AIMC Topic: Gene Frequency

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Fast and accurate deep learning scans for signatures of natural selection in genomes using FASTER-NN.

Communications biology Jan 15, 2025
Deep learning classification models based on Convolutional Neural Networks (CNNs) are increasingly used in population genetic inference for detecting signatures of natural selection. Prevailing detection methods treat the design of the classifier as ...
Selection, Genetic Genome Genetics, Population Genomics Gene Frequency Neural Networks, Computer Deep Learning Humans
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Artificial Intelligence-Driven Prediction Revealed CFTR Associated with Therapy Outcome of Breast Cancer: A Feasibility Study.

Oncology Jul 18, 2024
INTRODUCTION: In silico tools capable of predicting the functional consequences of genomic differences between individuals, many of which are AI-driven, have been the most effective over the past two decades for non-synonymous single nucleotide varia...
Treatment Outcome Feasibility Studies Cystic Fibrosis Transmembrane Conductance Regulator Gene Frequency Breast Neoplasms Middle Aged Polymorphism, Single Nucleotide Aged Adult Artificial Intelligence Female Humans
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INDELpred: Improving the prediction and interpretation of indel pathogenicity within the clinical genome.

HGG advances Jul 10, 2024
Small insertions and deletions (indels) are critical yet challenging genetic variations with significant clinical implications. However, the identification of pathogenic indels from neutral variants in clinical contexts remains an understudied proble...
Humans Gene Frequency INDEL Mutation Genomics Machine Learning Computational Biology Software Genome, Human
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Ancestry analysis using a self-developed 56 AIM-InDel loci and machine learning methods.

Forensic science international May 21, 2024
Insertion/deletion (InDel) polymorphisms can be used as one of the ancestry-informative markers in ancestry analysis. In this study, a self-developed panel consisting of 56 ancestry-informative InDels was used to investigate the genetic structures an...
East Asian People Ethnicity Gene Frequency Machine Learning China Genetics, Population DNA Fingerprinting Polymorphism, Genetic INDEL Mutation Humans
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AIVariant: a deep learning-based somatic variant detector for highly contaminated tumor samples.

Experimental & molecular medicine Aug 1, 2023
The detection of somatic DNA variants in tumor samples with low tumor purity or sequencing depth remains a daunting challenge despite numerous attempts to address this problem. In this study, we constructed a substantially extended set of actual posi...
Mutation Gene Frequency Humans Neoplasms Deep Learning Algorithms Computational Biology
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Gene-specific machine learning for pathogenicity prediction of rare BRCA1 and BRCA2 missense variants.

Scientific reports Jun 28, 2023
Machine learning-based pathogenicity prediction helps interpret rare missense variants of BRCA1 and BRCA2, which are associated with hereditary cancers. Recent studies have shown that classifiers trained using variants of a specific gene or a set of ...
Neural Networks, Computer Machine Learning Gene Frequency Virulence Mutation, Missense
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Improving variant calling using population data and deep learning.

BMC bioinformatics May 12, 2023
Large-scale population variant data is often used to filter and aid interpretation of variant calls in a single sample. These approaches do not incorporate population information directly into the process of variant calling, and are often limited to ...
Humans High-Throughput Nucleotide Sequencing Deep Learning Polymorphism, Single Nucleotide Genome, Human Genome-Wide Association Study Whole Genome Sequencing Gene Frequency
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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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Machine learning-based identification and characterization of 15 novel pathogenic SUOX missense mutations.

Molecular genetics and metabolism Aug 8, 2021
Isolated sulfite oxidase deficiency (ISOD) is a rare hereditary metabolic disease caused by absence of functional sulfite oxidase (SO) due to mutations of the SUOX gene. SO oxidizes toxic sulfite and sulfite accumulation is associated with neurologic...
Genetic Variation Gene Frequency Mutation, Missense Infant, Newborn Databases, Genetic Machine Learning Genome Humans Brain Oxidoreductases Acting on Sulfur Group Donors
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Detecting adaptive introgression in human evolution using convolutional neural networks.

eLife May 25, 2021
Studies in a variety of species have shown evidence for positively selected variants introduced into a population via introgression from another, distantly related population-a process known as adaptive introgression. However, there are few explicit ...
Mutation Gene Frequency Humans Genotype Neural Networks, Computer Evolution, Molecular
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