Related papers: Genetic Paralog Analysis and Simulations
Elections constitute a paradigm of decision-making problems that have puzzled experts of different disciplines for decades. We study two decision-making problems, where groups make decisions that impact only themselves as a group. In both…
Gene duplication is believed to play a major role in the evolution of genomic complexity. The presence of a duplicate removes the constraint of natural selection upon the gene, leading to its likely loss of function or, occasionally, the…
We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The…
To recognize and mitigate the harms of generative AI systems, it is crucial to consider whether and how different societal groups are represented by these systems. A critical gap emerges when naively measuring or improving who is…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
We study the impact of a hard selective sweep on the genealogy of partially linked neutral loci in the vicinity of the positively selected allele. We consider a sexual population of stochastically varying size and, focusing on two…
Several genetic programming systems are created, each solving a different problem. In these systems, the median number of generations G needed to evolve a working program is measured. The behavior of G is observed as the difficulty of the…
We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…
In bioequivalence design, power analyses dictate how much data must be collected to detect the absence of clinically important effects. Power is computed as a tail probability in the sampling distribution of the pertinent test statistics.…
Using Monte Carlo simulations on different system sizes we determine with high precision the critical thresholds of two families of directed percolation models on a square lattice. The thresholds decrease exponentially with the degree of…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
We consider two processes that have been used to study gene duplication, Watterson's [Genetics 105 (1983) 745--766] double recessive null model and Lynch and Force's [Genetics 154 (2000) 459--473] subfunctionalization model. Though the…
We study the coupled dynamics of two populations of random replicators by means of statistical mechanics methods, and focus on the effects of relative population size, strategy correlations and heterogeneities in the respective co-operation…
Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in amoeba. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as point mutation…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Spreading from a seed is studied by Monte Carlo simulation on a square lattice with two types of sites affecting the rates of birth and death. These systems exhibit a critical transition between survival and extinction. For time- dependent…
Statistical mechanics determines the abundance of different arrangements of matter depending on cost-benefit balances. Its formalism and phenomenology percolate throughout biological processes and set limits to effective computation. Under…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
We investigate the effects on cosmological clustering statistics of empirical biasing, where the galaxy distribution is a local transformation of the present-day Eulerian density field. The effects of the suppression of galaxy numbers in…