AIMC Topic: Genome, Human

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DeepCNV: a deep learning approach for authenticating copy number variations.

Briefings in bioinformatics Sep 2, 2021
Copy number variations (CNVs) are an important class of variations contributing to the pathogenesis of many disease phenotypes. Detecting CNVs from genomic data remains difficult, and the most currently applied methods suffer from an unacceptably hig...
Humans Deep Learning ROC Curve Datasets as Topic Genome, Human False Positive Reactions Disease DNA Copy Number Variations Area Under Curve Benchmarking
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A deep learning approach for filtering structural variants in short read sequencing data.

Briefings in bioinformatics Jul 20, 2021
Short read whole genome sequencing has become widely used to detect structural variants in human genetic studies and clinical practices. However, accurate detection of structural variants is a challenging task. Especially existing structural variant ...
Deep Learning Whole Genome Sequencing High-Throughput Nucleotide Sequencing Genome, Human Humans Software
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Prediction of driver variants in the cancer genome via machine learning methodologies.

Briefings in bioinformatics Jul 20, 2021
Sequencing technologies have led to the identification of many variants in the human genome which could act as disease-drivers. As a consequence, a variety of bioinformatics tools have been proposed for predicting which variants may drive disease, an...
Genome, Human Neoplasms Genomics Computational Biology Machine Learning Humans Software
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Opportunities and challenges for the computational interpretation of rare variation in clinically important genes.

American journal of human genetics Apr 1, 2021
Genome sequencing is enabling precision medicine-tailoring treatment to the unique constellation of variants in an individual's genome. The impact of recurrent pathogenic variants is often understood, however there is a long tail of rare genetic vari...
Machine Learning Precision Medicine Infant, Newborn Pharmacogenetics Humans Genome, Human Metabolism, Inborn Errors Genomics Genetic Variation Genetics, Medical
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A machine learning-based framework for modeling transcription elongation.

Proceedings of the National Academy of Sciences of the United States of America Feb 9, 2021
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gen...
Binding Sites RNA Polymerase II Nucleotide Motifs RNA Splicing Base Sequence Genome, Human Histones RNA Splice Sites Transcription Elongation, Genetic Machine Learning Epigenesis, Genetic DNA Methylation HeLa Cells HEK293 Cells Protein Processing, Post-Translational Models, Biological Humans
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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...
Computer Simulation Animals Humans Alzheimer Disease Genetic Predisposition to Disease High-Throughput Screening Assays Polymorphism, Single Nucleotide Genome, Human RNA, Messenger Phospholipase C gamma RNA Splicing Deep Learning Disease Models, Animal Genome-Wide Association Study Exons Mice
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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...
Genetic Association Studies Computational Biology Software Databases, Genetic Humans Phenotype Genome, Human Genome-Wide Association Study Epistasis, Genetic Machine Learning Polymorphism, Single Nucleotide Genotype
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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...
Genome, Human Epistasis, Genetic Quantitative Trait, Heritable Inheritance Patterns Macular Degeneration Data Mining Alzheimer Disease Computational Biology Crohn Disease Plants Phenotype Neoplasms Genome-Wide Association Study Polymorphism, Single Nucleotide Humans Machine Learning
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Sequence-Based Deep Learning Frameworks on Enhancer-Promoter Interactions Prediction.

Current pharmaceutical design Jan 1, 2021
Enhancer-promoter interactions (EPIs) in the human genome are of great significance to transcriptional regulation, which tightly controls gene expression. Identification of EPIs can help us better decipher gene regulation and understand disease mecha...
Promoter Regions, Genetic Regulatory Sequences, Nucleic Acid Humans Neural Networks, Computer Deep Learning Genome, Human
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The reactome pathway knowledgebase.

Nucleic acids research Jan 8, 2020
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data mo...
Databases, Chemical Genome, Human Signal Transduction Humans Metabolic Networks and Pathways Software Knowledge Bases Protein Interaction Maps Databases, Pharmaceutical
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