AIMC Topic: Phenotype

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A Knowledge-Based Machine Learning Approach to Gene Prioritisation in Amyotrophic Lateral Sclerosis.

Genes Jun 19, 2020
Amyotrophic lateral sclerosis is a neurodegenerative disease of the upper and lower motor neurons resulting in death from neuromuscular respiratory failure, typically within two to five years of first symptoms. Several rare disruptive gene variants h...
Motor Neurons Genetic Association Studies Amyotrophic Lateral Sclerosis Neurodegenerative Diseases Knowledge Bases Humans Machine Learning Phenotype Genome-Wide Association Study Genetic Predisposition to Disease Genotype
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Cardiovascular/stroke risk prevention: A new machine learning framework integrating carotid ultrasound image-based phenotypes and its harmonics with conventional risk factors.

Indian heart journal Jun 18, 2020
MOTIVATION: Machine learning (ML)-based stroke risk stratification systems have typically focused on conventional risk factors (CRF) (AtheroRisk-conventional). Besides CRF, carotid ultrasound image phenotypes (CUSIP) have shown to be powerful phenoty...
Ultrasonography Follow-Up Studies Stroke Carotid Artery, Common Machine Learning Phenotype Retrospective Studies Risk Factors Risk Assessment Humans
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Predicting direct hepatocyte toxicity in humans by combining high-throughput imaging of HepaRG cells and machine learning-based phenotypic profiling.

Archives of toxicology Jun 12, 2020
Accurate prediction of drug- and chemical-induced hepatotoxicity remains to be a problem for pharmaceutical companies as well as other industries and regulators. The goal of the current study was to develop an in vitro/in silico method for the rapid ...
Humans Machine Learning Phenotype Risk Assessment Cellular Senescence Cell Death Hepatocytes High-Throughput Screening Assays Toxicity Tests Image Processing, Computer-Assisted Hep G2 Cells Dose-Response Relationship, Drug DNA Damage Microscopy, Fluorescence Proto-Oncogene Mas Transcription Factor RelA Chemical and Drug Induced Liver Injury Primary Cell Culture Actin Cytoskeleton
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Differentiating molecular etiologies of Angelman syndrome through facial phenotyping using deep learning.

American journal of medical genetics. Part A Jun 11, 2020
Angelman syndrome (AS) is caused by several genetic mechanisms that impair the expression of maternally-inherited UBE3A through deletions, paternal uniparental disomy (UPD), UBE3A pathogenic variants, or imprinting defects. Current methods of differe...
Maternal Inheritance Angelman Syndrome Uniparental Disomy Adult Male Infant Deep Learning Adolescent Child, Preschool Child Face Genomic Imprinting Ubiquitin-Protein Ligases Humans Phenotype Female Young Adult
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Machine learning uncovers cell identity regulator by histone code.

Nature communications Jun 1, 2020
Conversion between cell types, e.g., by induced expression of master transcription factors, holds great promise for cellular therapy. Our ability to manipulate cell identity is constrained by incomplete information on cell identity genes (CIGs) and t...
Machine Learning Algorithms Phenotype RNA-Seq Gene Regulatory Networks Humans Gene Expression Regulation Cells Pluripotent Stem Cells Histone Code Chromatin Immunoprecipitation Sequencing Epigenesis, Genetic Transcription Factors Databases, Genetic Human Umbilical Vein Endothelial Cells Regenerative Medicine
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Environmental influences on evolvable robots.

PloS one May 29, 2020
The field of Evolutionary Robotics addresses the challenge of automatically designing robotic systems. Furthermore, the field can also support biological investigations related to evolution. In this paper, we evolve (simulated) modular robots under d...
Environment Algorithms Phenotype Robotics Seasons
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CytoCensus, mapping cell identity and division in tissues and organs using machine learning.

eLife May 19, 2020
A major challenge in cell and developmental biology is the automated identification and quantitation of cells in complex multilayered tissues. We developed CytoCensus: an easily deployed implementation of supervised machine learning that extends conv...
Mutation Retina Zebrafish Embryo, Mammalian Machine Learning Microscopy, Video Larva Animals, Genetically Modified Phenotype Organoids Brain Automation Time Factors Female Image Processing, Computer-Assisted Drosophila melanogaster Reproducibility of Results Mice Cell Division Animals Tissue Culture Techniques Male Time-Lapse Imaging
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Unsupervised Cluster Analysis of Patients With Aortic Stenosis Reveals Distinct Population With Different Phenotypes and Outcomes.

Circulation. Cardiovascular imaging May 18, 2020
BACKGROUND: There is a lack of studies investigating the heterogeneity of patients with aortic stenosis (AS). We explored whether cluster analysis identifies distinct subgroups with different prognostic significances in AS.
Humans Middle Aged Cause of Death Decision Support Techniques Comorbidity Phenotype Risk Factors Severity of Illness Index Aged Cluster Analysis Prospective Studies Hemodynamics Aged, 80 and over Aortic Valve Stenosis Prognosis Age Factors Male Aortic Valve Female Echocardiography Unsupervised Machine Learning Reproducibility of Results Predictive Value of Tests
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Active deep learning to detect demographic traits in free-form clinical notes.

Journal of biomedical informatics May 16, 2020
The free-form portions of clinical notes are a significant source of information for research, but before they can be used, they must be de-identified to protect patients' privacy. De-identification efforts have focused on known identifier types (nam...
Problem-Based Learning Humans Demography Phenotype Deep Learning Confidentiality
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Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature.

eLife May 14, 2020
The transcriptional activation and repression during NK cell ontology are poorly understood. Here, using single-cell RNA-sequencing, we reveal a novel role for T-bet in suppressing the immature gene signature during murine NK cell development. Based ...
Regulatory-Associated Protein of mTOR T-Box Domain Proteins T-bet Transcription Factor Cluster Analysis Mice, Inbred C57BL Gene Expression Profiling Gene Expression Regulation Mice, Knockout Transcriptome Machine Learning Killer Cells, Natural Proto-Oncogene Proteins c-akt Single-Cell Analysis Phenotype Forkhead Box Protein O1 Bone Marrow Cells RNA-Seq Animals Mechanistic Target of Rapamycin Complex 2 Genotype Rapamycin-Insensitive Companion of mTOR Protein
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