Related papers: Effective Protein-Protein Interaction Exploration …
Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…
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…
Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of…
Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used…
Background: Protein-protein interaction (PPI) network analyses are highly valuable in deciphering and understanding the intricate organisation of cellular functions. Nevertheless, the majority of available protein-protein interaction…
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…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…
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…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
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) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. It is not clear, however, how such dramatic evolutionary process has contributed to shape the large scale topology of…
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…