AIMC Topic: Phenotype

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PhenPath: a tool for characterizing biological functions underlying different phenotypes.

BMC genomics Jul 16, 2019
BACKGROUND: Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or few biological functions. For...
Humans Phenotype Computational Biology Disease Databases, Genetic Biological Ontologies
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Phenotype annotation with the ontology of microbial phenotypes (OMP).

Journal of biomedical semantics Jul 15, 2019
BACKGROUND: Microbial genetics has formed a foundation for understanding many aspects of biology. Systematic annotation that supports computational data mining should reveal further insights for microbes, microbiomes, and conserved functions beyond m...
Metadata Biological Ontologies Data Curation Phenotype Microbiology
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Machine and deep learning meet genome-scale metabolic modeling.

PLoS computational biology Jul 11, 2019
Omic data analysis is steadily growing as a driver of basic and applied molecular biology research. Core to the interpretation of complex and heterogeneous biological phenotypes are computational approaches in the fields of statistics and machine lea...
Computational Biology Machine Learning Metabolic Networks and Pathways Phenotype Genome Deep Learning Genotype
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AMC-Net: Asymmetric and multi-scale convolutional neural network for multi-label HPA classification.

Computer methods and programs in biomedicine Jul 9, 2019
BACKGROUND AND OBJECTIVES: The multi-label Human Protein Atlas (HPA) classification can yield a better understanding of human diseases and help doctors to enhance the automatic analysis of biomedical images. The existing automatic protein recognition...
Algorithms Phenotype Reproducibility of Results Image Processing, Computer-Assisted Humans Neural Networks, Computer Microscopy Probability Microtubules Pattern Recognition, Automated Proteins Databases, Protein Microscopy, Fluorescence Cell Nucleus False Positive Reactions
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Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models.

BMC bioinformatics Jul 2, 2019
BACKGROUND: In spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensionality, given the disbalance bet...
Humans Genomics Signal Transduction Proteins Fanconi Anemia Machine Learning Phenotype Databases, Factual
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HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology.

Journal of biomedical informatics Jun 27, 2019
BACKGROUND: In precision medicine, deep phenotyping is defined as the precise and comprehensive analysis of phenotypic abnormalities, aiming to acquire a better understanding of the natural history of a disease and its genotype-phenotype associations...
Semantics Electronic Health Records Area Under Curve Databases, Genetic Phenotype ROC Curve Biological Ontologies Medical Informatics Humans Genetic Association Studies Models, Statistical Rare Diseases Computer Simulation Machine Learning Precision Medicine Algorithms
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Identification of a Multiplex Biomarker Panel for Hypertrophic Cardiomyopathy Using Quantitative Proteomics and Machine Learning.

Molecular & cellular proteomics : MCP Jun 26, 2019
Hypertrophic cardiomyopathy (HCM) is defined by pathological left ventricular hypertrophy (LVH). It is the commonest inherited cardiac condition and a significant number of high risk cases still go undetected until a sudden cardiac death (SCD) event....
Hypertrophy, Left Ventricular Sarcomeres Proteomics Predictive Value of Tests Humans Machine Learning Mutation Young Adult Phenotype Cardiomyopathy, Hypertrophic Adult Prospective Studies Male Peptides Middle Aged Severity of Illness Index Case-Control Studies Biomarkers Female Aged
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Identifying pre-disease signals before metabolic syndrome in mice by dynamical network biomarkers.

Scientific reports Jun 24, 2019
The establishment of new therapeutic strategies for metabolic syndrome is urgently needed because metabolic syndrome, which is characterized by several disorders, such as hypertension, increases the risk of lifestyle-related diseases. One approach is...
Humans Biomarkers Animals Neural Networks, Computer Phenotype Metabolic Syndrome Models, Biological Disease Progression Symptom Assessment Mice Computational Biology
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MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks.

BMC bioinformatics Jun 20, 2019
BACKGROUND: Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified different microbiome profiles in...
Metagenomics Phenotype ROC Curve Models, Theoretical Area Under Curve Microbiota Neural Networks, Computer Support Vector Machine Machine Learning Databases, Genetic Humans Algorithms
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Detection and Classification of Novel Renal Histologic Phenotypes Using Deep Neural Networks.

The American journal of pathology Jun 18, 2019
With the advent and increased accessibility of deep neural networks (DNNs), complex properties of histologic images can be rigorously and reproducibly quantified. We used DNN-based transfer learning to analyze histologic images of periodic acid-Schif...
Neural Pathways Aldehyde Oxidoreductases Phenotype Animals Male Kidney Mice, Knockout Image Processing, Computer-Assisted Mice Neural Networks, Computer
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