Related papers: Identifying species network features from gene tre…

Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in…

Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…

Ecological networks offer powerful insights into community function, but without first characterizing these networks accurately, our ability to detect and interpret changes under environmental stress is limited. We develop an approach to…

Many complex networks, ranging from social to biological systems, exhibit structural patterns consistent with an underlying hyperbolic geometry. Revealing the dimensionality of this latent space can disentangle the structural complexity of…

When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include lineage sorting, horizontal gene transfer, and gene…

Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…

The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured in ways that are otherwise inaccessible to observation. Here, we introduce the $n$-tangle method to directly compare two…

Cycles, which can be found in many different kinds of networks, make the problems more intractable, especially when dealing with dynamical processes on networks. On the contrary, tree networks in which no cycle exists, are simplifications…

Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…

Community detection is considered as a fundamental task in analyzing social networks. Even though many techniques have been proposed for community detection, most of them are based exclusively on the connectivity structures. However, there…

An efficient structural identifiability analysis algorithm is developed in this study for a broad range of network structures. The proposed method adopts the Wright's path coefficient method to generate identifiability equations in forms of…

We study the properties of metrics aimed at the characterization of grid-like ordering in complex networks. These metrics are based on the global and local behavior of cycles of order four, which are the minimal structures able to identify…

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…

Several natural and theoretical networks can be broken down into smaller portions, or subgraphs corresponding to neighborhoods. The more frequent of these neighborhoods can then be understood as motifs of the network, being therefore…

Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…

Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…