AIMC Topic: Phenotype

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Application of neural networks with back-propagation to genome-enabled prediction of complex traits in Holstein-Friesian and German Fleckvieh cattle.

Genetics, selection, evolution : GSE Mar 31, 2015
BACKGROUND: Recently, artificial neural networks (ANN) have been proposed as promising machines for marker-based genomic predictions of complex traits in animal and plant breeding. ANN are universal approximators of complex functions, that can captur...
Neural Networks, Computer Male Cattle Polymorphism, Single Nucleotide Genotype Lactation Algorithms Phenotype Female Animals Dairying Genome Quantitative Trait, Heritable Milk Linear Models Breeding Crosses, Genetic
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De novo transcriptome assembly of pummelo and molecular marker development.

PloS one Mar 23, 2015
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtai...
Cluster Analysis Phenotype Genetic Markers Reproducibility of Results Gene Library Phylogeny High-Throughput Nucleotide Sequencing Citrus Microsatellite Repeats Gene Expression Profiling Molecular Sequence Annotation Physical Chromosome Mapping Gene Frequency Transcriptome Gene Ontology Polymorphism, Single Nucleotide Nucleotide Motifs
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Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature.

BMC bioinformatics Mar 18, 2015
BACKGROUND: Systems approaches to studying drug-side-effect (drug-SE) associations are emerging as an active research area for both drug target discovery and drug repositioning. However, a comprehensive drug-SE association knowledge base does not exi...
Knowledge Bases Drug Repositioning Search Engine Data Mining Humans Pharmaceutical Preparations Databases, Pharmaceutical Biological Ontologies Periodicals as Topic MEDLINE Artificial Intelligence Drug-Related Side Effects and Adverse Reactions Phenotype Drug Discovery
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Automatic concept recognition using the human phenotype ontology reference and test suite corpora.

Database : the journal of biological databases and curation Feb 27, 2015
Concept recognition tools rely on the availability of textual corpora to assess their performance and enable the identification of areas for improvement. Typically, corpora are developed for specific purposes, such as gene name recognition. Gene and ...
Phenotype Data Mining Gene Ontology Humans Software
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HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.

PloS one Feb 9, 2015
BACKGROUND: Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the con...
Databases, Genetic Disease Gene Ontology Genes Software Phenotype Genetic Predisposition to Disease Computational Biology Humans
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Identification of Type 2 Diabetes Risk Factors Using Phenotypes Consisting of Anthropometry and Triglycerides based on Machine Learning.

IEEE journal of biomedical and health informatics Feb 6, 2015
The hypertriglyceridemic waist (HW) phenotype is strongly associated with type 2 diabetes; however, to date, no study has assessed the predictive power of phenotypes based on individual anthropometric measurements and triglyceride (TG) levels. The ai...
Diabetes Mellitus, Type 2 Anthropometry Triglycerides Adult Humans Cross-Sectional Studies Machine Learning Male Phenotype Middle Aged Risk Factors Retrospective Studies Aged Female Aged, 80 and over
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Aber-OWL: a framework for ontology-based data access in biology.

BMC bioinformatics Jan 28, 2015
BACKGROUND: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within t...
Phenotype Databases, Factual Heart Septal Defects, Ventricular Language Humans Semantics Genome-Wide Association Study Software Biological Ontologies Computational Biology Knowledge Models, Genetic Apoptosis Regulatory Proteins Internet
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Validation of electronic health record phenotyping of bipolar disorder cases and controls.

The American journal of psychiatry Dec 12, 2014
OBJECTIVE: The study was designed to validate use of electronic health records (EHRs) for diagnosing bipolar disorder and classifying control subjects.
Electronic Health Records Female Reproducibility of Results Aged Humans Algorithms Phenotype Case-Control Studies Adult Bipolar Disorder Cohort Studies Sensitivity and Specificity Predictive Value of Tests Male Natural Language Processing Middle Aged
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Quantitative analysis of mitochondrial morphology and membrane potential in living cells using high-content imaging, machine learning, and morphological binning.

Biochimica et biophysica acta Nov 13, 2014
Understanding the processes of mitochondrial dynamics (fission, fusion, biogenesis, and mitophagy) has been hampered by the lack of automated, deterministic methods to measure mitochondrial morphology from microscopic images. A method to quantify mit...
tert-Butylhydroperoxide Carbonyl Cyanide m-Chlorophenyl Hydrazone Cell Respiration Sodium-Potassium-Exchanging ATPase Stress, Physiological Cell Membrane Electron Transport Phenotype Animals Imaging, Three-Dimensional Mice Membrane Potential, Mitochondrial Oxidants Mitochondria Cell Line Cell Survival Artificial Intelligence
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UGMDR: a unified conceptual framework for detection of multifactor interactions underlying complex traits.

Heredity Oct 22, 2014
Biological outcomes are governed by multiple genetic and environmental factors that act in concert. Determining multifactor interactions is the primary topic of interest in recent genetics studies but presents enormous statistical and mathematical ch...
Multifactorial Inheritance Algorithms Phenotype Computer Simulation Polymorphism, Single Nucleotide Humans Linear Models Logistic Models Proportional Hazards Models Models, Genetic Multifactor Dimensionality Reduction
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