AIMC Topic: Polymorphism, Single Nucleotide

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Spatial rank-based multifactor dimensionality reduction to detect gene-gene interactions for multivariate phenotypes.

BMC bioinformatics Oct 4, 2021
BACKGROUND: Identifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionality reduction (MDR) is a popul...
Polymorphism, Single Nucleotide Models, Genetic Epistasis, Genetic Multifactor Dimensionality Reduction Algorithms Phenotype Computer Simulation Genome-Wide Association Study
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LightGBM: accelerated genomically designed crop breeding through ensemble learning.

Genome biology Sep 20, 2021
LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize lines. LightGBM exhibits superior performa...
Decision Trees Zea mays Crops, Agricultural Plant Breeding Machine Learning Software Genome-Wide Association Study Genomics Polymorphism, Single Nucleotide
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Genetic dissection of complex traits using hierarchical biological knowledge.

PLoS computational biology Sep 17, 2021
Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical bio...
Neural Networks, Computer Machine Learning Phenotype Genome-Wide Association Study Metabolic Networks and Pathways Copper Mutation Glucose Polymorphism, Single Nucleotide Computational Biology Systems Biology Models, Genetic Benomyl Nucleotidyltransferases Gene Ontology Glycine Hydroxyurea Knowledge Bases Chromosome Mapping Saccharomyces cerevisiae Multifactorial Inheritance
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NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks.

Genome biology Sep 6, 2021
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs usin...
INDEL Mutation Chromosome Mapping Major Histocompatibility Complex Nanopore Sequencing Humans High-Throughput Nucleotide Sequencing Neural Networks, Computer Haplotypes Base Sequence Polymorphism, Single Nucleotide Genome, Human Nanoparticles Benchmarking Alleles
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Assigning function to SNPs: Considerations when interpreting genetic variation.

Seminars in cell & developmental biology Aug 24, 2021
Assigning function to single nucleotide polymorphisms (SNPs) to understand the mechanisms that link genetic and phenotypic variation and disease is an area of intensive research that is necessary to contribute to the continuing development of precisi...
Precision Medicine Polymorphism, Single Nucleotide Genetic Variation Humans Machine Learning
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Interleukin-37 gene polymorphism and susceptibility to pulmonary tuberculosis among Iraqi patients.

The Indian journal of tuberculosis Aug 12, 2021
BACKGROUND: Control of tuberculosis (TB) depends on a balance between host's immune factors and bacterial evasion strategies. Interleukin-37 (IL-37) is among the immunomodulatory factors that have been proposed to influence susceptibility to tubercul...
Polymorphism, Single Nucleotide Humans Interleukins Case-Control Studies Iraq Genetic Predisposition to Disease Tuberculosis, Pulmonary
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A deep learning model for predicting next-generation sequencing depth from DNA sequence.

Nature communications Jul 19, 2021
Targeted high-throughput DNA sequencing is a primary approach for genomics and molecular diagnostics, and more recently as a readout for DNA information storage. Oligonucleotide probes used to enrich gene loci of interest have different hybridization...
Humans DNA High-Throughput Nucleotide Sequencing Deep Learning DNA Probes Genomics Base Sequence Polymorphism, Single Nucleotide Sequence Analysis, DNA
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An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism.

Scientific reports Jul 7, 2021
Venous thromboembolism is the third common cardiovascular disease and is composed of two entities, deep vein thrombosis (DVT) and its potential fatal form, pulmonary embolism (PE). While PE is observed in ~ 40% of patients with documented DVT, there ...
Pulmonary Embolism Receptors, Cell Surface Humans Genetic Predisposition to Disease Neural Networks, Computer Polymorphism, Single Nucleotide COVID-19 Proteomics Phenotype Female Adult Male Genome-Wide Association Study
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Risk prediction for delayed clearance of high-dose methotrexate in pediatric hematological malignancies by machine learning.

International journal of hematology Jun 25, 2021
This study aimed to establish a predictive model to identify children with hematologic malignancy at high risk for delayed clearance of high-dose methotrexate (HD-MTX) based on machine learning. A total of 205 patients were recruited. Five variables ...
Methotrexate Alleles Antimetabolites, Antineoplastic Humans Polymorphism, Single Nucleotide Pharmacogenomic Testing Hematologic Neoplasms Machine Learning Genotype Risk Assessment Biomarkers Nomograms Child Reproducibility of Results ROC Curve
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Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen.

Nature communications Jun 10, 2021
Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere...
INDEL Mutation Chromosomes Arabidopsis Retroelements Crossing Over, Genetic Genes, Duplicate Sequence Inversion Pedigree Meiosis Eukaryota Genome Genetic Variation Polymorphism, Genetic Genomics Ascomycota Polymorphism, Single Nucleotide Machine Learning Models, Genetic Computer Simulation Evolution, Molecular Phylogeny Genome-Wide Association Study
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