Related papers: A p-Adic Model of DNA Sequence and Genetic Code
Cell imaging and analysis are fundamental to biomedical research because cells are the basic functional units of life. Among different cell-related analysis, cell counting and detection are widely used. In this paper, we focus on one common…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the…
This paper introduces new tools for genomic signal processing, which can assist for genomic attribute extracting or describing biologically meaningful features embedded in a DNA. The codongrams and a2grams are offered as an alternative to…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has…
A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D, G, A, U, C}, where the letter D represents one or more hypothetical bases with…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…
The mathematical basis of p-adic Higgs mechanism discussed in papers [email protected] 9410058-62 is considered in this paper. The basic properties of p-adic numbers, of their algebraic extensions and the so called canonical…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…
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…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…