AIMC Topic: Phenotype

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Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning.

Nature methods Mar 18, 2019
Recent advances in large-scale single-cell RNA-seq enable fine-grained characterization of phenotypically distinct cellular states in heterogeneous tissues. We present scScope, a scalable deep-learning-based approach that can accurately and rapidly i...
Single-Cell Analysis Mice Computational Biology Sequence Analysis, RNA Leukocytes, Mononuclear Gene Expression Profiling Transcriptome Deep Learning Brain Mapping Principal Component Analysis Retina RNA Intestines Inflammation Databases, Genetic Cluster Analysis Software Algorithms Phenotype Computer Simulation Reproducibility of Results Animals
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Rare disease knowledge enrichment through a data-driven approach.

BMC medical informatics and decision making Feb 14, 2019
BACKGROUND: Existing resources to assist the diagnosis of rare diseases are usually curated from the literature that can be limited for clinical use. It often takes substantial effort before the suspicion of a rare disease is even raised to utilize t...
Data Mining Rare Diseases Humans Algorithms Phenotype Electronic Health Records Knowledge Bases
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DeepPVP: phenotype-based prioritization of causative variants using deep learning.

BMC bioinformatics Feb 6, 2019
BACKGROUND: Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In these methods, pathogenicity ...
Genetic Variation Gene Frequency Exome Sequencing Exome Neural Networks, Computer Software Phenotype Deep Learning Humans
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Severe Dengue Prognosis Using Human Genome Data and Machine Learning.

IEEE transactions on bio-medical engineering Feb 4, 2019
UNLABELLED: Dengue has become one of the most important worldwide arthropod-borne diseases. Dengue phenotypes are based on laboratorial and clinical exams, which are known to be inaccurate.
Humans Machine Learning Phenotype Genome, Human Severe Dengue Case-Control Studies Polymorphism, Single Nucleotide Genotype Predictive Value of Tests Prognosis Sensitivity and Specificity Brazil
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Contribution of Cardiovascular Reserve to Prognostic Categories of Heart Failure With Preserved Ejection Fraction: A Classification Based on Machine Learning.

Journal of the American Society of Echocardiography : official publication of the American Society of Echocardiography Feb 1, 2019
BACKGROUND: The authors used cluster analysis of data from cardiovascular domains associated with exercise intolerance to help define prognostic phenotypes of patients with heart failure with preserved ejection fraction (HFpEF).
Male Stroke Volume Echocardiography Middle Aged Biomarkers Prognosis Female Aged Heart Function Tests Longitudinal Studies Exercise Test Heart Failure Exercise Tolerance Humans Machine Learning Phenotype Prospective Studies
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Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis.

Genetics in medicine : official journal of the American College of Medical Genetics Jan 24, 2019
PURPOSE: Despite the successful progress next-generation sequencing technologies has achieved in diagnosing the genetic cause of rare Mendelian diseases, the current diagnostic rate is still far from satisfactory because of heterogeneity, imprecision...
Mutation Phenotype Rare Diseases Genetic Testing Humans Genomics Exome Genetic Variation Machine Learning Genotype High-Throughput Nucleotide Sequencing Software Computational Biology
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Multi-task learning improves ancestral state reconstruction.

Theoretical population biology Jan 11, 2019
We consider the ancestral state reconstruction problem where we need to infer phenotypes of ancestors using observations from present-day species. For this problem, we propose a multi-task learning method that uses regularized maximum likelihood to e...
Phylogeny Stochastic Processes Humans Models, Biological Phenotype Biological Evolution Mammals Machine Learning Computer Simulation Likelihood Functions Learning Animals
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Identifying facial phenotypes of genetic disorders using deep learning.

Nature medicine Jan 7, 2019
Syndromic genetic conditions, in aggregate, affect 8% of the population. Many syndromes have recognizable facial features that are highly informative to clinical geneticists. Recent studies show that facial analysis technologies measured up to the ca...
Syndrome Genetic Diseases, Inborn Phenotype Facies Humans Deep Learning Algorithms Image Processing, Computer-Assisted Genotype
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Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide.

Molecular psychiatry Jan 4, 2019
Suicide accounts for nearly 800,000 deaths per year worldwide with rates of both deaths and attempts rising. Family studies have estimated substantial heritability of suicidal behavior; however, collecting the sample sizes necessary for successful ge...
Female Risk Factors Mental Health Male Suicide, Attempted Suicidal Ideation Genome-Wide Association Study Health Surveys Humans Machine Learning Phenotype Electronic Health Records Tennessee Biological Specimen Banks Probability White People United Kingdom
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Computer vision-based phenotyping for improvement of plant productivity: a machine learning perspective.

GigaScience Jan 1, 2019
Employing computer vision to extract useful information from images and videos is becoming a key technique for identifying phenotypic changes in plants. Here, we review the emerging aspects of computer vision for automated plant phenotyping. Recent a...
Remote Sensing Technology Crops, Agricultural Neural Networks, Computer Plant Breeding Machine Learning Phenotype
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