Related papers: Topological network alignment uncovers biological …
We present a method that compares the protein interaction networks of two species to detect functionally similar (conserved) protein modules between them. The method is based on an algorithm we developed to identify matching subgraphs…
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and…
Our Microbiome Network Alignment Algorithm (MiNAA) aligns two microbial networks using a combination of the GRAph ALigner (GRAAL) algorithm and the Hungarian algorithm. Network alignment algorithms find pairs of nodes (one node from the…
The widespread relevance of complex networks is a valuable tool in the analysis of a broad range of systems. There is a demand for tools which enable the extraction of meaningful information and allow the comparison between different…
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…
Optimization for deep networks is currently a very active area of research. As neural networks become deeper, the ability in manually optimizing the network becomes harder. Mini-batch normalization, identification of effective respective…
Images of natural systems may represent patterns of network-like structure, which could reveal important information about the topological properties of the underlying subject. However, the image itself does not automatically provide a…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
The study of neuronal morphology is important not only for its potential relationship with neuronal dynamics, but also as a means to classify diverse types of cells and compare than among species, organs, and conditions. In the present…
The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured in ways that are otherwise inaccessible to observation. Here, we introduce the $n$-tangle method to directly compare two…
Networks are abundant in the life sciences. Outstanding challenges include how to characterize similarities between networks, and in extension how to integrate information across networks. Yet, network alignment remains a core algorithmic…
Homeostasis is widely observed in biological systems and refers to their ability to maintain an output quantity approximately constant despite variations in external disturbances. Mathematically, homeostasis can be formulated through an…
We use mathematical methods from the theory of tailored random graphs to study systematically the effects of sampling on topological features of large biological signalling networks. Our aim in doing so is to increase our quantitative…
Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of…
We provide an efficient algorithm for determining how a road network has evolved over time, given two snapshot instances from different dates. To allow for such determinations across different databases and even against hand drawn maps, we…