AIMC Topic: Genetic Variation

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Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation.

Journal of chemical information and modeling Apr 18, 2024
Research in the human genome sciences generates a substantial amount of genetic data for hundreds of thousands of individuals, which concomitantly increases the number of variants of unknown significance (VUS). Bioinformatic analyses can successfully...
Proto-Oncogene Proteins c-myc Models, Molecular Genetic Variation Protein Conformation NF-E2-Related Factor 2 Genome, Human Humans Machine Learning Computational Biology
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Personal transcriptome variation is poorly explained by current genomic deep learning models.

Nature genetics Nov 30, 2023
Genomic deep learning models can predict genome-wide epigenetic features and gene expression levels directly from DNA sequence. While current models perform well at predicting gene expression levels across genes in different cell types from the refer...
Deep Learning Genomics Genetic Variation Humans Transcriptome Genome
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Predicting pathogenic protein variants.

Science (New York, N.Y.) Sep 19, 2023
Machine-learning algorithm uses structure prediction to spot disease-causing mutations.
Disease Mutation, Missense Mutant Proteins Genetic Variation Protein Conformation Algorithms Sequence Analysis, DNA Machine Learning
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Modeling islet enhancers using deep learning identifies candidate causal variants at loci associated with T2D and glycemic traits.

Proceedings of the National Academy of Sciences of the United States of America Aug 21, 2023
Genetic association studies have identified hundreds of independent signals associated with type 2 diabetes (T2D) and related traits. Despite these successes, the identification of specific causal variants underlying a genetic association signal rema...
Enhancer Elements, Genetic Islets of Langerhans Diabetes Mellitus, Type 2 Genetic Variation Computer Simulation Deep Learning Humans
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Sampling effect in predicting the evolutionary response of populations to climate change.

Molecular ecology resources Jun 30, 2023
Genomic data and machine learning approaches have gained interest due to their potential to identify adaptive genetic variation across populations and to assess species vulnerability to climate change. By identifying gene-environment associations for...
Genetic Variation Climate Change Genetics, Population Polymorphism, Single Nucleotide
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Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.

Science (New York, N.Y.) Apr 28, 2023
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challe...
Animals Mammals Enhancer Elements, Genetic Machine Learning Genetic Variation Phenotype
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Estimating resistance surfaces using gradient forest and allelic frequencies.

Molecular ecology resources Mar 10, 2023
Understanding landscape connectivity has become a global priority for mitigating the impact of landscape fragmentation on biodiversity. Connectivity methods that use link-based methods traditionally rely on relating pairwise genetic distance between ...
Genetic Variation Gene Frequency Genetics, Population Computer Simulation Biodiversity
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Expectile Neural Networks for Genetic Data Analysis of Complex Diseases.

IEEE/ACM transactions on computational biology and bioinformatics Feb 6, 2023
The genetic etiologies of common diseases are highly complex and heterogeneous. Classic methods, such as linear regression, have successfully identified numerous variants associated with complex diseases. Nonetheless, for most diseases, the identifie...
Neural Networks, Computer Linear Models Phenotype Genetic Variation
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Predicting Antigenic Distance from Genetic Data for PRRSV-Type 1: Applications of Machine Learning.

Microbiology spectrum Dec 13, 2022
The control of porcine reproductive and respiratory syndrome (PRRS) remains a significant challenge due to the genetic and antigenic variability of the causative virus (PRRSV). Predominantly, PRRSV management includes using vaccines and live virus in...
Porcine Reproductive and Respiratory Syndrome Porcine respiratory and reproductive syndrome virus Cross Protection Antigenic Variation Genetic Variation Swine Machine Learning Cross Reactions Phylogeny Animals
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A machine learning approach based on ACMG/AMP guidelines for genomic variant classification and prioritization.

Scientific reports Feb 15, 2022
Genomic variant interpretation is a critical step of the diagnostic procedure, often supported by the application of tools that may predict the damaging impact of each variant or provide a guidelines-based classification. We propose the application o...
Genetic Testing Computer Simulation Software Genetic Variation Genomics Humans Neoplasms Genome, Human Research Design Machine Learning Genetic Predisposition to Disease Logistic Models Cohort Studies High-Throughput Nucleotide Sequencing Bayes Theorem Practice Guidelines as Topic
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