Related papers: Genetic Paralog Analysis and Simulations
We consider the optimization problem of constructing a binary orthogonal array (OA) starting from a bigger one, by removing a specified amount of lines. In particular, we develop a genetic algorithm (GA) where the underlying chromosomes are…
We study weighted particle systems in which new generations are resampled from current particles with probabilities proportional to their weights. This covers a broad class of sequential Monte Carlo (SMC) methods, widely-used in applied…
Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray…
Combination of the power spectrum and bispectrum is a powerful way of breaking degeneracies between galaxy bias and cosmological parameters, enabling us to maximize the constraining power from galaxy surveys. Recent cosmological constraints…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
For a family of models of evolving population under selection, which can be described by noisy traveling wave equations, the coalescence times along the genealogical tree scale like $\log^\alpha N$, where $N$ is the size of the population,…
Xenophobic interactions play a role as important as homophilic ones in shaping many dynamical processes on social networks, such as opinion formation, social balance, or epidemic spreading. In this paper, we use belief propagation and Monte…
We consider the general branching random walk under minimal assumptions, which in particular guarantee that the empirical particle distribution admits an almost sure central limit theorem. For such a process, we study the large time decay…
Biological genomes are divided into coding and non-coding regions. Introns are non-coding parts within genes, while the remaining non-coding parts are intergenic sequences. To study the evolutionary significance of recombination inside…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
In the context of countable groups of polynomial volume growth, we consider a large class of random walks that are allowed to take long jumps along multiple subgroups according to power law distributions. For such a random walk, we study…
Commonly recognized evolutionarily relevant effects of sexual reproduction include increased diversity, accelerated adaptation, and constrained accumulation of deleterious mutations, along with a secondary effect of species genotype…
Large differences between the properties of the known sample of cataclysmic variable stars (CVs) and the predictions of the theory of binary star evolution have long been recognised. However, because all existing CV samples suffer from…
We analyse numerically the effects of small population size in the initial transient regime of a simple example population dynamics. These effects play an important role for the numerical determination of large deviation functions of…
We present a method to quantify spatial fluctuations of the substitution rate on different length scales throughout genomes of eukaryotes. The fluctuations on large length scales are found to be predominantly a consequence of a…
We consider a population with non-overlapping generations, whose size goes to infinity. It is described by a discrete genealogy which may be time non-homogeneous and we pay special attention to branching trees in varying environments. A…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
Defining the energy function as the negative logarithm of the density, we explore the energy landscape of a distribution via the tree of sublevel sets of its energy. This tree represents the hierarchy among the connected components of the…
Group sequential designs drive innovation in clinical, industrial, and corporate settings. Early stopping for failure in sequential designs conserves experimental resources, whereas early stopping for success accelerates access to improved…