Related papers: Symmetry Analysis Of Genetic Code And Determinativ…
A theoretical construction of the genetic material establishes the unique and ideal character of DNA. A similar conclusion is reached for amino acids and proteins.
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…
The grammars used in grammar-based Genetic Programming (GP) methods have a significant impact on the quality of the solutions generated since they define the search space by restricting the solutions to its syntax. In this work, we propose…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…
Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…
Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…
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…
We introduce a categorical language in which it is possible to talk about DNA sequencing, alignment methods, CRISPR, homologous recombination, haplotypes, and genetic linkage. This language takes the form of a class of limit-sketches whose…
The genesis of the stand genetic code is considered as a result of a fusion of two AU- and GC-codes distributed in two dominant and two recessive domains. The fusion of these codes is described with simple empirical rules. This formal…
We introduce GENomic Encoding REpresentation with Language Model (GENEREL), a framework designed to bridge genetic and biomedical knowledge bases. What sets GENEREL apart is its ability to fine-tune language models to infuse biological…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Ultrametric approach to the genetic code and the genome is considered and developed. $p$-Adic degeneracy of the genetic code is pointed out. Ultrametric tree of the codon space is presented. It is shown that codons and amino acids can be…
Probability theory can be studied synthetically as the computational effect embodied by a commutative monad. In the recently proposed Markov categories, one works with an abstraction of the Kleisli category and then defines deterministic…
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…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers…
Using concepts of physics of elementary particles concerning the breaking of symmetry and grannd unified theory we propose to study with the algebraic approximation the degeneracy finded in the genetic code with the incorporation of a…
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…