AIMC Topic: Phenotype

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Machine Learning for High-Throughput Stress Phenotyping in Plants.

Trends in plant science Dec 1, 2015
Advances in automated and high-throughput imaging technologies have resulted in a deluge of high-resolution images and sensor data of plants. However, extracting patterns and features from this large corpus of data requires the use of machine learnin...
Plants High-Throughput Screening Assays Stress, Physiological Breeding Machine Learning Phenotype
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Powerful Tests for Multi-Marker Association Analysis Using Ensemble Learning.

PloS one Nov 30, 2015
Multi-marker approaches have received a lot of attention recently in genome wide association studies and can enhance power to detect new associations under certain conditions. Gene-, gene-set- and pathway-based association tests are increasingly bein...
Asthma Humans Genome-Wide Association Study Machine Learning Polymorphism, Single Nucleotide Genetic Markers Phenotype
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Lynx: a knowledge base and an analytical workbench for integrative medicine.

Nucleic acids research Nov 20, 2015
Lynx (http://lynx.ci.uchicago.edu) is a web-based database and a knowledge extraction engine. It supports annotation and analysis of high-throughput experimental data and generation of weighted hypotheses regarding genes and molecular mechanisms cont...
Genes Databases, Genetic Knowledge Bases Integrative Medicine Data Mining Humans Molecular Sequence Annotation Phenotype Gene Regulatory Networks
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Genome-Wide Locations of Potential Epimutations Associated with Environmentally Induced Epigenetic Transgenerational Inheritance of Disease Using a Sequential Machine Learning Prediction Approach.

PloS one Nov 16, 2015
Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation involves germline transmitted epimutations. The primary epimutations identified involve altered differential DNA methylation regions (DMRs). Differen...
Databases, Genetic Sequence Analysis, DNA DNA Methylation Cluster Analysis Genetic Predisposition to Disease Humans DDT Computational Biology Machine Learning Methoxychlor Epigenesis, Genetic Environmental Exposure Phenotype Female Sertoli Cells Bayes Theorem Reproducibility of Results Mutation Male Granulosa Cells Spermatozoa Genome-Wide Association Study CpG Islands Chromosomes
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Causal Phenotype Discovery via Deep Networks.

AMIA ... Annual Symposium proceedings. AMIA Symposium Nov 5, 2015
The rapid growth of digital health databases has attracted many researchers interested in using modern computational methods to discover and model patterns of health and illness in a research program known as computational phenotyping. Much of the wo...
Physiology Critical Illness Intensive Care Units Disease Humans Neural Networks, Computer Machine Learning Algorithms Phenotype Databases, Factual
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OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization.

Bioinformatics (Oxford, England) Aug 12, 2015
MOTIVATION: Exome sequencing has become a de facto standard method for Mendelian disease gene discovery in recent years, yet identifying disease-causing mutations among thousands of candidate variants remains a non-trivial task.
Humans Algorithms Phenotype Transcriptome Biological Ontologies Disease Exome Polymorphism, Single Nucleotide Genotype Computational Biology
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A Comparative Study on Multifactor Dimensionality Reduction Methods for Detecting Gene-Gene Interactions with the Survival Phenotype.

BioMed research international Aug 3, 2015
Genome-wide association studies (GWAS) have extensively analyzed single SNP effects on a wide variety of common and complex diseases and found many genetic variants associated with diseases. However, there is still a large portion of the genetic vari...
Genome-Wide Association Study Genetic Predisposition to Disease Polymorphism, Single Nucleotide Genotype Epistasis, Genetic Multifactor Dimensionality Reduction Humans Algorithms Phenotype Computer Simulation
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A systematic comparison of feature space effects on disease classifier performance for phenotype identification of five diseases.

Journal of biomedical informatics Aug 1, 2015
Automated phenotype identification plays a critical role in cohort selection and bioinformatics data mining. Natural Language Processing (NLP)-informed classification techniques can robustly identify phenotypes in unstructured medical notes. In this ...
Humans Sensitivity and Specificity Diabetes Mellitus Cardiovascular Diseases Support Vector Machine Diagnosis, Computer-Assisted Natural Language Processing Obesity Phenotype Decision Support Systems, Clinical Data Mining Electronic Health Records New York Reproducibility of Results Pattern Recognition, Automated
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Multivariate Quantitative Multifactor Dimensionality Reduction for Detecting Gene-Gene Interactions.

Human heredity Jul 28, 2015
OBJECTIVES: To determine gene-gene interactions and missing heritability of complex diseases is a challenging topic in genome-wide association studies. The multifactor dimensionality reduction (MDR) method is one of the most commonly used methods for...
Humans Multifactor Dimensionality Reduction Polymorphism, Single Nucleotide Lipid Metabolism Phenotype Computer Simulation Multivariate Analysis Gene Regulatory Networks Epistasis, Genetic
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A Robust e-Epidemiology Tool in Phenotyping Heart Failure with Differentiation for Preserved and Reduced Ejection Fraction: the Electronic Medical Records and Genomics (eMERGE) Network.

Journal of cardiovascular translational research Jul 21, 2015
Identifying populations of heart failure (HF) patients is paramount to research efforts aimed at developing strategies to effectively reduce the burden of this disease. The use of electronic medical record (EMR) data for this purpose is challenging g...
Natural Language Processing Heart Failure Data Mining Electronic Health Records Female Reproducibility of Results Male Ventricular Function, Left Stroke Volume United States Humans Algorithms Phenotype
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