AIMC Topic: Genetic Variation

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Predicting geographic location from genetic variation with deep neural networks.

eLife Jun 8, 2020
Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of kn...
Humans Neural Networks, Computer Animals Genome, Human Animal Distribution Demography Anopheles Genomics Genotype Plasmodium falciparum Genetic Variation
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Artificial intelligence as the next step towards precision pathology.

Journal of internal medicine Mar 3, 2020
Pathology is the cornerstone of cancer care. The need for accuracy in histopathologic diagnosis of cancer is increasing as personalized cancer therapy requires accurate biomarker assessment. The appearance of digital image analysis holds promise to i...
Pathology, Clinical Image Processing, Computer-Assisted Genetic Variation Survival Analysis Humans Artificial Intelligence Prognosis Neoplasms
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Machine-learning based patient classification using Hepatitis B virus full-length genome quasispecies from Asian and European cohorts.

Scientific reports Dec 11, 2019
Chronic infection with Hepatitis B virus (HBV) is a major risk factor for the development of advanced liver disease including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The relative contribution of virological factors to disease progres...
Humans Machine Learning Female Hepatitis B virus DNA, Viral Hepatitis B, Chronic Genetic Variation Male Disease Progression Liver Neoplasms Carcinoma, Hepatocellular Genome, Viral Quasispecies
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PharmVar GeneFocus: CYP2D6.

Clinical pharmacology and therapeutics Dec 9, 2019
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus. CYP2D6 genetic variation impacts the metabolism of numerous drugs and, thus, can impact drug efficacy and safety. This GeneFocu...
Genetic Variation Polymorphism, Genetic Cytochrome P-450 CYP2D6 Pharmacogenetics Databases, Genetic Humans Pharmaceutical Preparations Knowledge Bases
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Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing.

Cells Nov 26, 2019
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient's variant landscape, the ability to characterize variants causing splicing defects ha...
Molecular Sequence Annotation RNA Precursors RNA Splicing Computational Biology Humans Models, Biological Machine Learning Genetic Variation Genomics Genetic Predisposition to Disease
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Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

Nature communications Nov 20, 2019
A gene is considered essential if loss of function results in loss of viability, fitness or in disease. This concept is well established for coding genes; however, non-coding regions are thought less likely to be determinants of critical functions. H...
Genes, Reporter Chromatin Computer Simulation Introns DNA INDEL Mutation Gene Expression Enhancer Elements, Genetic Mutation Humans Supervised Machine Learning Genetic Variation Genome, Human Nucleic Acid Conformation
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CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network.

Scientific reports Nov 15, 2019
With recent advances in DNA sequencing technologies, fast acquisition of large-scale genomic data has become commonplace. For cancer studies, in particular, there is an increasing need for the classification of cancer type based on somatic alteration...
Linear Models Genetic Testing Workflow Genetic Variation Machine Learning Algorithms Databases, Factual Reproducibility of Results Neoplasms Genomics Mutation Humans Neural Networks, Computer
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Dysmorphology in a Genomic Era.

Clinics in perinatology Oct 31, 2019
Dysmorphology is the practice of defining the morphologic phenotype of syndromic disorders. Genomic sequencing has advanced our understanding of human variation and molecular dysmorphology has evolved in response to the science of relating embryologi...
Genetic Variation Abnormalities, Multiple Genetic Counseling Genetics, Medical Humans Genomics Genome, Human Genotype Phenotype Neonatal Screening Infant, Newborn Diagnosis, Differential Terminology as Topic Genetic Testing
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Artificial intelligence reveals environmental constraints on colour diversity in insects.

Nature communications Oct 7, 2019
Explaining colour variation among animals at broad geographic scales remains challenging. Here we demonstrate how deep learning-a form of artificial intelligence-can reveal subtle but robust patterns of colour feature variation along an ecological gr...
Species Specificity Skin Pigmentation Moths Genetic Variation Insecta Climate Altitude Deep Learning Color Biodiversity Artificial Intelligence Temperature Animals Phylogeny
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Designing Eukaryotic Gene Expression Regulation Using Machine Learning.

Trends in biotechnology Aug 17, 2019
Controlling the expression of genes is one of the key challenges of synthetic biology. Until recently fine-tuned control has been out of reach, particularly in eukaryotes owing to their complexity of gene regulation. With advances in machine learning...
Flow Cytometry Eukaryota Machine Learning Genetic Variation Genetic Engineering Algorithms Synthetic Biology Eukaryotic Cells Models, Genetic Gene Expression Regulation
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