Related papers: Phyllotaxis, a model
During development, highly ordered structures emerge as cells collectively coordinate with each other. While recent advances have clarified how individual cells process and respond to external signals, understanding collective cellular…
We demonstrate that the pattern forming partial differential equation derived from the auxin distribution model proposed by Meyerowitz, Traas and others gives rise to all spiral phyllotaxis properties observed on plants. We show how the…
The original problem of phyllotaxis was focused on the regular arrangements of leaves on mature stems represented by common fractions such as 1/2, 1/3, 2/5, 3/8, 5/13, etc. The phyllotaxis fraction is not fixed for each plant but it may…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Recently proposed budding tree is a decision tree algorithm in which every node is part internal node and part leaf. This allows representing every decision tree in a continuous parameter space, and therefore a budding tree can be jointly…
Phyllotaxis, the regular arrangement of leaves or other lateral organs in plants including pineapples, sunflowers and some cacti, has attracted scientific interest for centuries. More recently there has been interest in phyllotaxis within…
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…
Self-propulsion and navigation due to the sensing of environmental conditions - such as durotaxis and chemotaxis - are remarkable properties of biological cells that cannot be reproduced by single-component self-propelled particles. We…
We demonstrate that active rotations in chemically signalling particles, such as autochemotactic {\it E. coli} close to walls, create a route for pattern formation based on a nonlinear yet deterministic instability mechanism. For slow…
The origin of allometric scaling patterns that are multiples of 1/4 has long fascinated biologists. While not universal, scaling relationships with exponents that are close to multiples of 1/4 are common and have been described in all major…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Many patterning events in multi-cellular organisms rely on cell-to-cell contact signaling, such as the Notch pathway in metazoans. A particularly interesting phenomenon in this form of communication is lateral inhibition where a cell that…
Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
Gyrotactic algae are bottom heavy, motile cells whose swimming direction is determined by a balance between a buoyancy torque directing them upwards and fluid velocity gradients. Gyrotaxis has, in recent years, become a paradigmatic model…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…