Related papers: A new integrated symmetrical table for genetic cod…
We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime…
The genetic code is considered to be universal. In order to test if some statistical properties of the coding bacterial genome were due to inherent properties of the genetic code, we compared the autocorrelation function, the scaling…
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…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution. Quantum computation is a new computational paradigm which exploits quantum resources to speed up information processing tasks. Therefore, it is…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
This article is interested in the origin of the genetic code, it puts forward a scenario of a simultaneous selection of the bases and amino acids and setting up of a correlation between them. Each amino acid is associated with a pair of its…
Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…
There has been much research on codes over $\mathbb{Z}_4$, sometimes called quaternary codes, for over a decade. Yet, no database is available for best known quaternary codes. This work introduces a new database for quaternary codes. It…
This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters,…
The biological distinction between the base positions in the codon, the chemical types of bases (purine and pyrimidine) and their hydrogen bond number have been the most relevant codon properties used in the genetic code analysis. Now,…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution, which are characterized by successfully finding robust solutions for optimization problems. Here, we propose a subroutine-based quantum genetic…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
Evolutionary multitasking has recently emerged as a novel paradigm that enables the similarities and/or latent complementarities (if present) between distinct optimization tasks to be exploited in an autonomous manner simply by solving them…
Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and…