Related papers: Conspiracy in bacterial genomes
Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we apply them to statistical modeling of peptides by…
We give a probabilistic interpretation of the configurational partition function of the logarithmic sector of critical cosmological topologically massive gravity, in which the Hurwitz numbers considered in our previous works assume the role…
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
We discuss the statistical properties of parton distributions within the framework of the NNPDF methodology. We present various tests of statistical consistency, in particular that the distribution of results does not depend on the…
This study investigates entropy's potential for analyzing scientific research patterns across disciplines. Originating from thermodynamics, entropy now measures uncertainty and diversity in information systems. We examine Shannon Entropy,…
In this paper, we address a longstanding challenge in self-organized criticality (SOC) systems: establishing a connection between sandpiles and complex networks. Our approach employs a similarity-based transfer function characterized by two…
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal…
Learning directionality between variables is crucial yet challenging, especially for mechanistic relationships without a priori ordering assumptions. We propose a coefficient of asymmetry to quantify directional asymmetry using Shannon's…
We investigate stochastic comparisons between exponential family distributions and their mixtures with respect to the usual stochastic order, the hazard rate order, the reversed hazard rate order, and the likelihood ratio order. A general…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any…
We recall the physical features of the parton distributions in the quantum statistical approach of the nucleon. Some predictions from a next-to-leading order QCD analysis are compared to recent experimental results. We also consider their…
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…
Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely…
In this paper introduces a new family of continuous distributions namely the Poison transmuted-G family of distribution is proposed by inducing two addition parameter on the base line G distribution. Some of its mathematical properties…
Any continuous curve in a higher dimensional space can be considered a trajectory that can be parameterized by a single variable, usually taken as time. It is well known that a continuous curve can have a fractional dimensionality, which…
The fractional order generalization of Shannon entropy proposed by Ubriaco has been studied for discrete distributions. In the current paper, we conduct a detailed study of the continuous analogue of this entropy termed as fractional…
The application of the Shannon entropy to study the relationship between information and structures has yielded insights into molecular and material systems. However, the difficulty in directly observing and manipulating atoms and molecules…
We reveal the rule with which we predicted, and verified by detailed numerical calculations on dozens of specific cases over the last decade, the emergence of hidden induced states and the formation of quartets of order parameters. The rule…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…