Related papers: The Reconstruction of Science Phylogeny
The problem of identifying common concepts in the sciences and deciding when new ideas have emerged is an open one. Metascience researchers have sought to formalize principles underlying stages in the life-cycle of scientific research,…
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
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…
Concepts in a certain domain of science are linked via intrinsic connections reflecting the structure of knowledge. To get a qualitative insight and a quantitative description of this structure, we perform empirical analysis and modeling of…
With the expansion of scientific research, the number of scientific research is increasing. A new urgent problem is raised that how to keep these researches in a proper way. Therefore, knowledge mapping methods come into being, providing a…
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Network ecologists investigate the structure, function, and evolution of ecological systems using network models and analyses. For example, network techniques have been used to study community interactions (i.e., food-webs, mutualisms),…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Scientific knowledge is growing rapidly, making it difficult to track progress and high-level conceptual links across broad disciplines. While tools like citation networks and search engines help retrieve related papers, they lack the…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
Experimental evolution has yielded surprising insights into human history and evolution by shedding light on the roles of chance and contingency in history and evolution, and on the deep evolutionary roots of cooperation, conflict and kin…
Bibliometric studies based on the Web of Science (WOS) database have become an increasingly popular method for analysing the structure of scientific research. So do network approaches, which, based on empirical data, make it possible to…
Whether or not biodiversity dynamics tend toward stable equilibria remains an unsolved question in ecology and evolution with important implications for our understanding of diversity and its conservation. Phylo/population genetic models…