AIMC Topic: Models, Genetic

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Predicting CRISPR/Cas9-Induced Mutations for Precise Genome Editing.

Trends in biotechnology Sep 13, 2019
SpCas9 creates blunt end cuts in the genome and generates random and unpredictable mutations through error-prone repair systems. However, a growing body of recent evidence points instead to Cas9-induced staggered end generation, nonrandomness of muta...
Mutation Gene Editing DNA Repair Machine Learning DNA End-Joining Repair Models, Genetic CRISPR-Cas Systems
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Designing Eukaryotic Gene Expression Regulation Using Machine Learning.

Trends in biotechnology Aug 17, 2019
Controlling the expression of genes is one of the key challenges of synthetic biology. Until recently fine-tuned control has been out of reach, particularly in eukaryotes owing to their complexity of gene regulation. With advances in machine learning...
Synthetic Biology Machine Learning Eukaryotic Cells Gene Expression Regulation Eukaryota Algorithms Genetic Engineering Models, Genetic Flow Cytometry Genetic Variation
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Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response.

BMC biology Jul 30, 2019
BACKGROUND: Identification of functional non-coding variants and their mechanistic interpretation is a major challenge of modern genomics, especially for precision medicine. Transcription factor (TF) binding profiles and epigenomic landscapes in refe...
Transcription Factors Gene Expression Regulation Male Protein Binding Polymorphism, Single Nucleotide Models, Genetic Humans Machine Learning Female
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A Guide for Using Deep Learning for Complex Trait Genomic Prediction.

Genes Jul 20, 2019
Deep learning (DL) has emerged as a powerful tool to make accurate predictions from complex data such as image, text, or video. However, its ability to predict phenotypic values from molecular data is less well studied. Here, we describe the theoreti...
Software Deep Learning Models, Genetic Genetic Code Multifactorial Inheritance
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.

Scientific reports Jul 17, 2019
Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machin...
Neural Networks, Computer Female Male Deep Learning Humans Decision Trees Polymorphism, Single Nucleotide Area Under Curve Genotype Crohn Disease Logistic Models Genome-Wide Association Study Alleles Models, Genetic Nonlinear Dynamics ROC Curve Genotyping Techniques Genetic Predisposition to Disease INDEL Mutation
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Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.

Genome research Jun 27, 2019
A central challenge in human genomics is to understand the cellular, evolutionary, and clinical significance of genetic variants. Here, we introduce a unified population-genetic and machine-learning model, called inear llele-pecific election nferenc ...
Genetics, Population Machine Learning Inheritance Patterns Autism Spectrum Disorder Genetic Variation Humans Polymorphism, Single Nucleotide Genetic Fitness Neoplasms Base Sequence Genomics Proteome Genome, Human Models, Genetic Selection, Genetic Alleles
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Machine-learning to stratify diabetic patients using novel cardiac biomarkers and integrative genomics.

Cardiovascular diabetology Jun 11, 2019
BACKGROUND: Diabetes mellitus is a chronic disease that impacts an increasing percentage of people each year. Among its comorbidities, diabetics are two to four times more likely to develop cardiovascular diseases. While HbA1c remains the primary dia...
Glycated Hemoglobin Humans Genetic Markers DNA, Mitochondrial Middle Aged Risk Assessment CpG Islands Systems Integration Epigenesis, Genetic Disease Progression Prognosis Mitochondria, Heart Models, Genetic Diabetes Mellitus, Type 2 Female Diabetic Cardiomyopathies Risk Factors Support Vector Machine Male DNA Methylation Genomics Genetic Predisposition to Disease Polymorphism, Single Nucleotide
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Kinetics of -induced gene silencing can be predicted from combinations of epigenetic and genomic features.

Genome research Jun 7, 2019
To initiate X-Chromosome inactivation (XCI), the long noncoding RNA mediates chromosome-wide gene silencing of one X Chromosome in female mammals to equalize gene dosage between the sexes. The efficiency of gene silencing is highly variable across g...
Genome Embryonic Stem Cells Gene Silencing Genes, X-Linked X Chromosome Inactivation Models, Genetic Cell Line RNA, Long Noncoding Kinetics Animals Mice Epigenesis, Genetic Machine Learning Female
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A novel matrix of sequence descriptors for predicting protein-protein interactions from amino acid sequences.

PloS one Jun 7, 2019
Protein-protein interactions (PPIs) play an important role in the life activities of organisms. With the availability of large amounts of protein sequence data, PPIs prediction methods have attracted increasing attention. A variety of protein sequenc...
Models, Genetic Humans Deep Learning Databases, Protein Protein Interaction Maps Sequence Analysis, Protein
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A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation.

Cell Jun 6, 2019
Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over ...
Humans HEK293 Cells Base Sequence Mutagenesis Polyadenylation 3' Untranslated Regions RNA Cleavage Models, Genetic Databases, Genetic Gene Expression Synthetic Biology Transcriptome Deep Learning RNA-Seq RNA, Messenger
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