AIMC Topic: Genome, Human

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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...
Models, Genetic Whole Genome Sequencing Genome, Human Genomic Structural Variation Humans Deep Learning Genomics
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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...
Computational Biology Cluster Analysis Mutation Metagenomics Artificial Intelligence SARS-CoV-2 Time Factors Genome, Human Genome, Viral RNA, Transfer Codon Usage Humans
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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...
Humans Deep Learning Genome-Wide Association Study Computational Biology Genome, Human Models, Genetic Promoter Regions, Genetic Mutation Molecular Sequence Annotation Genes, Reporter Gene Expression Regulation Enhancer Elements, Genetic Regulatory Sequences, Nucleic Acid Transcription Initiation, Genetic
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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...
Genome, Human INDEL Mutation Chromosome Mapping Major Histocompatibility Complex Alleles High-Throughput Nucleotide Sequencing Humans Haplotypes Base Sequence Neural Networks, Computer Polymorphism, Single Nucleotide Nanoparticles Nanopore Sequencing Benchmarking
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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...
Gene Expression Regulation, Developmental Humans Gene Regulatory Networks Genetic Association Studies Computational Biology Models, Genetic Transcription Factors Multigene Family Genome, Human Tissue Distribution Neoplasms Machine Learning Transcriptome Software Genome-Wide Association Study Female Protein Interaction Maps Male
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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 ...
Genome, Human Polymorphism, Genetic Promoter Regions, Genetic Humans Enhancer Elements, Genetic Neural Networks, Computer Animals Microsatellite Repeats A549 Cells Deep Learning Neurodegenerative Diseases Mice High-Throughput Nucleotide Sequencing Computational Biology Base Sequence Transcription Initiation Site Transcription Initiation, Genetic
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Feasibility of predicting allele specific expression from DNA sequencing using machine learning.

Scientific reports May 19, 2021
Allele specific expression (ASE) concerns divergent expression quantity of alternative alleles and is measured by RNA sequencing. Multiple studies show that ASE plays a role in hereditary diseases by modulating penetrance or phenotype severity. Howev...
Feasibility Studies Polymorphism, Single Nucleotide Alleles Models, Genetic Humans Gene Expression Regulation Sequence Analysis, DNA Machine Learning Genome, Human Bias ROC Curve
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Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance.

Nature communications May 11, 2021
Resistance to ionizing radiation, a first-line therapy for many cancers, is a major clinical challenge. Personalized prediction of tumor radiosensitivity is not currently implemented clinically due to insufficient accuracy of existing machine learnin...
Databases, Genetic Neoplasm Proteins Radiation, Ionizing Humans Metabolic Networks and Pathways Machine Learning Cell Line, Tumor Datasets as Topic Survival Analysis Neoplasms Gene Expression Regulation, Neoplastic Genome, Human Transcriptome Treatment Outcome Radiation Tolerance Atlases as Topic
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