Protein-protein interactions: Methods, databases, and applications in virus-host study

Almost all the cellular processes in a living system are controlled by proteins:They regulate gene expression,catalyze chemical reactions,transport small molecules across membranes,and transmit signal across membranes.Even,a viral infection is often initiated through virus-host protein interactions.Protein-protein interactions(PPIs)are the physical contacts between two or more proteins and they represent complex biological functions.Nowadays,PPIs have been used to construct PPI networks to study complex pathways for revealing the functions of unknown proteins.Scientists have used PPIs to find the molecular basis of certain diseases and also some potential drug targets.In this review,we will discuss how PPI networks are essential to understand the molecular basis of virus-host relationships and several databases which are dedicated to virus-host interaction studies.Here,we present a short but comprehensive review on PPIs,including the experimental and computational methods of finding PPIs,the databases dedicated to virus-host PPIs,and the associated various applications in protein interaction networks of some lethal viruses with their hosts.

Computational and bioinformatics tools for understanding disease mechanisms

Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states.The utilization of protein/gene interaction and genetic variation databases,coupled with pathway analysis can facilitate the identification of potential drug targets.By bridging the gap between molecular-level information and disease understanding,this review contributes insights into the impactful utilization of computational methods,paving the way for targeted interventions and therapeutic advancements in biomedical research.

Banian: A Cross-Platform Interactive Query System for Structured Big Data

The rapid growth of structured data has presented new technological challenges in the research fields of big data and relational database. In this paper, we present an efficient system for managing and analyzing PB level structured data called Banian. Banian overcomes the storage structure limitation of relational database and effectively integrates interactive query with large-scale storage management. It provides a uniform query interface for cross-platform datasets and thus shows favorable compatibility and scalability. Banian＇s system architecture mainly includes three layers：（1） a storage layer using HDFS for the distributed storage of massive data;（2） a scheduling and execution layer employing the splitting and scheduling technology of parallel database; and（3）an application layer providing a cross-platform query interface and supporting standard SQL. We evaluate Banian using PB level Internet data and the TPC-H benchmark. The results show that when compared with Hive, Banian improves the query performance to a maximum of 30 times and achieves better scalability and concurrency.