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Proteins execute various activities required by biological cells. Further, they structurally support and pro-mote important biochemical reactions which functionally are sparked by active-sites. Active-sites are regions where reac-tions and…
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…
Predicting compound-protein affinity is critical for accelerating drug discovery. Recent progress made by machine learning focuses on accuracy but leaves much to be desired for interpretability. Through molecular contacts underlying…
Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already…
Pro-inflammatory peptides (PIPs) play critical roles in immune signaling and inflammation but are difficult to identify experimentally due to costly and time-consuming assays. To address this challenge, we present KEMP-PIP, a hybrid machine…
Process Mining is a famous technique which is frequently applied to Software Development Processes, while being neglected in Human-Computer Interaction (HCI) recommendation applications. Organizations usually train employees to interact…
A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often…
Large-scale Electronic Health Record (EHR) databases have become indispensable in supporting clinical decision-making through data-driven treatment recommendations. However, existing medication recommender methods often struggle with a user…
Drug-Drug Interactions (DDIs) significantly influence therapeutic efficacy and patient safety. As experimental discovery is resource-intensive and time-consuming, efficient computational methodologies have become essential. The predominant…
Large-scale industrial recommender systems are usually confronted with computational problems due to the enormous corpus size. To retrieve and recommend the most relevant items to users under response time limits, resorting to an efficient…
Background: Breast cancer is a multifactorial disease, genetic and environmental factors will affect its incidence probability. Breast cancer metastasis is one of the main cause of breast cancer related deaths reported by the American…
Parkinson's disease (PD) is a slowly progressing neurodegenerative disease with early manifestation of motor signs. Recently, there has been a growing interest in developing automatic tools that can assess motor function in PD patients.…
Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively…
In the big data era, the relationship between entries becomes more and more complex. Many graph (or network) algorithms have already paid attention to dynamic networks, which are more suitable than static ones for fitting the complex…
Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…
The AMIDER, Advanced Multidisciplinary Integrated-Database for Exploring new Research, is a newly developed research data catalog to demonstrate an advanced database application. AMIDER is characterized as a multidisciplinary database…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
Parkinson's disease (PD) is a common neurodegenerative disease with a high degree of heterogeneity in its clinical features, rate of progression, and change of variables over time. In this work, we present a novel data-driven, network-based…
Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biological processes. Accurately predicting PTM sites and their…
The major histocompatibility complex (MHC) class-I pathway supports the detection of cancer and viruses by the immune system. It presents parts of proteins (peptides) from inside a cell on its membrane surface enabling visiting immune cells…