Related papers: Topological network alignment uncovers biological …
Biological network alignment aims to identify similar regions between networks of different species. Existing methods compute node "similarities" to rapidly identify from possible alignments the "high-scoring" alignments with respect to the…
Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them. The topological alignment of two Protein-Protein Interaction (PPI) networks should thus…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
Most real-world networks are embedded in latent geometries. If a node in a network is found in the vicinity of another node in the latent geometry, the two nodes have a disproportionately high probability of being connected by a link. The…
Motivation: Since susceptibility to diseases increases with age, studying aging gains importance. Analyses of gene expression or sequence data, which have been indispensable for investigating aging, have been limited to studying genes and…
Deep neural networks proved to be a very useful and powerful tool with many practical applications. They especially excel at learning from large data sets with labeled samples. However, in order to achieve good learning results, the network…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Biological network alignment is currently in a state of disarray, with more than two dozen network alignment tools having been introduced in the past decade, with no clear winner, and other new tools being published almost quarterly. Part…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel…
We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate…
The alignment of protein-protein interaction (PPI) networks has many applications, such as the detection of conserved biological network motifs, the prediction of protein interactions, and the reconstruction of phylogenetic trees [1, 2, 3].…
Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps…
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…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
Network alignment is the problem of matching the nodes of two graphs, maximizing the similarity of the matched nodes and the edges between them. This problem is encountered in a wide array of applications-from biological networks to social…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…