相关论文: Parallel Protein Community Detection in Large-scal…

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…

Here we present ComPPI, a cellular compartment specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis (http://ComPPI.LinkGroup.hu). ComPPI enables the user…

Discovering disease pathways, which can be defined as sets of proteins associated with a given disease, is an important problem that has the potential to provide clinically actionable insights for disease diagnosis, prognosis, and…

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…

Inference of new biological knowledge, e.g., prediction of protein function, from protein-protein interaction (PPI) networks has received attention in the post-genomic era. A popular strategy has been to cluster the network into…

Essential protein plays a crucial role in the process of cell life. The identification of essential proteins can not only promote the development of drug target technology, but also contribute to the mechanism of biological evolution. There…

Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification…

Network-based computational approaches to predict unknown genes associated with certain diseases are of considerable significance for uncovering the molecular basis of human diseases. In this paper, we proposed a kind of new…

Deep learning approaches achieved significant progress in predicting protein structures. These methods are often applied to protein-protein interactions (PPIs) yet require Multiple Sequence Alignment (MSA) which is unavailable for various…

Knowledge about protein-protein interactions is essential in understanding the biological processes such as metabolic pathways, DNA replication, and transcription etc. However, a majority of the existing Protein-Protein Interaction (PPI)…

Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…

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…

Most existing community-related studies focus on detection, which aim to find the community membership for each user from user friendship links. However, membership alone, without a complete profile of what a community is and how it…

Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language…

A lot of research effort has been put into community detection from all corners of academic interest such as physics, mathematics and computer science. In this paper I have proposed a Bi-Objective Genetic Algorithm for community detection…

The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…

Over the past decade, community detection in overlapping un-weighted networks, where nodes can belong to multiple communities, has been one of the most popular topics in modern network science. However, community detection in overlapping…

Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational methods have been devised to…

Community detection is considered as a fundamental task in analyzing social networks. Even though many techniques have been proposed for community detection, most of them are based exclusively on the connectivity structures. However, there…

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…