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Genome-Wide Association Study

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Prediction of Alzheimer's disease-specific phospholipase c gamma-1 SNV by deep learning-based approach for high-throughput screening.

Proceedings of the National Academy of Sciences of the United States of America Jan 19, 2021
Exon splicing triggered by unpredicted genetic mutation can cause translational variations in neurodegenerative disorders. In this study, we discover Alzheimer's disease (AD)-specific single-nucleotide variants (SNVs) and abnormal exon splicing of ph...
Humans Computer Simulation Animals Alzheimer Disease High-Throughput Screening Assays Genome, Human RNA Splicing Exons Phospholipase C gamma Genetic Predisposition to Disease Deep Learning Polymorphism, Single Nucleotide Genome-Wide Association Study RNA, Messenger Mice Disease Models, Animal
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Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations.

Nucleic acids research Jan 11, 2021
Assessing the causal tissues of human complex diseases is important for the prioritization of trait-associated genetic variants. Yet, the biological underpinnings of trait-associated variants are extremely difficult to infer due to statistical noise ...
Models, Genetic Transcription Factors Causality Epigenome Humans Linkage Disequilibrium Deep Learning Datasets as Topic Genetic Diseases, Inborn Organ Specificity Chromatin Immunoprecipitation Molecular Sequence Annotation Histone Code Binding Sites Genome-Wide Association Study Polymorphism, Single Nucleotide Epigenomics
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Protocol for Epistasis Detection with Machine Learning Using GenEpi Package.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
To develop medical treatments and prevention, the association between disease and genetic variants needs to be identified. The main goal of genome-wide association study (GWAS) is to discover the underlying reason for vulnerability to disease and uti...
Computational Biology Databases, Genetic Genome, Human Epistasis, Genetic Genome-Wide Association Study Polymorphism, Single Nucleotide Genotype Genetic Association Studies Humans Machine Learning Software Phenotype
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Brief Survey on Machine Learning in Epistasis.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
In biology, the term "epistasis" indicates the effect of the interaction of a gene with another gene. A gene can interact with an independently sorted gene, located far away on the chromosome or on an entirely different chromosome, and this interacti...
Crohn Disease Plants Macular Degeneration Data Mining Genome-Wide Association Study Polymorphism, Single Nucleotide Computational Biology Inheritance Patterns Alzheimer Disease Genome, Human Epistasis, Genetic Quantitative Trait, Heritable Humans Machine Learning Phenotype Neoplasms
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PheMap: a multi-resource knowledge base for high-throughput phenotyping within electronic health records.

Journal of the American Medical Informatics Association : JAMIA Nov 1, 2020
OBJECTIVE: Developing algorithms to extract phenotypes from electronic health records (EHRs) can be challenging and time-consuming. We developed PheMap, a high-throughput phenotyping approach that leverages multiple independent, online resources to s...
Diabetes Mellitus, Type 2 Electronic Health Records Polymorphism, Single Nucleotide Adult Knowledge Bases Humans Hypothyroidism Dementia Information Storage and Retrieval Algorithms Genome-Wide Association Study Natural Language Processing Terminology as Topic Phenotype
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Statistical and Machine Learning Methods for eQTL Analysis.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2020
An immense amount of observable diversity exists for all traits and across global populations. In the post-genomic era, equipped with efficient sequencing capabilities and better genotyping methods, we are now able to more fully appreciate how regula...
Chromosome Mapping Computational Biology Humans Data Interpretation, Statistical Machine Learning Gene Expression Genome-Wide Association Study Quantitative Trait Loci
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Convolutional Neural Network Visualization for Identification of Risk Genes in Bipolar Disorder.

Current molecular medicine Jan 1, 2020
BACKGROUND: Bipolar disorder (BD) is a type of chronic emotional disorder with a complex genetic structure. However, its genetic molecular mechanism is still unclear, which makes it insufficient to be diagnosed and treated.
Humans Neural Networks, Computer Bipolar Disorder Genome-Wide Association Study Genetic Predisposition to Disease Polymorphism, Single Nucleotide Molecular Sequence Annotation
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Convolutional neural network model to predict causal risk factors that share complex regulatory features.

Nucleic acids research Dec 16, 2019
Major progress in disease genetics has been made through genome-wide association studies (GWASs). One of the key tasks for post-GWAS analyses is to identify causal noncoding variants with regulatory function. Here, on the basis of >2000 functional fe...
Genetic Predisposition to Disease Mental Disorders Regulatory Sequences, Nucleic Acid Humans Polymorphism, Single Nucleotide Neural Networks, Computer Risk Factors Autoimmune Diseases Genome-Wide Association Study Quantitative Trait Loci
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Identification of disease-associated loci using machine learning for genotype and network data integration.

Bioinformatics (Oxford, England) Dec 15, 2019
MOTIVATION: Integration of different omics data could markedly help to identify biological signatures, understand the missing heritability of complex diseases and ultimately achieve personalized medicine. Standard regression models used in Genome-Wid...
Genome-Wide Association Study Humans Gene Regulatory Networks Machine Learning Polymorphism, Single Nucleotide Phenotype Genotype
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A guide to machine learning for bacterial host attribution using genome sequence data.

Microbial genomics Dec 1, 2019
With the ever-expanding number of available sequences from bacterial genomes, and the expectation that this data type will be the primary one generated from both diagnostic and research laboratories for the foreseeable future, then there is both an o...
Salmonella typhimurium Swine Humans Birds Whole Genome Sequencing Host Specificity Machine Learning Genome-Wide Association Study Salmonella Infections Salmonella Infections, Animal Cattle Animals Genome, Bacterial
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