相关论文: Global alignment of protein-protein interaction ne…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
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…
PPI network alignment aims to find topological and functional similarities between networks of different species. Several alignment approaches have been proposed. Each of these approaches relies on a different alignment method and uses…
One of the most difficult problems difficult problem in systems biology is to discover protein-protein interactions as well as their associated functions. The analysis and alignment of protein-protein interaction networks (PPIN), which are…
Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the…
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…
The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation…
Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere…
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].…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
The function of a protein is defined by its interaction partners. Thus, topology-driven network alignment of the protein-protein interaction (PPI) networks of two species should uncover similar interaction patterns and allow identification…
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…
We explore the application of graph coloring to biological networks, specifically protein-protein interaction (PPI) networks. First, we find that given similar conditions (i.e. number of nodes, number of links, degree distribution and…
Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently,…
Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…
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 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…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used…