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...

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...

Correction: Revealing Topological Organization of Human Brain Functional Networks with Resting-State Functional Near Infrared Spectroscopy

dx.plos.org/10.1371/annotation/8941aee3-4bb8-42a0-b09a-e7c416beeef7

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...

Correction: Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks

dx.plos.org/10.1371/annotation/e1599064-95cc-47c9-bbcc-042202bf0423

Correction: Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks

dx.plos.org/10.1371/annotation/0a0bed45-e421-4f6a-8d7f-f48194a14516

Correction: Voting-Based Cancer Module Identification by Combining Topological and Data-Driven Properties

dx.plos.org/10.1371/journal.pone.0096883

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...

Correction: Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks

dx.plos.org/10.1371/annotation/b3e79f42-7316-4ff8-9762-514120463813