Related papers: Functional geometry of protein-protein interaction…
Biological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins, drugs) and edges represent relational ties among these objects (binds-to, interacts-with, regulates). This…
In the big data era, the relationship between entries becomes more and more complex. Many graph (or network) algorithms have already paid attention to dynamic networks, which are more suitable than static ones for fitting the complex…
A large variety of interacting complex systems are characterized by interactions occurring between more than two nodes. These systems are described by simplicial complexes. Simplicial complexes are formed by simplices (nodes, links,…
Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…
With the advent of high-throughput wet lab technologies the amount of protein interaction data available publicly has increased substantially, in turn spurring a plethora of computational methods for in silico knowledge discovery from this…
Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…
Directed protein networks with only a few thousand of nodes are rather complex and do not allow to extract easily the effective influence of one protein to another taking into account all indirect pathways via the global network.…
The past two decades have seen significant successes in our understanding of complex networked systems, from the mapping of real-world social, biological and technological networks to the establishment of generative models recovering their…
Protein interactions constitute the fundamental building block of almost every life activity. Identifying protein communities from Protein-Protein Interaction (PPI) networks is essential to understand the principles of cellular organization…
Higher-order connectivity patterns such as small induced sub-graphs called graphlets (network motifs) are vital to understand the important components (modules/functional units) governing the configuration and behavior of complex networks.…
Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and…
Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we…
Protein-protein interaction (PPI) networks consist of the physical and/or functional interactions between the proteins of an organism. Since the biophysical and high-throughput methods used to form PPI networks are expensive,…
Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness…
Background. Human aging is linked to many prevalent diseases. The aging process is highly influenced by genetic factors. Hence, it is important to identify human aging-related genes. We focus on supervised prediction of such genes. Gene…
Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole…
This work describes how the formalization of complex network concepts in terms of discrete mathematics, especially mathematical morphology, allows a series of generalizations and important results ranging from new measurements of the…
Simplicial complexes are higher-order combinatorial structures which have been used to represent real-world complex systems. In this paper, we concentrate on the local patterns in simplicial complexes called simplets, a generalization of…
How and where proteins interface with one another can ultimately impact the proteins' functions along with a range of other biological processes. As such, precise computational methods for protein interface prediction (PIP) come highly…
Discovering patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary…