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Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing ground for drug repurposing…
Prediction of protein-ligand interactions (PLI) plays a crucial role in drug discovery as it guides the identification and optimization of molecules that effectively bind to target proteins. Despite remarkable advances in deep…
Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
A novel group of small non-coding RNA, known as microRNA (miRNA) is predicted to regulate as high as 90% of the coding genes in human. The diversity and abundance of miRNA targets offer an enormous level of combinatorial possibilities and…
We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess…
Within a case study on the protein-protein interaction network (PIN) of Drosophila melanogaster we investigate the relation between the network's spectral properties and its structural features such as the prevalence of specific subgraphs…
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of compound-protein interactions for rational drug discovery. Existing deep learning-based methods utilize only the single modality of protein sequences…
Protein-protein interactions (PPIs) perform important roles on biological functions. Researches of mutants on protein interactions can further understand PPIs. In the past, many researchers have developed databases that stored mutants on…
A graph with semantically attributed nodes are a common data structure in a wide range of domains. It could be interlinked web data or citation networks of scientific publications. The essential problem for such a data type is to determine…
Omics data analysis is crucial for studying complex diseases, but its high dimensionality and heterogeneity challenge classical statistical and machine learning methods. Graph neural networks have emerged as promising alternatives, yet the…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
Protein-protein interactions (PPIs) are critical for various biological processes, and understanding their dynamics is essential for decoding molecular mechanisms and advancing fields such as cancer research and drug discovery. Mutations in…
Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful…
Protein-protein interaction (PPI) prediction plays a pivotal role in deciphering cellular functions and disease mechanisms. To address the limitations of traditional experimental methods and existing computational approaches in cross-modal…
Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs…
Understanding the mathematical properties of graphs underling biological systems could give hints on the evolutionary mechanisms behind these structures. In this article we perform a complete statistical analysis over thousands of graphs…
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly replaced the Delta variant as a dominating SARS-CoV-2 variant because of natural selection, which favors the variant with higher infectivity and…