AIMC Topic: Phenotype

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PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease.

Bioinformatics (Oxford, England) Oct 1, 2019
MOTIVATION: Whole-exome sequencing (WES) is now being used in clinical practice for the diagnosis of the causal genes of Mendelian diseases. In order to make the diagnosis, however, the clinical phenotypes [e.g. Human Phenotype Ontology (HPO) terms] ...
Computational Biology Natural Language Processing Exome Sequencing Humans Software Phenotype
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Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.

Current protocols in human genetics Sep 1, 2019
The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnost...
Diagnosis, Differential Whole Genome Sequencing Biological Ontologies Phenotype Genetic Diseases, Inborn Humans Computational Biology Exome Software Databases, Genetic
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Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits.

Systematic biology Sep 1, 2019
Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. Thes...
Classification Anatomy Biological Evolution Animals Models, Statistical Biological Ontologies Phenotype
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TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes.

Nucleic acids research Aug 22, 2019
Genome-wide association studies (GWAS) associate single nucleotide polymorphisms (SNPs) to complex phenotypes. Most human SNPs fall in non-coding regions and are likely regulatory SNPs, but linkage disequilibrium (LD) blocks make it difficult to dist...
Genetic Predisposition to Disease Polymorphism, Single Nucleotide Computational Biology Phenotype Genome-Wide Association Study Quantitative Trait Loci Linkage Disequilibrium Regulatory Sequences, Nucleic Acid Internet Supervised Machine Learning Gene Expression Regulation Humans
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Doc2Hpo: a web application for efficient and accurate HPO concept curation.

Nucleic acids research Jul 2, 2019
We present Doc2Hpo, an interactive web application that enables interactive and efficient phenotype concept curation from clinical text with automated concept normalization using the Human Phenotype Ontology (HPO). Users can edit the HPO concepts aut...
User-Computer Interface Internet Biological Ontologies Data Curation Genes Humans Software Phenotype
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OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction.

Bioinformatics (Oxford, England) Jun 1, 2019
MOTIVATION: Ontologies are widely used in biology for data annotation, integration and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of information tha...
Semantics Biological Ontologies Phenotype Animals Mice
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New Phenotypes for Sepsis: The Promise and Problem of Applying Machine Learning and Artificial Intelligence in Clinical Research.

JAMA May 28, 2019
Machine Learning Humans Artificial Intelligence Phenotype Sepsis
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A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth.

GigaScience May 1, 2019
BACKGROUND: Tracking and predicting the growth performance of plants in different environments is critical for predicting the impact of global climate change. Automated approaches for image capture and analysis have allowed for substantial increases ...
Arabidopsis Phenotype Imaging, Three-Dimensional Deep Learning Plant Development Photometry
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Leveraging machine vision in cell-based diagnostics to do more with less.

Nature materials May 1, 2019
Machine Learning Diagnostic Techniques and Procedures Software Algorithms Humans Biopsy Neural Networks, Computer Prognosis Cytological Techniques Image Processing, Computer-Assisted Phenotype Diagnosis, Computer-Assisted Microfluidics Diagnostic Imaging Biomarkers Single-Cell Analysis Precision Medicine
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Avoiding common pitfalls in machine learning omic data science.

Nature materials May 1, 2019
Humans Machine Learning Algorithms Phenotype Data Science Genomics Oligonucleotide Array Sequence Analysis Proteomics Computational Biology Medical Errors Models, Theoretical Cell Biology Genetic Variation
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