Related papers: Quantifying the common genetic variability of bact…

Reconstructing who infected whom is a central challenge in analysing epidemiological data. Recently, advances in sequencing technology have led to increasing interest in Bayesian approaches to inferring who infected whom using genetic data…

In this work, we analyze if it is possible to distinguish between different clones of the same bacteria species (Klebsiella pneumoniae) based only on microscopic images. It is a challenging task, previously considered impossible due to the…

We motivate and explore the basic features of generalized contagion, a model mechanism that unifies fundamental models of biological and social contagion. Generalized contagion builds on the elementary observation that spreading and…

Bacteria populations rely on mechanisms such as quorum sensing to coordinate complex tasks that cannot be achieved by a single bacterium. Quorum sensing is used to measure the local bacteria population density, and it controls cooperation…

Genome-Wide Association Studies (GWAS) help identify genetic variations in people with diseases such as Parkinson's disease (PD), which are less common in those without the disease. Thus, GWAS data can be used to identify genetic variations…

Competition between random genetic drift and natural selection plays a central role in evolution: Whereas non-beneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer…

Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…

The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…

The identification of sets of co-regulated genes that share a common function is a key question of modern genomics. Bayesian profile regression is a semi-supervised mixture modelling approach that makes use of a response to guide inference…

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…

It is of great interest to quantify the contributions of genetic variation to brain structure and function, which are usually measured by high-dimensional imaging data (e.g., magnetic resonance imaging). In addition to the variance, the…

Background: Prior to the current genomic era it was suggested that the number of protein-coding genes that an organism made use of was a valid measure of its complexity. It is now clear, however, that major incongruities exist and that…

This paper develops a theory for characterisation of DNA sequences based on their measure representation. The measures are shown to be random cascades generated by an infinitely divisible distribution. This probability distribution is…

Variable selection has played a critical role in modern statistical learning and scientific discoveries. Numerous regularization and Bayesian variable selection methods have been developed in the past two decades for variable selection, but…

The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds…

Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an…

The development of a complex disease is an intricate interplay of genetic and environmental factors. "Heritability" is defined as the proportion of total trait variance due to genetic factors within a given population. Studies with…

Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…

Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…

In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…