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Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
Comparative graph and network analysis play an important role in both systems biology and pattern recognition, but existing surveys on the topic have historically ignored or underserved one or the other of these fields. We present an…
Modeling the effects of mutations on the binding affinity plays a crucial role in protein engineering and drug design. In this study, we develop a novel deep learning based framework, named GraphPPI, to predict the binding affinity changes…
Biomedical information graphs are crucial for interaction discovering of biomedical information in modern age, such as identification of multifarious molecular interactions and drug discovery, which attracts increasing interests in…
The actin cytoskeleton is composed of multiple networks which are specialized for several processes such as cell motility or cell division. Each of these networks are composed of organized actin microfilaments which are decorated with…
Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…
Complex networks have become essential tools for understanding diverse phenomena in social systems, traffic systems, biomolecular systems, and financial systems. Identifying critical nodes is a central theme in contemporary research,…
Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…
Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally…
It is of paramount importance to uncover influential nodes to control diffusion phenomena in a network. In recent works, there is a growing trend to investigate the role of the community structure to solve this issue. Up to now, the vast…
The IACOB and OWN surveys are two ambitious complementary observational projects which have made available a large multi-epoch spectroscopic database of optical high resolution spectra of Galactic massive O-type stars. As a first step in…
We perform factor analysis on the raw data of the four major neighborhood and shortest paths-based centrality metrics (Degree, Eigenvector, Betweeenness and Closeness) and propose a novel quantitative measure called the…
Network theory-based approaches provide valuable insights into the variations in global structural connectivity between differing dynamical states of proteins. Our objective is to review network-based analyses to elucidate such variations,…
Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional…
Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein…
In multi-domain proteins, the domains are connected by a flexible unstructured region called as protein domain linker. The accurate demarcation of these linkers holds a key to understanding of their biochemical and evolutionary attributes.…