相关论文: Genetic Variability of Splicing Sites

In ecology and population dynamics, gene-flow refers to the transfer of a trait from one population to another. This phenomenon appears in studying the evolution of social features, such as languages. From the mathematical point of view,…

When organisms adapt to spatially heterogeneous environments, selection may drive divergence at multiple genes. If populations under divergent selection also exchange migrants, we expect genetic differentiation to be high at selected loci,…

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 consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…

The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to have more than one clearly different phenotypes. We present a model for…

The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…

In many models of genotypic evolution, the vector of genotype populations satisfies a system of linear ordinary differential equations. This system of equations models a competition between differential replication rates (fitness) and…

In this paper we explore the features of a graph generated by random walkers with nodes that have evolutionary attractiveness and Boltzmann-like transition probabilities that depend both on the euclidean distance between the nodes and on…

The notion that transcription factors bind DNA only through specific, consensus binding sites has been recently questioned. In a pioneering study by Pugh and Venters no specific consensus motif for the positioning of the human…

Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…

Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence-dependence of the local unzipping of double-stranded DNA, the first step…

Between-species coevolution, and in particular antagonistic host-parasite coevolution, is a major process shaping within-species diversity. In this paper we investigate the role of various stochastic processes affecting the outcome of the…

Scattering transforms are non-trainable deep convolutional architectures that exploit the multi-scale resolution of a wavelet filter bank to obtain an appropriate representation of data. More importantly, they are proven invariant to…

The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong non-linear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that…

Many transcription factors bind to DNA with a remarkable lack of specificity, so that regulatory binding sites compete with an enormous number of non-regulatory 'decoy' sites. For an auto-regulated gene, we show decoy sites decrease noise…

Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…

Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…

The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…

Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…

A precise estimate of allele and haplotype polymorphism is of great interest in theoretical population genetics, but also has practical applications, such as bone marrow registries management. Allele polymorphism is driven mainly by point…