MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes

Network-based multi-omics integrative analysis methods in drug discovery: a systematic review

The integration of multi-omics data from diverse high-throughput technologies has revolutionized drug discovery. While various network-based methods have been developed to integrate multi-omics data, systematic evaluation and comparison of these methods remain challenging. This review aims to analyze network-based approaches for multi-omics integration and evaluate their applications in drug discovery. We conducted a comprehensive review of literature (2015-2024) on network-based multi-omics integration methods in drug discovery, and categorized methods into four primary types: network propagation/diffusion, similarity-based approaches, graph neural networks, and network inference models. We also discussed the applications of the methods in three scenario of drug discovery, including drug target identification, drug response prediction, and drug repurposing, and finally evaluated the performance of the methods by highlighting their advantages and limitations in specific applications. While network-based multi-omics integration has shown promise in drug discovery, challenges remain in computational scalability, data integration, and biological interpretation. Future developments should focus on incorporating temporal and spatial dynamics, improving model interpretability, and establishing standardized evaluation frameworks.

SAMNA: accurate alignment of multiple biological networks based on simulated annealing

Proteins are important parts of the biological structures and encode a lot of biological information. Protein-protein interaction network alignment is a model for analyzing proteins that helps discover conserved functions between organisms and predict unknown functions. In particular, multi-network alignment aims at finding the mapping relationship among multiple network nodes, so as to transfer the knowledge across species. However, with the increasing complexity of PPI networks, how to perform network alignment more accurately and efficiently is a new challenge. This paper proposes a new global network alignment algorithm called Simulated Annealing Multiple Network Alignment (SAMNA), using both network topology and sequence homology information. To generate the alignment, SAMNA first generates cross-network candidate clusters by a clustering algorithm on a k-partite similarity graph constructed with sequence similarity information, and then selects candidate cluster nodes as alignment results and optimizes them using an improved simulated annealing algorithm. Finally, the SAMNA algorithm was experimented on synthetic and real-world network datasets, and the results showed that SAMNA outperformed the state-of-the-art algorithm in biological performance.

Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context

At the heart of the cellular machinery through the regulation of cellular functions, protein-protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.

BioAlign: An Accurate Global PPI Network Alignment Algorithm

Motivation

The advancement of high-throughput PPI profiling techniques results in generating a large amount of PPI data. The alignment of the PPI networks uncovers the relationship between the species that can help understand the biological systems. The comparative study reveals the conserved biological interactions of the proteins across the species. It can also help study the biological pathways and signal networks of the cells. Although several network alignment algorithms are developed to study and compare the PPI data, the development of the aligner that aligns the PPI networks with high biological similarity and coverage is still challenging.

Results

This paper presents a novel global network alignment algorithm, BioAlign, that incorporates a significant amount of biological information. Existing studies use global sequence and/or 3D-structure similarity to align the PPI networks. In contrast, BioAlign uses the local sequence similarity, predicted secondary structure motifs, and remote homology in addition to global sequence and 3D-structure similarity. The extra sources of biological information help BioAlign to align the proteins with high biological similarity. BioAlign produces significantly better results in terms of AFS and Coverage (6-32 and 7-34 with respect to MF and BP, respectively) than the existing algorithms. BioAlign aligns a much larger number of proteins that have high biological similarities as compared to the existing aligners. BioAlign helps in studying the functionally similar protein pairs across the species.