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Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…

In knowledge bases such as Wikidata, it is possible to assert a large set of properties for entities, ranging from generic ones such as name and place of birth to highly profession-specific or background-specific ones such as doctoral…

Neurons have a polarized structure, including dendrites and axons, and compartment-specific functions can be affected by dwelling mitochondria. It is known that the morphology of mitochondria is closely related to the functions of neurons…

Motivation: Exploring drug-protein interactions (DPIs) work as a pivotal step in drug discovery. The fast expansion of available biological data enables computational methods effectively assist in experimental methods. Among them, deep…

Significant differences in protein structures hinder the generalization of existing drug-target interaction (DTI) models, which often rely heavily on pre-learned binding principles or detailed annotations. In contrast, BioBridge designs an…

In recent years, there has been remarkable progress in machine learning for protein-protein interactions. However, prior work has predominantly focused on improving learning algorithms, with less attention paid to evaluation strategies and…

Accurate prediction of drug-target interactions (DTI) is crucial for drug discovery. Recently, deep learning (DL) models for show promising performance for DTI prediction. However, these models can be difficult to use for both computer…

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…

Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model…

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…

The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory processes, such as gene splicing, gene…

Decoding protein-protein interactions (PPIs) at the residue level is crucial for understanding cellular mechanisms and developing targeted therapeutics. We present Seq2Bind Webserver, a computational framework that leverages fine-tuned…

In this paper, we consider the statistical analysis of a protein interaction network. We propose a Bayesian model that uses a hierarchy of probabilistic assumptions about the way proteins interact with one another in order to: (i) identify…

Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often…

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide…

We present a novel dual-head deep learning architecture for protein-protein interaction modeling that enables simultaneous prediction of binding affinity ($\Delta G$) and mutation-induced affinity changes ($\Delta\Delta G$) using only…

The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing…

Increased proliferation is a key driver of tumorigenesis, and quantification of mitotic activity is a standard task for prognostication. The goal of this systematic review is scholarly analysis of all available references on mitotic…

Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…

In recent years, applications of data mining methods are become more popular in many fields of medical diagnosis and evaluations. The data mining methods are appropriate tools for discovering and extracting of available knowledge in medical…