相关论文: A mathematical model for gene evolution after whol…

A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…

We consider a multitype Galton-Watson process that allows for the mutation and reversion of individual types in discrete and continuous time. In this setting, we explicitly compute the time evolution of quantities such as the mean and…

We propose a population-based Evolutionary Stochastic Gradient Descent (ESGD) framework for optimizing deep neural networks. ESGD combines SGD and gradient-free evolutionary algorithms as complementary algorithms in one framework in which…

BACKGROUND: The uncoupling protein (UCP) genes belong to the superfamily of electron transport carriers of the mitochondrial inner membrane. Members of the uncoupling protein family are involved in thermogenesis and determining the…

Estimation of distribution algorithms (EDA) are stochastic optimization algorithms. EDA establishes a probability model to describe the distribution of solution from the perspective of population macroscopically by statistical learning…

We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…

Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common…

Reproducibility of a deep-learning fully convolutional neural network is evaluated by training several times the same network on identical conditions (database, hyperparameters, hardware) with non-deterministic Graphics Processings Unit…

A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…

In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…

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…

Gene trees record the combination of gene level events, such as duplication, transfer and loss, and species level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene…

DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet…

Understanding the evolutionary relationship among species is of fundamental importance to the biological sciences. The location of the root in any phylogenetic tree is critical as it gives an order to evolutionary events. None of the…

Fundamental properties of macroscopic gene-mating dynamic evolutionary systems are investigated. We focus on a single locus, any number of alleles in a two-gender dioecious population, for a large class of systems within population…

Binary neutron star mergers are one of the ultimate events of massive binary star evolution, and our understanding of their parent system is still in its infancy. Upcoming gravitational wave detections, coupled with multi-wavelength…

Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…

Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of…

Understanding the evolution of dust and molecular hydrogen (H$_2$) is a critical aspect of galaxy evolution, as they affect star formation and the spectral energy distribution of galaxies. We use the $N$-body/smoothed-particle-hydrodynamics…

Replication helps ensure that a genotype-phenotype association observed in a genome-wide association (GWA) study represents a credible association and is not a chance finding or an artifact due to uncontrolled biases. We discuss…