Related papers: Simulating Genomes and Populations in the Mutation…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
The development of coalescent theory paved the way to statistical inference from population genetic data. In the genomic era, however, coalescent models are limited due to the complexity of the underlying ancestral recombination graph. The…
We consider the directed evolution of a population after an intervention that has significantly altered the underlying fitness landscape. We model the space of genotypes as a distributive lattice; the fitness landscape is a real-valued…
Backward simulation is an approximate inference technique for Bayesian belief networks. It differs from existing simulation methods in that it starts simulation from the known evidence and works backward (i.e., contrary to the direction of…
Simulation of population dynamics is a central research theme in computational biology, which contributes to understanding the interactions between predators and preys. Conventional mathematical tools of this theme, however, are incapable…
Dynamic models are widely used to mathematically describe biological phenomena that evolve over time. One important area of application is leukaemia research, where leukaemia cells are genetically modified in preclinical studies to explore…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
Assessing the statistical power to detect susceptibility variants plays a critical role in GWA studies both from the prospective and retrospective points of view. Power is empirically estimated by simulating phenotypes under a disease model…
Respondent-driven sampling is a form of link-tracing network sampling, which is widely used to study hard-to-reach populations, often to estimate population proportions. Previous treatments of this process have used a with-replacement…
In this paper we consider the evolution of the HIV infection under a highly effective treatment based on a combination of RTI and/or PI drugs. This is usually modelled with a set of ODEs where the drug efficacy is a constant. In this paper…
We compare and contrast the long-time dynamical properties of two individual-based models of biological coevolution. Selection occurs via multispecies, stochastic population dynamics with reproduction probabilities that depend nonlinearly…
The intratumor heterogeneity has been recognized to characterize cancer cells impairing the efficacy of cancer treatments. We here propose an extension of constraint-based modeling approach in order to simulate metabolism of cell…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
Computer simulations of complex population genetic models are an essential tool for making sense of the large-scale datasets of multiple genome sequences from a single species that are becoming increasingly available. A widely used approach…
SLiM is an efficient forward population genetic simulation designed for studying the effects of linkage and selection on a chromosome-wide scale. The program can incorporate complex scenarios of demography and population substructure,…
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the…
Fitting generative models to sequential data typically involves two recursive computations through time, one forward and one backward. The latter could be a computation of the loss gradient (as in backpropagation through time), or an…
Ending the HIV/AIDS pandemic is among the Sustainable Development Goals for the next decade. In order to overcome the gap between the need for care and the available resources, better understanding of HIV epidemics is needed to guide policy…
Most population models assume that individuals within a given population are identical, that is, the fundamental role of variation is ignored. Here we develop a general approach to modeling heterogeneous populations with discrete…
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…