Related papers: A simple model to study phylogeographies and speci…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…

Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and…

A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…

The behavior of ecological systems mainly relies on the interactions between the species it involves. We consider the problem of inferring the species interaction network from abundance data. To be relevant, any network inference…

Natural ecosystems are characterized by striking diversity of form and functions and yet exhibit deep symmetries emerging across scales of space, time and organizational complexity. Species-area relationships and species-abundance…

A taxonomy is a standardized framework to classify and organize items into categories. Hierarchical taxonomies are ubiquitous, ranging from the classification of organisms to the file system on a computer. Characterizing the typical…

Pattern forming systems allow for a wealth of states, where wavelengths and orientation of patterns varies and defects disrupt patches of monocrystalline regions. Growth of patterns has long been recognized as a strong selection mechanism.…

In many networks, including networks of protein-protein interactions, interdisciplinary collaboration networks, and semantic networks, connections are established between nodes with complementary rather than similar properties. While…

Network science provides a universal framework for modeling complex systems, contrasting the reductionist approach generally adopted in physics. In a prototypical study, we utilize network models created from spectroscopic data of atoms to…

This paper presents an alternative approach of analyzing possibly multitype point patterns in space and space-time that occur on network structures, and introduces several different graph-related intensity measures. The proposed formalism…

We propose a general theory for surface patterning in many different biological systems, including mite and insect cuticles, pollen grains, fungal spores, and insect eggs. The patterns of interest are often intricate and diverse, yet an…

The use of science to understand its own structure is becoming popular, but understanding the organization of knowledge areas is still limited because some patterns are only discoverable with proper computational treatment of large-scale…

We review theoretical approaches to the understanding of food webs. After an overview of the available food web data, we discuss three different classes of models. The first class comprise static models, which assign links between species…

We study diffusion-driven pattern-formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing…

Hierarchical crack patterns that arise during the drying of thin films of colloidal dispersions or polymer solutions on a solid substrate are of interest both from a fundamental standpoint and in the context of the creation of transparent…

This doctoral work focuses on three main problems related to social networks: (1) Orchestrating Network Formation: We consider the problem of orchestrating formation of a social network having a certain given topology that may be desirable…

The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…

This study uses positional analysis to describe the student interaction networks in four research-based introductory physics curricula. Positional analysis is a technique for simplifying the structure of a network into blocks of actors…

Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…