AIMC Topic: Genome, Human

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DeepC: predicting 3D genome folding using megabase-scale transfer learning.

Nature methods Oct 12, 2020
Predicting the impact of noncoding genetic variation requires interpreting it in the context of three-dimensional genome architecture. We have developed deepC, a transfer-learning-based deep neural network that accurately predicts genome folding from...
Humans Neural Networks, Computer Computer Simulation Genomics CCCTC-Binding Factor Genomic Structural Variation Models, Genetic Base Sequence Genome, Human Chromatin
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Sequence-to-function deep learning frameworks for engineered riboregulators.

Nature communications Oct 7, 2020
While synthetic biology has revolutionized our approaches to medicine, agriculture, and energy, the design of completely novel biological circuit components beyond naturally-derived templates remains challenging due to poorly understood design rules....
Humans Computer Simulation Genome, Human Genome, Viral Mutagenesis Biotechnology Genetic Engineering Riboswitch Natural Language Processing Datasets as Topic Synthetic Biology Base Sequence Deep Learning Models, Genetic Structure-Activity Relationship
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LncLocation: Efficient Subcellular Location Prediction of Long Non-Coding RNA-Based Multi-Source Heterogeneous Feature Fusion.

International journal of molecular sciences Oct 1, 2020
Recent studies uncover that subcellular location of long non-coding RNAs (lncRNAs) can provide significant information on its function. Due to the lack of experimental data, the number of lncRNAs is very limited, experimentally verified subcellular l...
RNA, Long Noncoding Benchmarking Exosomes Datasets as Topic Animals Computational Biology Support Vector Machine Databases, Genetic Terminology as Topic Cytoplasm Ribosomes Eukaryotic Cells Cell Nucleus Gene Expression Regulation Base Sequence Genome, Human Humans Software
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Evaluating the informativeness of deep learning annotations for human complex diseases.

Nature communications Sep 17, 2020
Deep learning models have shown great promise in predicting regulatory effects from DNA sequence, but their informativeness for human complex diseases is not fully understood. Here, we evaluate genome-wide SNP annotations from two previous deep learn...
Molecular Sequence Annotation Histones Linkage Disequilibrium Deep Learning Genome-Wide Association Study Genetic Predisposition to Disease Polymorphism, Single Nucleotide Models, Genetic Alleles Genome, Human Disease Humans Phenotype
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MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals.

Genomics, proteomics & bioinformatics Sep 8, 2020
Mosaic variants resulting from postzygotic mutations are prevalent in the human genome and play important roles in human diseases. However, except for cancer-related variants, there is no collection of postzygotic mosaic variants in noncancer disease...
Genome, Human Zygote Disease Health Databases, Genetic Mutation Knowledge Bases Mosaicism Humans Software Phenotype User-Computer Interface
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DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework.

Computational and mathematical methods in medicine Sep 1, 2020
Although sequencing a human genome has become affordable, identifying genetic variants from whole-genome sequence data is still a hurdle for researchers without adequate computing equipment or bioinformatics support. GATK is a gold standard method fo...
High-Throughput Nucleotide Sequencing Cost-Benefit Analysis Genome, Human Cloud Computing Deep Learning Humans Computational Biology Neural Networks, Computer Whole Genome Sequencing Software Genetic Variation
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Frequency spectra characterization of noncoding human genomic sequences.

Genes & genomics Aug 31, 2020
BACKGROUND: Noncoding sequences have been demonstrated to possess regulatory functions. Its classification is challenging because they do not show well-defined nucleotide patterns that can correlate with their biological functions. Genomic signal pro...
Genomics Nucleotides Genome, Human Humans Regulatory Sequences, Nucleic Acid Machine Learning Algorithms
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A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer.

BMC cancer Aug 28, 2020
BACKGROUND: Cell-free DNA's (cfDNA) use as a biomarker in cancer is challenging due to genetic heterogeneity of malignancies and rarity of tumor-derived molecules. Here we describe and demonstrate a novel machine-learning guided panel design strategy...
Middle Aged Cohort Studies Sequence Analysis, DNA Prostatic Neoplasms Mutation Whole Genome Sequencing Base Sequence Genome, Human Aged, 80 and over Adult Biomarkers, Tumor Male Humans Machine Learning Aged Circulating Tumor DNA
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A Comparative Study of Supervised Machine Learning Algorithms for the Prediction of Long-Range Chromatin Interactions.

Genes Aug 24, 2020
The role of three-dimensional genome organization as a critical regulator of gene expression has become increasingly clear over the last decade. Most of our understanding of this association comes from the study of long range chromatin interaction ma...
K562 Cells Gene Expression Regulation, Leukemic Chromatin Computer Simulation Support Vector Machine Supervised Machine Learning Genome, Human Humans Algorithms
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Artificial intelligence powered statistical genetics in biobanks.

Journal of human genetics Aug 11, 2020
Large-scale, sometimes nationwide, prospective genomic cohorts biobanking rich biological specimens such as blood, urine and tissues, have been established and released their vast amount of data in several countries. These genetic and epidemiological...
Humans Artificial Intelligence Reproducibility of Results Genome-Wide Association Study Genomics Polymorphism, Single Nucleotide Genetic Association Studies Computational Biology Biological Specimen Banks Genome, Human
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