AIMC Topic: Polymorphism, Single Nucleotide

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Improving variant calling using population data and deep learning.

BMC bioinformatics May 12, 2023
Large-scale population variant data is often used to filter and aid interpretation of variant calls in a single sample. These approaches do not incorporate population information directly into the process of variant calling, and are often limited to ...
Deep Learning Genome-Wide Association Study Humans High-Throughput Nucleotide Sequencing Genome, Human Gene Frequency Polymorphism, Single Nucleotide Whole Genome Sequencing
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Inference of chronic obstructive pulmonary disease with deep learning on raw spirograms identifies new genetic loci and improves risk models.

Nature genetics Apr 17, 2023
Chronic obstructive pulmonary disease (COPD), the third leading cause of death worldwide, is highly heritable. While COPD is clinically defined by applying thresholds to summary measures of lung function, a quantitative liability score has more power...
Humans Genetic Loci Genome-Wide Association Study Pulmonary Disease, Chronic Obstructive Polymorphism, Single Nucleotide Deep Learning
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Automatic extraction of ranked SNP-phenotype associations from text using a BERT-LSTM-based method.

BMC bioinformatics Apr 12, 2023
Extraction of associations of singular nucleotide polymorphism (SNP) and phenotypes from biomedical literature is a vital task in BioNLP. Recently, some methods have been developed to extract mutation-diseases affiliations. However, no accessible met...
Random Forest Machine Learning Polymorphism, Single Nucleotide Mutation Phenotype
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Genetic Risk Assessment of Nonsyndromic Cleft Lip with or without Cleft Palate by Linking Genetic Networks and Deep Learning Models.

International journal of molecular sciences Feb 25, 2023
Recent deep learning algorithms have further improved risk classification capabilities. However, an appropriate feature selection method is required to overcome dimensionality issues in population-based genetic studies. In this Korean case-control st...
Interferon Regulatory Factors Polymorphism, Single Nucleotide Genotype Cleft Lip Cleft Palate Gene Regulatory Networks Genetic Predisposition to Disease Case-Control Studies Risk Factors Deep Learning Risk Assessment Humans
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Uncovering the complex genetic architecture of human plasma lipidome using machine learning methods.

Scientific reports Feb 22, 2023
Genetic architecture of plasma lipidome provides insights into regulation of lipid metabolism and related diseases. We applied an unsupervised machine learning method, PGMRA, to discover phenotype-genotype many-to-many relations between genotype and ...
Machine Learning Phenotype Humans Unsupervised Machine Learning Lipidomics Polymorphism, Single Nucleotide Genotype
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Symphonizing pileup and full-alignment for deep learning-based long-read variant calling.

Nature computational science Dec 19, 2022
Deep learning-based variant callers are becoming the standard and have achieved superior single nucleotide polymorphisms calling performance using long reads. Here we present Clair3, which leverages two major method categories: pileup calling handles...
Polymorphism, Single Nucleotide High-Throughput Nucleotide Sequencing Deep Learning
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Evaluation of six machine learning classification algorithms in pig breed identification using SNPs array data.

Animal genetics Dec 2, 2022
Breed identification utilizing multiple information sources and methods is widely applicated in the field of animal genetics and breeding. Simultaneously, with the development of artificial intelligence, the integration of high-throughput genomic dat...
Artificial Intelligence Machine Learning Algorithms Animals Polymorphism, Single Nucleotide Swine Genomics
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Artificial intelligence model with deep learning in nonalcoholic fatty liver disease diagnosis: genetic based artificial neural networks.

Nucleosides, nucleotides & nucleic acids Nov 30, 2022
Nonalcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease in the world. The NAFLD spectrum includes simple steatosis, steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Genetic, nutritio...
Humans Deep Learning Insulin Resistance Non-alcoholic Fatty Liver Disease Neural Networks, Computer Carcinoma, Hepatocellular Liver Neoplasms Artificial Intelligence Polymorphism, Single Nucleotide
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Artificial Intelligence Based Study Association between p53 Gene Polymorphism and Endometriosis: A Systematic Review and Meta-analysis.

Computational intelligence and neuroscience Nov 18, 2022
BACKGROUND: The P53 gene is critical to the onset and progression of cancers. Currently, relevant study findings indicate that the p53 gene may have a strong association with the risk of endometriosis, but these findings have not been united. To gath...
Polymorphism, Single Nucleotide Female Tumor Suppressor Protein p53 Humans Endometriosis Genetic Predisposition to Disease Artificial Intelligence
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Gene-gene interaction detection with deep learning.

Communications biology Nov 12, 2022
The extent to which genetic interactions affect observed phenotypes is generally unknown because current interaction detection approaches only consider simple interactions between top SNPs of genes. We introduce an open-source framework for increasin...
Polymorphism, Single Nucleotide Epistasis, Genetic Neural Networks, Computer Phenotype Deep Learning
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