AIMC Topic: Genome, Human

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Cell type-specific interpretation of noncoding variants using deep learning-based methods.

GigaScience Mar 27, 2023
Interpretation of noncoding genomic variants is one of the most important challenges in human genetics. Machine learning methods have emerged recently as a powerful tool to solve this problem. State-of-the-art approaches allow prediction of transcrip...
Deep Learning Genome, Human Humans Neural Networks, Computer Machine Learning
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Cue: a deep-learning framework for structural variant discovery and genotyping.

Nature methods Mar 23, 2023
Structural variants (SVs) are a major driver of genetic diversity and disease in the human genome and their discovery is imperative to advances in precision medicine. Existing SV callers rely on hand-engineered features and heuristics to model SVs, w...
Humans Software Cues Genome, Human Genomic Structural Variation Deep Learning Genotype
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Detecting genomic deletions from high-throughput sequence data with unsupervised learning.

BMC bioinformatics Jan 27, 2023
BACKGROUND: Structural variation (SV), which ranges from 50 bp to [Formula: see text] 3 Mb in size, is an important type of genetic variations. Deletion is a type of SV in which a part of a chromosome or a sequence of DNA is lost during DNA replicati...
Humans Software Genomics Genomic Structural Variation High-Throughput Nucleotide Sequencing Sequence Analysis, DNA Genome, Human Unsupervised Machine Learning
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Perspectives on the future of dysmorphology.

American journal of medical genetics. Part A Dec 9, 2022
The field of clinical genetics and genomics continues to evolve. In the past few decades, milestones like the initial sequencing of the human genome, dramatic changes in sequencing technologies, and the introduction of artificial intelligence, have u...
Humans Artificial Intelligence Genomics Genome, Human
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Context dependent prediction in DNA sequence using neural networks.

PeerJ Sep 20, 2022
One way to better understand the structure in DNA is by learning to predict the sequence. Here, we trained a model to predict the missing base at any given position, given its left and right flanking contexts. Our best-performing model was a neural n...
Humans Neural Networks, Computer Genome, Human Nucleosomes Animals DNA Mice Base Sequence
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Automated filtering of genome-wide large deletions through an ensemble deep learning framework.

Methods (San Diego, Calif.) Aug 28, 2022
Computational methods based on whole genome linked-reads and short-reads have been successful in genome assembly and detection of structural variants (SVs). Numerous variant callers that rely on linked-reads and short reads can detect genetic variati...
Sequence Analysis Base Sequence Genome, Human Humans Sequence Analysis, DNA Deep Learning High-Throughput Nucleotide Sequencing
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Haplotype and population structure inference using neural networks in whole-genome sequencing data.

Genome research Aug 25, 2022
Accurate inference of population structure is important in many studies of population genetics. Here we present HaploNet, a method for performing dimensionality reduction and clustering of genetic data. The method is based on local clustering of phas...
Genome, Human Genetics, Population Neural Networks, Computer Principal Component Analysis Whole Genome Sequencing Haplotypes Humans
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A review of deep learning applications in human genomics using next-generation sequencing data.

Human genomics Jul 25, 2022
Genomics is advancing towards data-driven science. Through the advent of high-throughput data generating technologies in human genomics, we are overwhelmed with the heap of genomic data. To extract knowledge and pattern out of this genomic data, arti...
Genome, Human Humans Genomics Artificial Intelligence High-Throughput Nucleotide Sequencing Deep Learning
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A hybrid metaheuristic-deep learning technique for the pan-classification of cancer based on DNA methylation.

BMC bioinformatics Jul 11, 2022
BACKGROUND: DNA Methylation is one of the most important epigenetic processes that are crucial to regulating the functioning of the human genome without altering the DNA sequence. DNA Methylation data for cancer patients are becoming more accessible ...
Humans Female Male Genome, Human Epigenesis, Genetic DNA Methylation Deep Learning Lung Neoplasms
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THRONE: A New Approach for Accurate Prediction of Human RNA N7-Methylguanosine Sites.

Journal of molecular biology Mar 16, 2022
N-methylguanosine (m7G) is an essential, ubiquitous, and positively charged modification at the 5' cap of eukaryotic mRNA, modulating its export, translation, and splicing processes. Although several machine learning (ML)-based computational predicto...
Software Computational Biology Humans Machine Learning RNA Caps Sequence Analysis, RNA Guanosine Genome, Human
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