solutions. Two relaxation modes are detected: the high- and the low-frequency mode. Dependence of the…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
ds-RNA and standard ds-DNA show specific structural differences in their di-nucleotide steps, piled along the helical axis. Modeling the helices of short fragments by a 3D mesoscopic Hamiltonian model, I use path integral techniques to…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
The presence of low dimensional chaos in the protein secondary structures, using the binary coded $\alpha$-helices and $\beta$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on the…
In this work, we study the DNA codes from the ring R = Z4 + wZ4, where w^2 = 2+2w with 16 elements. We establish a one to one correspondence between the elements of the ring R and all the DNA codewords of length 2 by defining a…
The discovery of new crystalline materials calls for generative models that handle periodic boundary conditions, crystallographic symmetries, and physical constraints, while scaling to large and structurally diverse unit cells. We propose a…
Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on…
As long as human beings exist on this earth, there will be confidential images intended for limited audience. These images have to be transmitted in such a way that no unauthorized person gets knowledge of them. DNA sequences play a vital…
In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
Computing the similarity between two DNA sequences is of vital importance in bioscience, yet it can be computationally expensive on classical hardware. For example, the edit distance with move operations (EDM), a DNA similarity measure of…