Related papers: Characterizing virulence differences in a parasito…
Inferring parameters related to the aggregation pattern of parasites and to their dispersal propensity is important for predicting their ecological consequences and evolutionary potential. Nonetheless, it is notoriously difficult to infer…
Background: Pseudomonas aeruginosa has emerged as a significant opportunistic bacterial pathogen that causes nosocomial infections in healthcare settings resulting in treatment failure throughout the world. This study was carried out to…
We present a maximum entropy framework to separate intrinsic and extrinsic contributions to noisy gene expression solely from the profile of expression. We express the experimentally accessible probability distribution of the copy number of…
The genetic basis of phenotypic differences between species is among the most longstanding questions in evolutionary biology. How new genes form and the processes selection acts to produce differences across species are fundamental to…
Traditionally, studies of coevolving systems have considered cases where a parasite may inhabit only a single host. The case where a parasite may infect many hosts, widespread parasitism, has until recently gained little traction. This is…
We develop a model for speciation due to postzygotic incompatibility generated by autoimmune reactions. The model is based on predator-prey interactions between a host plants and their pathogens. Such interactions are often…
Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…
Clinical variant classification of pathogenic versus benign genetic variants remains a pivotal challenge in clinical genetics. Recently, the proposition of protein language models has improved the generic variant effect prediction (VEP)…
Viruses are known to tolerate wide ranges of pH and salt conditions and to withstand internal pressures as high as 100 atmospheres. In this paper we investigate the mechanical properties of viral capsids, calling explicit attention to the…
We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic…
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses…
Reaction-diffusion waves have long been used to describe the growth and spread of populations undergoing a spatial range expansion. Such waves are generally classed as either pulled, where the dynamics are driven by the very tip of the…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
In this paper we study invasion probabilities and invasion times of cooperative parasites spreading in spatially structured host populations. The spatial structure of the host population is given by a random geometric graph on $[0,1]^n$,…
We present an SI epidemic model whereby a continuous variable captures variability in proliferative potential and resistance to infection among susceptibles. The occurrence of heritable, spontaneous changes in these phenotype and the…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
The epidemiological behavior of Plasmodium vivax malaria occurs across spatial scales including within-host, population, and metapopulation levels. On the within-host scale, P. vivax sporozoites inoculated in a host may form latent…
The inhabitants of the bush lupine in coastal California have been the subject of scientific scrutiny in recent years. Observations of a host-parasitoid interaction in the shrub's foliage, in which victims are significantly less motile than…
Protein-protein interactions (PPIs) between a virus and its host govern infection, replication, and pathogenesis. While high-throughput mapping has identified thousands of virus-host associations, much of the virus-host interactome remains…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…