AIMC Topic: Gene Ontology

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Discovering the mechanism of action of drugs with a sparse explainable network.

EBioMedicine Aug 24, 2023
BACKGROUND: Although Deep Neural Networks (DDNs) have been successful in predicting the efficacy of cancer drugs, the lack of explainability in their decision-making process is a significant challenge. Previous research proposed mimicking the Gene On...
Humans Artificial Intelligence Mutation Gene Ontology Cell Line Drug Repositioning
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Screening of the shared pathogenic genes of ulcerative colitis and colorectal cancer by integrated bioinformatics analysis.

Journal of cellular and molecular medicine Jul 26, 2023
Ulcerative colitis (UC) is one of the high-risk pathogenic factors for colorectal cancer (CRC). However, the shared gene and signalling mechanisms between UC and CRC remain unclear. The goal of this study was to delve more into the probable causal re...
Signal Transduction Databases, Genetic Computational Biology Gene Expression Regulation, Neoplastic Colitis, Ulcerative Gene Ontology Colorectal Neoplasms Gene Expression Profiling Protein Interaction Maps Gene Regulatory Networks Humans
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Predicting lifespan-extending chemical compounds for with machine learning and biologically interpretable features.

Aging Jul 13, 2023
Recently, there has been a growing interest in the development of pharmacological interventions targeting ageing, as well as in the use of machine learning for analysing ageing-related data. In this work, we use machine learning methods to analyse da...
Machine Learning Algorithms Caenorhabditis elegans Longevity Glutathione Aging Databases, Pharmaceutical Gene Ontology Oxidation-Reduction
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Self-prediction of relations in GO facilitates its quality auditing.

Journal of biomedical informatics Jul 10, 2023
As applications of the gene ontology (GO) increase rapidly in the biomedical field, quality auditing of it is becoming more and more important. Existing auditing methods are mostly based on rules, observed patterns or hypotheses. In this study, we pr...
Biological Ontologies Gene Ontology Machine Learning
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GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2023
The measurement of gene functional similarity plays a critical role in numerous biological applications, such as gene clustering, the construction of gene similarity networks. However, most existing approaches still rely heavily on traditional comput...
Cluster Analysis Knowledge Bases Gene Ontology Reproducibility of Results Gene Regulatory Networks
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A Deep Learning Framework for Predicting Protein Functions With Co-Occurrence of GO Terms.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2023
The understanding of protein functions is critical to many biological problems such as the development of new drugs and new crops. To reduce the huge gap between the increase of protein sequences and annotations of protein functions, many methods hav...
Gene Ontology Proteins Amino Acid Sequence Deep Learning
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Identifying the tumor location-associated candidate genes in development of new drugs for colorectal cancer using machine-learning-based approach.

Medical & biological engineering & computing Aug 10, 2022
Numerous studies have been conducted to elucidate the relation of tumor proximity to cancer prognosis and treatment efficacy in colorectal cancer. However, the molecular pathways and prognoses of left- and right-sided colorectal cancers are different...
Humans Machine Learning Colorectal Neoplasms Gene Ontology
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DeepIDA: Predicting Isoform-Disease Associations by Data Fusion and Deep Neural Networks.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
Alternative splicing produces different isoforms from the same gene locus, it is an important mechanism for regulating gene expression and proteome diversity. Although the prediction of gene(ncRNA)-disease associations has been extensively studied, f...
Gene Ontology Alternative Splicing Proteome Protein Isoforms Neural Networks, Computer Computational Biology
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Gene Identification and Potential Drug Therapy for Drug-Resistant Melanoma with Bioinformatics and Deep Learning Technology.

Disease markers Jul 23, 2022
BACKGROUND: Melanomas are skin malignant tumors that arise from melanocytes which are primarily treated with surgery, chemotherapy, targeted therapy, immunotherapy, radiation therapy, etc. Targeted therapy is a promising approach to treating advanced...
Gene Ontology Melanoma Computational Biology Gene Expression Profiling Gene Expression Regulation, Neoplastic Technology Deep Learning Prognosis Humans Protein Interaction Maps
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NILINKER: Attention-based approach to NIL Entity Linking.

Journal of biomedical informatics Jul 8, 2022
The existence of unlinkable (NIL) entities is a major hurdle affecting the performance of Named Entity Linking approaches, and, consequently, the performance of downstream models that depend on them. Existing approaches to deal with NIL entities focu...
Neural Networks, Computer Data Mining Gene Ontology Cluster Analysis Knowledge Bases
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