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Gene Ontology

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Evolving knowledge graph similarity for supervised learning in complex biomedical domains.

BMC bioinformatics
BACKGROUND: In recent years, biomedical ontologies have become important for describing existing biological knowledge in the form of knowledge graphs. Data mining approaches that work with knowledge graphs have been proposed, but they are based on ve...

Seeking for potential pathogenic genes of major depressive disorder in the Gene Expression Omnibus database.

Asia-Pacific psychiatry : official journal of the Pacific Rim College of Psychiatrists
INTRODUCTION: Major depressive disorder (MDD) is one of the most common mental disorders worldwide. The aim of this study was to identify potential pathological genes in MDD.

More Agility to Semantic Similarities Algorithm Implementations.

International journal of environmental research and public health
Algorithms for measuring semantic similarity between Gene Ontology (GO) terms has become a popular area of research in bioinformatics as it can help to detect functional associations between genes and potential impact to the health and well-being of ...

Identification of infectious disease-associated host genes using machine learning techniques.

BMC bioinformatics
BACKGROUND: With the global spread of multidrug resistance in pathogenic microbes, infectious diseases emerge as a key public health concern of the recent time. Identification of host genes associated with infectious diseases will improve our underst...

GO2Vec: transforming GO terms and proteins to vector representations via graph embeddings.

BMC genomics
BACKGROUND: Semantic similarity between Gene Ontology (GO) terms is a fundamental measure for many bioinformatics applications, such as determining functional similarity between genes or proteins. Most previous research exploited information content ...

An improved catalogue of putative synaptic genes defined exclusively by temporal transcription profiles through an ensemble machine learning approach.

BMC genomics
BACKGROUND: Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Previously, we had trained an ensemble machine learning model to assign a probability of having synaptic function to every p...

Identification of distinct blood-based biomarkers in early stage of Parkinson's disease.

Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology
Parkinson's disease (PD) is a slowly progressive geriatric disease, which can be one of the leading causes of serious socioeconomic burden in the aging society. Clinical trials suggest that prompt treatment of early-stage Parkinson's disease (EPD) ma...

Identification of aberrantly methylated‑differentially expressed genes and gene ontology in prostate cancer.

Molecular medicine reports
Prostate cancer (PCa) is the most frequent urological malignancy in men worldwide. DNA methylation has an essential role in the etiology and pathogenesis of PCa. The purpose of the present study was to identify the aberrantly methylated‑differentiall...

DeepMiR2GO: Inferring Functions of Human MicroRNAs Using a Deep Multi-Label Classification Model.

International journal of molecular sciences
MicroRNAs (miRNAs) are a highly abundant collection of functional non-coding RNAs involved in cellular regulation and various complex human diseases. Although a large number of miRNAs have been identified, most of their physiological functions remain...

NNTox: Gene Ontology-Based Protein Toxicity Prediction Using Neural Network.

Scientific reports
With advancements in synthetic biology, the cost and the time needed for designing and synthesizing customized gene products have been steadily decreasing. Many research laboratories in academia as well as industry routinely create genetically engine...