AIMC Topic: Polymorphism, Single Nucleotide

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Machine learning identifies interacting genetic variants contributing to breast cancer risk: A case study in Finnish cases and controls.

Scientific reports Sep 3, 2018
We propose an effective machine learning approach to identify group of interacting single nucleotide polymorphisms (SNPs), which contribute most to the breast cancer (BC) risk by assuming dependencies among BCAC iCOGS SNPs. We adopt a gradient tree b...
Gene Regulatory Networks Genetic Predisposition to Disease Polymorphism, Single Nucleotide Gene Expression Regulation, Neoplastic Female Humans Breast Neoplasms Prognosis Case-Control Studies Genome-Wide Association Study Ubiquitin-Protein Ligases Finland Protein Interaction Mapping Support Vector Machine Estrogen Receptor alpha Base Sequence Genome, Human Risk
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A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik Aug 4, 2018
Key message New fast and accurate method for phasing and imputation of SNP chip genotypes within diploid bi-parental plant populations. This paper presents a new heuristic method for phasing and imputation of genomic data in diploid plant species. Ou...
Genetic Markers Plants Alleles Haplotypes Computer Heuristics Plant Breeding Computer Simulation Genomics Polymorphism, Single Nucleotide Genotype Software
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An unsupervised machine learning method for discovering patient clusters based on genetic signatures.

Journal of biomedical informatics Jul 29, 2018
INTRODUCTION: Many chronic disorders have genomic etiology, disease progression, clinical presentation, and response to treatment that vary on a patient-to-patient basis. Such variability creates a need to identify characteristics within patient popu...
Gene Regulatory Networks Polymorphism, Single Nucleotide Computational Biology Databases, Genetic Cluster Analysis Humans Unsupervised Machine Learning Algorithms Gene Ontology Precision Medicine Linkage Disequilibrium Genome-Wide Association Study
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Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution.

Journal of computational biology : a journal of computational molecular cell biology Jul 27, 2018
Expression quantitative trait loci (eQTL) analysis is an emerging method for establishing the impact of genetic variations (such as single nucleotide polymorphisms) on the expression levels of genes. Although different methods for evaluating the impa...
Polymorphism, Single Nucleotide Genotype Computational Biology Logistic Models Gene Expression Regulation Quantitative Trait Loci Machine Learning Algorithms Gene Expression Profiling Gene Regulatory Networks Humans
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Class Balanced Multifactor Dimensionality Reduction to Detect Gene-Gene Interactions.

IEEE/ACM transactions on computational biology and bioinformatics Jul 23, 2018
Detecting gene-gene interactions in single-nucleotide polymorphism data is vital for understanding disease susceptibility. However, existing approaches may be limited by the sample size in case-control studies. Herein, we propose a balance approach f...
Algorithms Polymorphism, Single Nucleotide Computational Biology Models, Genetic Epistasis, Genetic Multifactor Dimensionality Reduction
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Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.

Nature genetics Jul 16, 2018
Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understanding the transcriptional effects of genome variation. However, this is extremely difficult because ...
Models, Genetic Gene Expression Mutation Promoter Regions, Genetic Quantitative Trait Loci Deep Learning Genome-Wide Association Study Genetic Predisposition to Disease Polymorphism, Single Nucleotide Humans Algorithms Computer Simulation
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Machine learning algorithm-based risk prediction model of coronary artery disease.

Molecular biology reports Jul 11, 2018
In view of high mortality associated with coronary artery disease (CAD), development of an early predicting tool will be beneficial in reducing the burden of the disease. The database comprising demographic, conventional, folate/xenobiotic genetic ri...
Aged Adult Male Middle Aged Forecasting Female Risk Factors Folic Acid Epistasis, Genetic Multifactor Dimensionality Reduction Xenobiotics Case-Control Studies Genetic Predisposition to Disease Polymorphism, Single Nucleotide Coronary Artery Disease Humans Machine Learning Algorithms Cytochrome P-450 CYP1A1 Glycine Hydroxymethyltransferase
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PLANET-SNP pipeline: PLants based ANnotation and Establishment of True SNP pipeline.

Genomics Jul 3, 2018
Acute prediction of SNPs (Single Nucleotide Polymorphisms) from high throughput sequencing data is a challenging problem, having potential to explore possible variation within plants species. For the extraction of profitable information from bulk of ...
Polymorphism, Single Nucleotide Machine Learning Magnoliopsida Software Ploidies Genome-Wide Association Study
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Plasminogen activator inhibitor-1 is associated with the metabolism and development of advanced colonic polyps.

Translational research : the journal of laboratory and clinical medicine Jun 6, 2018
Implications of plasminogen activator inhibitor-1 (PAI-1) in colonic polyps remain elusive. A prospective study was conducted with 188 consecutive subjects who underwent colonoscopy at a tertiary referral center. Biochemical parameters, serum PAI-1 l...
Plasminogen Activator Inhibitor 1 Cholesterol, HDL Colonic Polyps Platelet Count Genotype Insulin Resistance Adenoma Prospective Studies Female Alanine Transaminase Humans Aged Triglycerides Male Homeostasis Middle Aged Colonoscopy ROC Curve Polymorphism, Single Nucleotide
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Leveraging multiple gene networks to prioritize GWAS candidate genes via network representation learning.

Methods (San Diego, Calif.) Jun 3, 2018
Genome-wide association studies (GWAS) have successfully discovered a number of disease-associated genetic variants in the past decade, providing an unprecedented opportunity for deciphering genetic basis of human inherited diseases. However, it is s...
Genetic Predisposition to Disease Polymorphism, Single Nucleotide Machine Learning Software Humans Genome-Wide Association Study Gene Regulatory Networks
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