AIMC Topic: Models, Genetic

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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....
Mutagenesis Biotechnology Genetic Engineering Computer Simulation Riboswitch Base Sequence Genome, Human Genome, Viral Deep Learning Humans Models, Genetic Datasets as Topic Structure-Activity Relationship Natural Language Processing Synthetic Biology
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A genotype imputation method for de-identified haplotype reference information by using recurrent neural network.

PLoS computational biology Oct 1, 2020
Genotype imputation estimates the genotypes of unobserved variants using the genotype data of other observed variants based on a collection of haplotypes for thousands of individuals, which is known as a haplotype reference panel. In general, more ac...
Genotype Models, Genetic Databases, Genetic Haplotypes Neural Networks, Computer Genomics Polymorphism, Single Nucleotide
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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...
Models, Genetic Alleles Genome, Human Histones Linkage Disequilibrium Disease Humans Deep Learning Genetic Predisposition to Disease Molecular Sequence Annotation Phenotype Genome-Wide Association Study Polymorphism, Single Nucleotide
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Impact of Gene Biomarker Discovery Tools Based on Protein-Protein Interaction and Machine Learning on Performance of Artificial Intelligence Models in Predicting Clinical Stages of Breast Cancer.

Interdisciplinary sciences, computational life sciences Sep 10, 2020
Breast cancer, as one of the most common diseases threatening the women's life, has attracted serious attention of the clinical and biomedical researchers worldwide. The genome-based studies along with their registered GEO datasets are frequent in th...
Breast Neoplasms Models, Genetic Area Under Curve Genetic Markers Humans Machine Learning Female
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Identification of the human DPR core promoter element using machine learning.

Nature Sep 9, 2020
The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of the signals that lead to the initiation of DNA transcription, but the downstream core promoter in humans has been difficult to understand. Here we analyse the human ...
Mutagenesis Transcription, Genetic Cells RNA Polymerase II Gene Expression Regulation Base Sequence Promoter Regions, Genetic Consensus Sequence TATA Box Humans Computer Simulation Models, Genetic HeLa Cells Datasets as Topic Support Vector Machine High-Throughput Nucleotide Sequencing
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Exploring gene-gene interaction in family-based data with an unsupervised machine learning method: EPISFA.

Genetic epidemiology Sep 1, 2020
Gene-gene interaction (G × G) is thought to fill the gap between the estimated heritability of complex diseases and the limited genetic proportion explained by identified single-nucleotide polymorphisms. The current tools for exploring G × G were oft...
Algorithms Case-Control Studies Models, Genetic Unsupervised Machine Learning Humans Epistasis, Genetic Multifactor Dimensionality Reduction Ischemic Stroke Linkage Disequilibrium Factor Analysis, Statistical Family
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A deep learning model to predict RNA-Seq expression of tumours from whole slide images.

Nature communications Aug 3, 2020
Deep learning methods for digital pathology analysis are an effective way to address multiple clinical questions, from diagnosis to prediction of treatment outcomes. These methods have also been used to predict gene mutations from pathology images, b...
Deep Learning Humans RNA-Seq Algorithms Image Processing, Computer-Assisted Gene Expression Regulation, Neoplastic Neoplasms Computational Biology Models, Genetic Gene Expression Profiling Microsatellite Instability
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Chances and challenges of machine learning-based disease classification in genetic association studies illustrated on age-related macular degeneration.

Genetic epidemiology Aug 2, 2020
Imaging technology and machine learning algorithms for disease classification set the stage for high-throughput phenotyping and promising new avenues for genome-wide association studies (GWAS). Despite emerging algorithms, there has been no successfu...
Diagnostic Errors Genome-Wide Association Study Models, Genetic United Kingdom Likelihood Functions Humans Proteins High-Temperature Requirement A Serine Peptidase 1 Algorithms Machine Learning Macular Degeneration Phenotype
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Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation.

Molecular ecology resources Jul 25, 2020
For the past decades, simulation-based likelihood-free inference methods have enabled researchers to address numerous population genetics problems. As the richness and amount of simulated and real genetic data keep increasing, the field has a strong ...
Bayes Theorem Computer Simulation Genetics, Population Deep Learning Animals Population Density Cattle Models, Genetic
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An enhanced machine learning tool for cis-eQTL mapping with regularization and confounder adjustments.

Genetic epidemiology Jul 22, 2020
Many expression quantitative trait loci (eQTL) studies have been conducted to investigate the biological effects of variants in gene regulation. However, these eQTL studies may suffer from low or moderate statistical power and overly conservative fal...
Genotype Models, Genetic Gene Expression Regulation Phenotype Quantitative Trait Loci Humans Gene Expression Profiling Confounding Factors, Epidemiologic Machine Learning Polymorphism, Single Nucleotide Algorithms
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