Search Results: topology

Combinational Reasoning of Quantitative Fuzzy Topological Relations for Simple Fuzzy Regions

dx.plos.org/10.1371/journal.pone.0117379
In recent years, formalization and reasoning of topological relations have become a hot topic as a means to generate knowledge about the relations between spatial objects at the conceptual and geometrical levels. These mechanisms have been widely used in spatial data query, spatial data mining, evaluation of equivalence and similarity in a spatial scene, as well as for consistency assessment of the topological relations of multi-resolution spatial databases. The concept of computation...

A Generalized Topological Entropy for Analyzing the Complexity of DNA Sequences

dx.plos.org/10.1371/journal.pone.0088519
Topological entropy is one of the most difficult entropies to be used to analyze the DNA sequences, due to the finite sample and high-dimensionality problems. In order to overcome these problems, a generalized topological entropy is introduced. The relationship between the topological entropy and the generalized topological entropy is compared, which shows the topological entropy is a special case of the generalized entropy. As an application the generalized topological entropy in int...

An Atlas of Network Topologies Reveals Design Principles for Caenorhabditis elegans Vulval Precursor Cell Fate Patterning

dx.plos.org/10.1371/journal.pone.0131397
The vulval precursor cell (VPC) fate patterning in Caenorhabditis elegans is a classic model experimental system for cell fate determination and patterning in development. Despite its apparent simplicity (six neighboring cells arranged in one dimension) and many experimental and computational efforts, the patterning strategy and mechanism remain controversial due to incomplete knowledge of the complex biology. Here, we carry out a comprehensive computational analysis and obtain a rese...

Discordance of Species Trees with Their Most Likely Gene Trees

dx.plos.org/10.1371/journal.pgen.0020068
Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from th...

Mechanistic Explanations for Restricted Evolutionary Paths That Emerge from Gene Regulatory Networks

dx.plos.org/10.1371/journal.pone.0061178
The extent and the nature of the constraints to evolutionary trajectories are central issues in biology. Constraints can be the result of systems dynamics causing a non-linear mapping between genotype and phenotype. How prevalent are these developmental constraints and what is their mechanistic basis? Although this has been extensively explored at the level of epistatic interactions between nucleotides within a gene, or amino acids within a protein, selection acts at the level...

Evolving Robust Gene Regulatory Networks

dx.plos.org/10.1371/journal.pone.0116258
Design and implementation of robust network modules is essential for construction of complex biological systems through hierarchical assembly of ‘parts’ and ‘devices’. The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology. The automatic designing capability of GRN topology that can exhibit robust behavior can dramatically change the current practice in synthetic biology. A recent study shows that Darwinian evolution can gradually deve...

Topological Data Analysis of Biological Aggregation Models

dx.plos.org/10.1371/journal.pone.0126383
We apply tools from topological data analysis to two mathematical models inspired by biological aggregations such as bird flocks, fish schools, and insect swarms. Our data consists of numerical simulation output from the models of Vicsek and D'Orsogna. These models are dynamical systems describing the movement of agents who interact via alignment, attraction, and/or repulsion. Each simulation time frame is a point cloud in position-velocity space. We analyze the topological structure ...

Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees

dx.plos.org/10.1371/journal.pone.0002651
Genomic regions participating in recombination events may support distinct topologies, and phylogenetic analyses should incorporate this heterogeneity. Existing phylogenetic methods for recombination detection are challenged by the enormous number of possible topologies, even for a moderate number of taxa. If, however, the detection analysis is conducted independently between each putative recombinant sequence and a set of reference parentals, potential recombinations between the recom...

Robust network topologies for generating oscillations with temperature-independent periods

dx.plos.org/10.1371/journal.pone.0171263
Nearly all living systems feature a temperature-independent oscillation period in circadian clocks. This ubiquitous property occurs at the system level and is rooted in the network architecture of the clock machinery. To investigate the mechanism of this prominent property of the circadian clock and provide general guidance for generating robust genetic oscillators with temperature-compensated oscillations, we theoretically explored the design principle and core network topologies pre...

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

dx.plos.org/10.1371/journal.pone.0004357
A recurrent topic in phylogenomics is the combination of various sequence alignments to reconstruct a tree that describes the evolutionary relationships within a group of species. However, such approach has been criticized for not being able to properly represent the topological diversity found among gene trees. To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection...

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