AIMC Topic: Genome, Human

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Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach.

BMC bioinformatics Nov 30, 2021
BACKGROUND: Deep learning is an active bioinformatics artificial intelligence field that is useful in solving many biological problems, including predicting altered epigenetics such as DNA methylation regions. Deep learning (DL) can learn an informat...
Animals Epigenesis, Genetic Rats DNA Methylation DNA Genome, Human Humans Artificial Intelligence Machine Learning
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Detecting immunotherapy-sensitive subtype in gastric cancer using histologic image-based deep learning.

Scientific reports Nov 22, 2021
Immune checkpoint inhibitor (ICI) therapy is widely used but effective only in a subset of gastric cancers. Epstein-Barr virus (EBV)-positive and microsatellite instability (MSI) / mismatch repair deficient (dMMR) tumors have been reported to be high...
Reproducibility of Results Stomach Neoplasms Deep Learning Immunotherapy Machine Learning Software Algorithms Databases, Factual DNA Mismatch Repair Humans Immunohistochemistry Neural Networks, Computer Treatment Outcome Genome, Human Lymphocytosis Herpesvirus 4, Human Area Under Curve Microsatellite Instability
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Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers.

PLoS computational biology Oct 11, 2021
Read-depths (RDs) are frequently used in identifying structural variants (SVs) from sequencing data. For existing RD-based SV callers, it is difficult for them to determine breakpoints in single-nucleotide resolution due to the noisiness of RD data a...
Humans Deep Learning Genomics Genomic Structural Variation Models, Genetic Whole Genome Sequencing Genome, Human
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AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome.

Genes & genetic systems Sep 27, 2021
In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable for big data analysis has become increasingly important. Unsupervised AI that can reveal novel know...
Genome, Viral Cluster Analysis Artificial Intelligence RNA, Transfer Humans Mutation SARS-CoV-2 Codon Usage Metagenomics Time Factors Genome, Human Computational Biology
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ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.

PLoS computational biology Sep 7, 2021
Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understan...
Promoter Regions, Genetic Molecular Sequence Annotation Enhancer Elements, Genetic Genes, Reporter Regulatory Sequences, Nucleic Acid Transcription Initiation, Genetic Models, Genetic Mutation Gene Expression Regulation Genome, Human Deep Learning Genome-Wide Association Study Computational Biology Humans
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NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks.

Genome biology Sep 6, 2021
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs usin...
Alleles High-Throughput Nucleotide Sequencing Haplotypes Base Sequence Polymorphism, Single Nucleotide Nanoparticles Benchmarking Nanopore Sequencing Genome, Human INDEL Mutation Chromosome Mapping Major Histocompatibility Complex Humans Neural Networks, Computer
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Discovering differential genome sequence activity with interpretable and efficient deep learning.

PLoS computational biology Aug 9, 2021
Discovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of disease related mutations. We introduce Expected Pattern Effect and Differential Expected Patt...
Humans Neural Networks, Computer Deep Learning Transcription Factors Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Genome, Human
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Prioritizing and characterizing functionally relevant genes across human tissues.

PLoS computational biology Jul 16, 2021
Knowledge of genes that are critical to a tissue's function remains difficult to ascertain and presents a major bottleneck toward a mechanistic understanding of genotype-phenotype links. Here, we present the first machine learning model-FUGUE-combini...
Machine Learning Tissue Distribution Software Gene Expression Regulation, Developmental Female Male Gene Regulatory Networks Genetic Association Studies Humans Computational Biology Transcription Factors Models, Genetic Multigene Family Genome, Human Neoplasms Transcriptome Genome-Wide Association Study Protein Interaction Maps
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Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning.

Scientific reports Jul 13, 2021
Over the past years, large consortia have been established to fuel the sequencing of whole genomes of many cancer patients. Despite the increased abundance in tools to study the impact of SNVs, non-coding SVs have been largely ignored in these data. ...
Neoplasms Genome, Human Chromatin Genomic Structural Variation Humans Machine Learning
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Nature communications Jun 2, 2021
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene ...
Transcription Initiation Site Neurodegenerative Diseases Transcription Initiation, Genetic High-Throughput Nucleotide Sequencing Humans Polymorphism, Genetic Base Sequence Promoter Regions, Genetic Neural Networks, Computer Genome, Human Enhancer Elements, Genetic Animals Deep Learning Microsatellite Repeats Mice Computational Biology A549 Cells
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