AIMC Topic: Alleles

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Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.

Nature genetics May 27, 2019
We address the challenge of detecting the contribution of noncoding mutations to disease with a deep-learning-based framework that predicts the specific regulatory effects and the deleterious impact of genetic variants. Applying this framework to 1,7...
Deep Learning Genomics Genetic Predisposition to Disease Genetic Association Studies Computational Biology Humans Algorithms Phenotype Autism Spectrum Disorder Genome, Human Transcription, Genetic RNA, Untranslated Genes, Reporter RNA Processing, Post-Transcriptional Gene Expression Mutation Alleles Gene Expression Regulation
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MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin.

BMC bioinformatics Feb 28, 2019
BACKGROUND: A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell lineages. MAE is highly cell-...
Machine Learning Software Reproducibility of Results Animals Mice Internet Alleles Humans Genes Chromatin
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Attribute selection and model evaluation for the maternal and paternal imprinted genes in bovine (Bos Taurus) using supervised machine learning algorithms.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie Jan 29, 2019
Imprinted genes display biased expression of paternal and maternal alleles in mammals. They are marked through epigenetic process during gametogenesis. Characterization of imprinted genes has expanded our understanding of the regulation and function ...
Humans Animals Cattle Genomic Imprinting Selection, Genetic Maternal Inheritance Paternal Inheritance Polymorphism, Single Nucleotide Long Interspersed Nucleotide Elements Supervised Machine Learning Alleles
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Factors involved in phenoconversion of CYP3A using 4β-hydroxycholesterol in stable kidney transplant recipients.

Pharmacological reports : PR Dec 15, 2018
BACKGROUND: Phenoconversion is a phenomenon whereby some genotypic extensive metabolizers transiently exhibit drug metabolizing enzyme activity at similar level as that of poor metabolizers. Renal failure is known to decrease CYP3A activity in humans...
Cytochrome P-450 CYP3A Humans Hydroxycholesterols Tumor Necrosis Factor-alpha Indican Middle Aged Kidney Transplantation Aged Genotype Interleukin-6 Young Adult Alleles Female Adult Parathyroid Hormone Male Polymorphism, Genetic
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Predictable and precise template-free CRISPR editing of pathogenic variants.

Nature Nov 7, 2018
Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a pre...
HCT116 Cells HEK293 Cells Base Sequence Gene Editing K562 Cells Reproducibility of Results Fibroblasts CRISPR-Cas Systems Alleles Menkes Kinky Hair Syndrome Templates, Genetic Substrate Specificity DNA Repair CRISPR-Associated Protein 9 Hermanski-Pudlak Syndrome Humans Machine Learning
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Increased risk of group B Streptococcus causing meningitis in infants with mannose-binding lectin deficiency.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases Oct 25, 2018
OBJECTIVES: To evaluate the association of mannose-binding lectin (MBL) deficiency with susceptibility and clinical features of group B Streptococcus (GBS) causing meningitis in Chinese infants.
Mannose-Binding Lectin Infant Meningitis, Bacterial Case-Control Studies Genetic Association Studies Humans Metabolism, Inborn Errors Young Adult China Alleles Female Adult Polymorphism, Genetic Genotype Streptococcal Infections Infant, Newborn Male Streptococcus agalactiae Risk Factors Middle Aged Disease Susceptibility
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Serum vitamin D deficiency and vitamin D receptor gene polymorphism are associated with increased risk of cardiovascular disease in a Chinese rural population.

Nutrition research (New York, N.Y.) Sep 13, 2018
Several studies have reported a conflicting association between vitamin D deficiency, vitamin D receptor (VDR) polymorphism, and the risk of cardiovascular disease (CVD). We hypothesized that serum 25(OH)D concentrations and single nucleotide polymor...
Male Cardiovascular Diseases Middle Aged China Biomarkers Asian People Blood Glucose Vitamin D Female Haplotypes Humans Polymorphism, Single Nucleotide Receptors, Calcitriol Aged Gene Frequency Genotype Vitamin D Deficiency Adult Triglycerides Logistic Models Alleles Rural Population
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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...
Genotype Genetic Markers Plants Alleles Haplotypes Computer Heuristics Plant Breeding Software Computer Simulation Genomics Polymorphism, Single Nucleotide
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A hybrid approach to increase the informedness of CE-based data using locus-specific thresholding and machine learning.

Forensic science international. Genetics Mar 31, 2018
The interpretation of genetic profiles require a robust and reliable method to discriminate true allelic information from noise, regardless of the instrumentation or methods used. Traditionally, static peak detection thresholds (analytical thresholds...
Alleles Electrophoresis, Capillary Artifacts DNA Fingerprinting Humans Machine Learning Algorithms
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Graphical classification of DNA sequences of HLA alleles by deep learning.

Human cell Jan 11, 2018
Alleles of human leukocyte antigen (HLA)-A DNAs are classified and expressed graphically by using artificial intelligence "Deep Learning (Stacked autoencoder)". Nucleotide sequence data corresponding to the length of 822 bp, collected from the Immuno...
Artificial Intelligence Sequence Analysis, DNA Alleles Base Sequence Databases, Nucleic Acid HLA-A Antigens Humans
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