Related papers: Bio-JOIE: Joint Representation Learning of Biologi…
Many large-scale knowledge bases simultaneously represent two views of knowledge graphs (KGs): an ontology view for abstract and commonsense concepts, and an instance view for specific entities that are instantiated from ontological…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. Meanwhile, knowledge bases (KBs) contain huge amounts of structured information of protein…
Because protein-protein interactions (PPIs) are crucial to understand living systems, harvesting these data is essential to probe disease development and discern gene/protein functions and biological processes. Some curated datasets contain…
Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…
Protein-protein interactions (PPIs) are essentials for many biological processes where two or more proteins physically bind together to achieve their functions. Modeling PPIs is useful for many biomedical applications, such as vaccine…
Interactions between SARS-CoV-2 and human proteins (SARS-CoV-2 PPIs) cause information transfer through biochemical pathways that contribute to the immunopathology of COVID-19. Here, we present a communication network model of the immune…
Protein-protein interaction networks provide a graph-level view of cellular organization, yet their functional modules are overlapping, noisy, and difficult to interpret from cluster assignments alone. Existing community-detection methods…
Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…
Discovery gene-disease links is important in biology and medicine areas, enabling disease identification and drug repurposing. Machine learning approaches accelerate this process by leveraging biological knowledge represented in ontologies…
Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection…
Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…
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…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot…
Predicting protein-protein interactions (PPIs) by learning informative representations from amino acid sequences is a challenging yet important problem in biology. Although various deep learning models in Siamese architecture have been…
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…
Automatically extracting Protein-Protein Interactions (PPI) from biomedical literature provides additional support for precision medicine efforts. This paper proposes a novel memory network-based model (MNM) for PPI extraction, which…
Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally…
Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…
Given the existing COVID-19 pandemic worldwide, it is critical to systematically study the interactions between hosts and coronaviruses including SARS-Cov, MERS-Cov, and SARS-CoV-2 (cause of COVID-19). We first created four host-pathogen…
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…