Related papers: Symmetry Analysis Of Genetic Code And Determinativ…
Advances in de novo synthesis of DNA and computational gene design methods make possible the customization of genes by direct manipulation of features such as codon bias and mRNA secondary structure. Codon context is another feature…
The deterministic selection-recombination equation describes the evolution of the genetic type composition of a population under selection and recombination in a law of large numbers regime. So far, an explicit solution has seemed out of…
The evolutionary edit distance between two individuals in a population, i.e., the amount of applications of any genetic operator it would take the evolutionary process to generate one individual starting from the other, seems like a…
This work proposes an extension to Structured Grammatical Evolution (SGE) called Co-evolutionary Probabilistic Structured Grammatical Evolution (Co-PSGE). In Co-PSGE each individual in the population is composed by a grammar and a genotype,…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
The goal of this thesis is to advance the exploration of the statistical language learning design space. In pursuit of that goal, the thesis makes two main theoretical contributions: (i) it identifies a new class of designs by specifying an…
The Genetic Algorithm is a heuristic that can be used to produce model independent solutions to an optimization problem, thus making it ideal for use in cosmology and more specifically in the analysis of type Ia supernovae data. In this…
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…
Identifying disease genes from human genome is an important and fundamental problem in biomedical research. Despite many publications of machine learning methods applied to discover new disease genes, it still remains a challenge because of…
Several notions of multiplicativity are introduced for forms of degree $d\geq 3$ over a field of characteristic 0 or greater than d. Examples of multiplicative and strongly multiplicative forms of higher degree are given. Conditions…
Quantifying differences in terminologies from various academic domains has been a longstanding problem yet to be solved. We propose a computational approach for analyzing linguistic variation among scientific research fields by capturing…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 "golden" amino acids, 7 of their…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…
A large number of inorganic and organic compounds are able to bind DNA and form complexes, among which drug-related molecules are important. Chromatin accessibility changes not only directly affects drug-DNA interactions, but also promote…
When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure. We review information-theoretic approaches to the…
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in…