Related papers: The Reconstruction of Science Phylogeny
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
Strategic diagrams and co-word analysis are widely employed to examine the conceptual structure of scientific domains and their development over time. Yet a structural inconsistency characterises dominant longitudinal implementations:…
Describing the evolution of science is a salient work not only for revealing the scientific trend but also for establishing a scientific classification system. In this paper, we investigate the evolution of science by observing the…
Infrastructure shapes societies and scientific discovery. Traditional scientific infrastructure, often static and fragmented, leads to issues like data silos, lack of interoperability and reproducibility, and unsustainable short-lived…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Identifying and understanding the large-scale biodiversity patterns in time and space is vital for conservation and addressing fundamental ecological and evolutionary questions. Network-based methods have proven useful for simplifying and…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
The ICT revolution has given birth to a world of digital traces. A wide number of knowledgedriven domains like science are daily fueled by unlimited flows of textual contents. In order to navigate across these growing constellations of…
Despite the apparent cross-disciplinary interactions among scientific fields, a formal description of their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…
One of the most interesting scientific challenges nowadays deals with the analysis and the understanding of complex networks' dynamics. A major issue is the definition of new frameworks for the exploration of the dynamics at play in real…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Understanding the changing structure of science over time is essential to elucidating how science evolves. We develop diachronic embeddings of scholarly periodicals to quantify "semantic changes" of periodicals across decades, allowing us…
The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are…