Related papers: Characterizing virulence differences in a parasito…
Motivation. Cancer heterogeneity is observed at multiple biological levels. To improve our understanding of these differences and their relevance in medicine, approaches to link organ- and tissue-level information from diagnostic images and…
The host immune response can often efficiently suppress a virus infection, which may lead to selection for immune-resistant viral variants within the host. For example, during HIV infection, an array of CTL immune response populations…
A two-species spatially extended system of hosts and parasitoids is studied. There are two distinct kinds of coexistence; one with populations distributed homogeneously in space and another one with spatiotemporal patterns. In the latter…
We investigate a discrete-time two-strain symbiotic epidemic model on complex networks with both random and long-range interactions. Our analysis examines how the co-infection recovery rate ($\mu$), the long-range decay exponent ($\alpha$),…
Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts with other sites in a structure have been shown to evolve more…
The behavior of two interacting populations, ``hosts''and ``parasites'', is investigated on Cayley trees and scale-free networks. In the former case analytical and numerical arguments elucidate a phase diagram, whose most interesting…
The motivation of this article is to improve inferences on the covariation in environmental exposures, motivated by data from a study of Toddlers Exposure to SVOCs in Indoor Environments (TESIE). The challenge is that the sample size is…
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The…
Dispersal of species is a fundamental ecological process in the evolution and maintenance of biodiversity. Limited control over ecological parameters has hindered progress in understanding of what enables species to colonise new area, as…
The integration of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data is crucial for understanding gene expression in spatial context. Existing methods for such integration have limited performance, with structural…
In many viruses, hundreds of proteins assemble an outer shell (capsid) around the viral nucleic acid to form an infectious virion. How the assembly process selects the viral genome amidst a vast excess of diverse cellular nucleic acids is…
We construct a seven-component model of the in-host dynamics of the Human Immunodeficiency Virus Type-1 (i.e, HIV) that accounts for latent infection and the propensity of viral mutation. A dynamical analysis is conducted and a theorem is…
In this study, we propose a novel model describing the coevolution between hosts and pathogens, based on a non-local partial differential equation formalism for populations structured by phenotypic traits. Our objective with this model is…
The defense response in plants challenged with pathogens is characterized by the activation of a diverse set of genes. Many of the same genes are induced in the defense responses of a wide range of plant species. How plant defense gene…
Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synthesis of gene products, which drives considerable…
Background: Structural Variations, SVs, in a genome can be linked to a disease or characteristic phenotype. The variations come in many types and it is a challenge, not only determining the variations accurately, but also conducting the…
Objectives: To enhance monitoring of high-burden foodborne pathogens, there is opportunity to combine pangenome data with network analysis. Methods: Salmonella enterica subspecies Enterica serovar Enteritidis isolates were referred to the…
Dynamic properties of spreading infection through a heterogeneous population are studied numerically and analytically using a dynamic variant of Watts and Strogatz Small World Network-based stochastic Susceptible-Exposed-Infectious-Removed…
We report a novel simulation strategy that enables us to identify key parameters controlling the experimentally measurable characteristics of structural protein tags on dsDNA construct translocating through a double nanopore setup. First,…
We study the behavior of epidemic routing in a delay tolerant network as a function of node density. Focusing on the probability of successful delivery to a destination within a deadline (PS), we show that PS experiences a phase transition…