Related papers: Simulating Genomes and Populations in the Mutation…
RNA viruses provide prominent examples of measurably evolving populations. In HIV infection, the development of drug resistance is of particular interest, because precise predictions of the outcome of this evolutionary process are a…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
When a biological population expands into new territory, genetic drift develops an enormous influence on evolution at the propagating front. In such range expansion processes, fluctuations in allele frequencies occur through stochastic…
Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
An agent-based computer simulation of death by inheritable mutations in a changing environment shows a maximal population, or avoids extinction, at so intermediate mutation rate of the individuals. Thus death seems needed to al for…
Antimicrobial resistance is an emerging global health crisis that is undermining advances in modern medicine and, if unmitigated, threatens to kill 10 million people per year worldwide by 2050. Research over the last decade has demonstrated…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution. Quantum computation is a new computational paradigm which exploits quantum resources to speed up information processing tasks. Therefore, it is…
Cross-sectional HIV incidence estimation leverages recency test results to determine the HIV incidence of a population of interest, where recency test uses biomarker profiles to infer whether an HIV-positive individual was "recently"…
Advances in healthcare and in the quality of life significantly increase human life expectancy. With the ageing of populations, new un-faced challenges are brought to science. The human body is naturally selected to be well-functioning…
The sexual version of the Penna model of biological ageing, simulated since 1996, is compared here with alternative forms of reproduction as well as with models not involving ageing. In particular we want to check how sexual forms of life…
Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…
Motivation: In predicting HIV therapy outcomes, a critical clinical question is whether using historical information can enhance predictive capabilities compared with current or latest available data analysis. This study analyses whether…
We consider resequencing studies of associated loci and the problem of prioritizing sequence variants for functional follow-up. Working within the multivariate linear regression framework helps us to account for correlation across variants,…
This paper investigates the effect of learning a forward model on the performance of a statistical forward planning agent. We transform Conway's Game of Life simulation into a single-player game where the objective can be either to preserve…
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a…
Development of resistance limits efficiency of present anticancer therapies and preventing it remains big challenge in cancer research. It is accepted, at intuitive level, that the resistance emerges as a consequence of cancer cells…
Population expansions trigger many biomedical and ecological transitions, from tumor growth to invasions of non-native species. Although population spreading often selects for more invasive phenotypes, we show that this outcome is far from…