AIMC Topic: Genome, Human

Clear Filters Showing 141 to 150 of 196 articles

Reinventing gene expression connectivity through regulatory and spatial structural empowerment via principal node aggregation graph neural network.

Nucleic acids research Jul 22, 2024
The intricacies of the human genome, manifested as a complex network of genes, transcend conventional representations in text or numerical matrices. The intricate gene-to-gene relationships inherent in this complexity find a more suitable depiction i...
Algorithms Protein Interaction Maps Humans Neural Networks, Computer Gene Expression Regulation Genome, Human Histone Code Gene Regulatory Networks Transcription Factors
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Geno-GCN: A Genome-specific Graph Convolutional Network for Diabetes Prediction.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference Jul 1, 2024
Drawing inspiration from convolutional neural networks, graph convolutional networks (GCNs) have been implemented in various applications. Yet, the integration of GCNs into clinical settings, particularly in the context of complex health conditions l...
Algorithms Computational Biology Humans Neural Networks, Computer Diabetes Mellitus, Type 2 Genomics Genome, Human Machine Learning
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NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data.

Bioinformatics (Oxford, England) Mar 4, 2024
MOTIVATION: Structural variants (SVs) play a causal role in numerous diseases but can be difficult to detect and accurately genotype (determine zygosity) with short-read genome sequencing data (SRS). Improving SV genotyping accuracy in SRS data, part...
Humans Software Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Genome, Human Deep Learning Genotype Genomic Structural Variation
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CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions.

Nucleic acids research Jan 5, 2024
Machine Learning-based scoring and classification of genetic variants aids the assessment of clinical findings and is employed to prioritize variants in diverse genetic studies and analyses. Combined Annotation-Dependent Depletion (CADD) is one of th...
Nucleotides Genome, Human Humans Software Genetic Variation Machine Learning
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Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants.

Toxicological sciences : an official journal of the Society of Toxicology Nov 28, 2023
The aryl hydrocarbon receptor (AhR) is an inducible transcription factor whose ligands include the potent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Ligand-activated AhR binds to DNA at dioxin response elements (DREs) conta...
Organ Specificity Basic Helix-Loop-Helix Transcription Factors Genome, Human Machine Learning Humans Receptors, Aryl Hydrocarbon
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DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome.

Briefings in bioinformatics Sep 20, 2023
Silencers are noncoding DNA sequence fragments located on the genome that suppress gene expression. The variation of silencers in specific cells is closely related to gene expression and cancer development. Computational approaches that exclusively r...
Multiomics Genome, Human Humans Cell Line Deep Learning Epigenesis, Genetic
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DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome.

Bioinformatics (Oxford, England) Jun 1, 2023
MOTIVATION: Enhancers are vital cis-regulatory elements that regulate gene expression. Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer regions in the genome. The tissue-specific expression of eRNAs is crucial in th...
Humans Deep Learning Genome, Human RNA, Long Noncoding Transcription, Genetic Histones Enhancer Elements, Genetic
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DeepOM: single-molecule optical genome mapping via deep learning.

Bioinformatics (Oxford, England) Mar 1, 2023
MOTIVATION: Efficient tapping into genomic information from a single microscopic image of an intact DNA molecule is an outstanding challenge and its solution will open new frontiers in molecular diagnostics. Here, a new computational method for optic...
Humans Software Deep Learning Genome, Human Genomics Restriction Mapping DNA
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Deep learning-assisted genome-wide characterization of massively parallel reporter assays.

Nucleic acids research Nov 11, 2022
Massively parallel reporter assay (MPRA) is a high-throughput method that enables the study of the regulatory activities of tens of thousands of DNA oligonucleotides in a single experiment. While MPRA experiments have grown in popularity, their small...
Sequence Analysis, DNA DNA Humans Deep Learning Genome, Human Regulatory Sequences, Nucleic Acid
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MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach.

Briefings in bioinformatics Sep 20, 2022
Structural variations (SVs) play important roles in human genetic diversity; deletions and insertions are two common types of SVs that have been proven to be associated with genetic diseases. Hence, accurately detecting and genotyping SVs is signific...
Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Deep Learning Genome, Human Humans Genotyping Techniques Genotype Software
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