Related papers: Codon Usage Bias Measured Through Entropy Approach
Efficient protein synthesis depends on the availability of charged tRNA molecules. With 61 different codons, shifting the balance among the tRNA abundances can lead to large changes in the protein synthesis rate. Previous theoretical work…
We frame the problem of selecting an optimal audio encoding scheme as a supervised learning task. Through uniform convergence theory, we guarantee approximately optimal codec selection while controlling for selection bias. We present…
The length of coding sequence series in microbial genomes were regarded as a fluctuating system and characterized by the methods of statistical physics. The distribution and the correlatin properties of 50 genomes including bacteria and…
Superdense Coding is a cornerstone in secure quantum communication, exploiting pre-shared entanglement to encode two classical bits within a single qubit. However, noise and decoherence deteriorate entanglement quality, restricting both…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
The noise of a device under test (DUT) is measured simultaneously with two instruments, each of which contributes its own background. The average cross power spectral density converges to the DUT power spectral density. This method enables…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
Considering vast amounts of genomic sequences of mostly unknown functionality, in-silico prediction of functional regions is an important enterprise. Many genomic browsers employ GC content, which was observed to be elevated in gene-rich…
Quantum computation will rely on quantum error correction to counteract decoherence. Successfully implementing an error correction protocol requires the fidelity of qubit operations to be well-above error correction thresholds. In…
An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content…
We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
The purpose of this study was to investigate how the entropy of a neuron cell can be measured using membrane ion current signals, which were recorded from neurons in the mouse medial prefrontal cortex (mPFC). The sample entropy and the…
We consider a scenario in which qubit-like probes are used to sense an external field that linearly affects their energy splitting. Following the frequency estimation approach in which one optimizes the state and sensing time of the probes…
Entropy measures of probability distributions are widely used measures in ecology, biology, genetics, and in other fields, to quantify species diversity of a community. Unfortunately, entropy-based diversity indices, or diversity indices…
Consider a measurement in which the current coming out of a mesoscopic sample is filtered around a given frequency, amplified, measured and squared. Then this process is repeated many times and the results are averaged. Often, two such…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
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…
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…
Entropy is a measure of heterogeneity widely used in applied sciences, often when data are collected over space. Recently, a number of approaches has been proposed to include spatial information in entropy. The aim of entropy is to…