Related papers: Codon Usage Bias Measured Through Entropy Approach

The cosinor model is frequently used to represent the oscillatory behavior of different genes over time. When data are collected from multiple individuals, the cosinor model is estimated with recorded gene expression levels and the 24 hour…

Rooted trees with probabilities are used to analyze properties of a variable length code. A bound is derived on the difference between the entropy rates of the code and a memoryless source. The bound is in terms of normalized informational…

The Shannon entropy is a fundamental measure for quantifying diversity and model complexity in fields such as information theory, ecology, and genetics. However, many existing studies assume that the number of species is known, an…

Quantitative methods for studying biodiversity have been traditionally rooted in the classical theory of finite frequency tables analysis. However, with the help of modern experimental tools, like high throughput sequencing, we now begin to…

We describe a method by which the decoherence time of a solid state qubit may be measured. The qubit is coded in the orbital degree of freedom of a single electron bound to a pair of donor impurities in a semiconductor host. The qubit is…

An additive noise channel is considered, in which the distribution of the noise is nonparametric and unknown. The problem of learning encoders and decoders based on noise samples is considered. For uncoded communication systems, the problem…

A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…

Optical frequency combs, named for their comb-like peaks in the spectrum, are essential for various sensing applications. As the technology develops, its performance has reached the standard quantum limit dictated by the quantum…

Entropy quantifies the number of bits required to store objects under certain given assumptions. While this is a well established concept for strings, in the context of tries the state-of-the-art regarding entropies is less developed. The…

Before new clinical measurement methods are implemented in clinical practice, it must be confirmed whether their results are equivalent to those of existing methods. The agreement of the trend between these methods is evaluated using the…

In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…

We present three measures of the dynamical coherence of channels, which are the generalization of several previous results. The measures are based on the generalized distance function between channels, which for example could be the…

Cross-entropy benchmarking is a central technique used to certify a quantum chip in recent experiments. To better understand its mathematical foundation and develop new benchmarking schemes, we introduce the concept of ergodicity to random…

Tight lower and upper bounds on the ratio of relative entropies of two probability distributions with respect to a common third one are established, where the three distributions are collinear in the standard $(n-1)$-simplex. These bounds…

In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…

Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…

A probability distribution over the Boolean cube is monotone if flipping the value of a coordinate from zero to one can only increase the probability of an element. Given samples of an unknown monotone distribution over the Boolean cube, we…

Electronic quantum entanglement between the central chain and the two electrodes in an infinite one-dimensional two-probe device system is studied. The entanglement entropy is calculated employing the nonequilibrium Green's function method…

Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon…