Related papers: A Selective Advantage for Conservative Viruses
This paper addresses the theoretical conditions necessary for some subject of study to survive forever. A probabilistic analysis leads to some prerequisite conditions for preserving, say, electronic data indefinitely into the future. The…
The paper continues the study of the phenomenon of local immunodeficiency (LI) in viral cross-immunoreactivity networks, with a focus on the roles and interactions between altruistic and persistent viral variants. As always, only the state…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
There is little doubt in scientific circles that--counting from the origin of life towards today--evolution has led to an increase in the amount of information stored within the genomes of the biosphere. This trend of increasing information…
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis,…
How does immune system evolve functional proteins - potent antibodies - in such a short time? We address this question using a microscopic, protein-level, sequence-based model of humoral immune response with explicitly defined interactions…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
The development of a large non-coding fraction in eukaryotic DNA and the phenomenon of the code-bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code…
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…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
We investigate the competition dynamics of two microbial or viral strains that live in an environment that switches periodically between two states. One of the strains is adapted to the long-term environment, but pays a short-term cost,…
We investigate a cyclic game system where organisms face an epidemic beyond being threatened by natural enemies. As a survival strategy, individuals of one out of the species usually safeguard themselves by approaching the enemies of their…
We consider a spatial stochastic model for a pathogen population growing inside a host that attempts to eliminate the pathogens through its immune system. The pathogen population is divided into different types. A pathogen can either…
We consider a stochastic model for an evolving population. We show that in the presence of genotype extinctions the population dies out for a low mutation probability but may survive for a high mutation probability. This turns upside down…
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…
This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…
Variation and selection are the core principles of Darwinian evolution, yet quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in…
We consider a general proportional odds model for survival data under binary treatment, where the functional form of the covariates is left unspecified. We derive the efficient score for the conditional survival odds ratio given the…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
Weak purifying selection, acting on many linked mutations, may play a major role in shaping patterns of molecular evolution in natural populations. Yet efforts to infer these effects from DNA sequence data are limited by our incomplete…