相关论文: Dimensions of Level-1 Group-Based Phylogenetic Net…

Extending previous results in the literature, random colored substitution networks and degree dimension are defined in this paper. The scale-freeness of these networks is proved by introducing a new definition for degree dimension that is…

Phylogenetic profiles - presence-absence patterns of genes across taxa - are rich information sources for inferring the evolutionary history of genes and gene families. When aggregated across many genes, these profiles can reveal…

Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…

Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…

Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations…

Rooted phylogenetic networks are rooted acyclic digraphs. They are used to model complex evolution where hybridization, recombination and other reticulation events play important roles. A rigorous definition of network compression is…

Identifying a subset of taxa that maximizes Phylogenetic Diversity (PD) is a cornerstone of quantitative conservation planning. Traditionally, PD is defined over a phylogenetic tree in which leaves resemble present-day taxa and the branch…

We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…

We derive the finite size dependence of the clustering coefficient of scale-free random graphs generated by the configuration model with degree distribution exponent $2<\gamma<3$. Degree heterogeneity increases the presence of triangles in…

We investigate the geometry of a family of log-linear statistical models called quasi-independence models. The toric fiber product is useful for understanding the geometry of parameter inference in these models because the maximum…

Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…

It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of…

We explore a systematic approach to studying the dynamics of evolving networks at a coarse-grained, system level. We emphasize the importance of finding good observables (network properties) in terms of which coarse grained models can be…

Real-world networks process structured connections since they have non-trivial vertex degree correlation and clustering. Here we propose a toy model of structure formation in real-world weighted network. In our model, a network evolves by…

Multiplex networks (a system of multiple networks that have different types of links but share a common set of nodes) arise naturally in a wide spectrum of fields. Theoretical studies show that in such multiplex networks, correlated edge…

Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…

In the paper, we present an incremental approach in the construction of scale free networks with hidden variables. The work arises from the necessity to generate that type of networks with a given number of links instead of obtaining a…

Scaling behavior of scale-free evolving networks arising in communications, citations, collaborations, etc. areas is studied. We derive universal scaling relations describing properties of such networks and indicate limits of their…

We propose a general geometric growth model for pseudofractal scale-free web, which is controlled by two tunable parameters. We derive exactly the main characteristics of the networks: degree distribution, second moment of degree…

We introduce a deterministic model for scale-free networks, whose degree distribution follows a power-law with the exponent $\gamma$. At each time step, each vertex generates its offsprings, whose number is proportional to the degree of…