Related papers: A Unified Model of Codon Reassignment in Alternati…
Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential…
The frequencies of A, C, G and T in mitochondrial DNA vary among species due to unequal rates of mutation between the bases. The frequencies of bases at four-fold degenerate sites respond directly to mutation pressure. At 1st and 2nd…
We investigated the error-minimization properties of putative primordial codes that consisted of 16 supercodons, with the third base being completely redundant, using a previously derived cost function and the error minimization percentage…
In this paper we investigate a neural network model in which weights between computational nodes are modified according to a local learning rule. To determine whether local learning rules are sufficient for learning, we encode the network…
Mutation is one of the most important stages of the genetic algorithm because of its impact on the exploration of global optima, and to overcome premature convergence. There are many types of mutation, and the problem lies in selection of…
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…
Recent studies have shown that retransmissions can cause heavy-tailed transmission delays even when packet sizes are light-tailed. Moreover, the impact of heavy-tailed delays persists even when packets size are upper bounded. The key…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
An algorithm is described that adaptively learns a non-linear mutation distribution. It works by training a denoising autoencoder (DA) online at each generation of a genetic algorithm to reconstruct a slowly decaying memory of the best…
The nature of the quantitative distribution of the 64 DNA codons in the human genome has been an issue of debate for over a decade. Some groups have proposed that the quantitative distribution of the DNA codons ordered as a rank-frequency…
We perform geometrization of genetics by representing genetic information by points of the 4-adic {\it information space.} By well known theorem of number theory this space can also be represented as the 2-adic space. The process of…
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…
The Moran model with recombination is considered, which describes the evolution of the genetic composition of a population under recombination and resampling. There are $n$ sites (or loci), a finite number of letters (or alleles) at every…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing…
Animal mitochondrial genomes usually have two transfer RNAs for Leucine: one, with anticodon UAG, translates the four-codon family CUN, whilst the other, with anticodon UAA, translates the two-codon family UUR. These two genes must differ…
A basic, and still largely unanswered, question in the context of Generative Adversarial Networks (GANs) is whether they are truly able to capture all the fundamental characteristics of the distributions they are trained on. In particular,…
Codon usage bias has a crucial impact on the translation efficiency and co-translational folding of proteins, necessitating the algorithmic development of codon optimization/harmonization methods, particularly for heterologous recombinant…