Related papers: Innovation as Evolution: Case Study Phylomemetic o…

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…

The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…

The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…

In this paper, we review some advances made recently in the study of mobile phone datasets. This area of research has emerged a decade ago, with the increasing availability of large-scale anonymized datasets, and has grown into a…

Cell-cell communication is essential for tissue development, regeneration and function, and its disruption can lead to diseases and developmental abnormalities. The revolution of single-cell genomics technologies offers unprecedented…

We construct a pathwise formulation of a growing population of cells, based on two different samplings of lineages within the population, namely the forward and backward samplings. We show that a general symmetry relation, called…

In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…

We propose a novel tree classification system called Treelogy, that fuses deep representations with hand-crafted features obtained from leaf images to perform leaf-based plant classification. Key to this system are segmentation of the leaf…

Evolution and development operate at different timescales; generations for the one, a lifetime for the other. These two processes, the basis of much of life on earth, interact in many non-trivial ways, but their temporal hierarchy --…

Offloading traffic through opportunistic communications has been recently proposed as a way to relieve the current overload of cellular networks. Opportunistic communication can occur when mobile device users are (temporarily) in each…

The iterative development process is a framework used to design products and applications across a wide range of domains. It centers around building prototypes, testing them, and updating based on the test results. We discuss how we applied…

We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…

How would a cellular network designed for high energy efficiency look like? To answer this fundamental question, we model cellular networks using stochastic geometry and optimize the energy efficiency with respect to the density of base…

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…

Innovation is to organizations what evolution is to organisms: it is how organisations adapt to changes in the environment and improve. Governments, institutions and firms that innovate are more likely to prosper and stand the test of time;…

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…

Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur,…

There are a number of ways to procedurally generate interesting three-dimensional shapes, and a method where a cellular neural network is combined with a mesh growth algorithm is presented here. The aim is to create a shape from a genetic…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

Population mobility can be studied readily and cheaply using cellphone data, since people's mobility can be approximately mapped into tower-mobile registries. We model people moving in a grid-like city, where edges of the grid are weighted…