Related papers: A framework for large scale phylogenetic analysis
Processing large complex networks recently attracted considerable interest. Complex graphs are useful in a wide range of applications from technological networks to biological systems like the human brain. Sometimes these networks are…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…
Complex networks are relational data sets commonly represented as graphs. The analysis of their intricate structure is relevant to many areas of science and commerce, and data sets may reach sizes that require distributed storage and…
Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…
Network theory has proven to be a powerful tool in describing and analyzing systems by modelling the relations between their constituent objects. In recent years great progress has been made by augmenting `traditional' network theory.…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree…
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,…
Neural networks are a prevalent and effective machine learning component, and their application is leading to significant scientific progress in many domains. As the field of neural network systems is fast growing, it is important to…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
With the advancement of computational network science, its research scope has significantly expanded beyond static graphs to encompass more complex structures. The introduction of streaming, temporal, multilayer, and hypernetwork approaches…
Due to the complexity of the human body, most diseases present a high inter-personal variability in the way they manifest, i.e. in their phenotype, which has important clinical repercussions - as for instance the difficulty in defining…
Graph algorithms play an important role in many computer science areas. In order to solve problems that can be modeled using graphs, it is necessary to use a data structure that can represent those graphs in an efficient manner. On top of…
Big graph mining is an important research area and it has attracted considerable attention. It allows to process, analyze, and extract meaningful information from large amounts of graph data. Big graph mining has been highly motivated not…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
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…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…