AIMC Topic: Genetic Variation

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WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

PLoS computational biology Nov 3, 2016
The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital componen...
Humans Machine Learning Software Algorithms High-Throughput Nucleotide Sequencing Pattern Recognition, Automated Sequence Homology, Amino Acid Genetic Speciation Animals Evolution, Molecular Proteins Genetic Variation
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Development of neuro-fuzzy model to explore gene-nutrient interactions modulating warfarin dose requirement.

Pharmacogenomics Jul 27, 2016
AIM: To investigate the influence of alterations in vitamin K (K1, K2 and K3) in modulating warfarin dose requirement.
Asian People Genetic Variation Vitamin K Polymorphism, Genetic Middle Aged Aged Adolescent Young Adult Humans Fuzzy Logic Child Adult Models, Neurological Genotype Female Male Anticoagulants Warfarin
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Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations.

PloS one Nov 24, 2015
Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biolog...
Iran Genetic Variation Olea Computational Biology Machine Learning Geography Decision Trees DNA, Plant Algorithms Bayes Theorem Genes, Plant Reproducibility of Results Alleles Microsatellite Repeats Genotype Phylogeography
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Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data.

PloS one Oct 5, 2015
It is becoming increasingly necessary to develop computerized methods for identifying the few disease-causing variants from hundreds discovered in each individual patient. This problem is especially relevant for Copy Number Variants (CNVs), which can...
Models, Genetic Causality Mutation Genetic Variation Humans Developmental Disabilities Gene Dosage Gene Regulatory Networks Gene Ontology Genetic Diseases, Inborn Genetic Predisposition to Disease Oligonucleotide Array Sequence Analysis Genetic Association Studies Congenital Abnormalities
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Model-Based Multifactor Dimensionality Reduction for Rare Variant Association Analysis.

Human heredity Jul 28, 2015
Genome-wide association studies have revealed a vast amount of common loci associated to human complex diseases. Still, a large proportion of heritability remains unexplained. The extent to which rare genetic variants (RVs) are able to explain a rele...
Humans Models, Genetic Genome-Wide Association Study Genetic Variation Multifactor Dimensionality Reduction Chromosomes, Human, Pair 4
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Better prediction of functional effects for sequence variants.

BMC genomics Jun 18, 2015
Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we introduce SNAP2, a novel neural network based classifier that improves over the state-of-the-a...
Evolution, Molecular Genetic Variation Protein Isoforms Humans Neural Networks, Computer Software Computational Biology
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PaPI: pseudo amino acid composition to score human protein-coding variants.

BMC bioinformatics Apr 19, 2015
BACKGROUND: High throughput sequencing technologies are able to identify the whole genomic variation of an individual. Gene-targeted and whole-exome experiments are mainly focused on coding sequence variants related to a single or multiple nucleotide...
Proteins Amino Acids Genetic Variation High-Throughput Nucleotide Sequencing Humans Artificial Intelligence Software Algorithms Genome, Human Exome
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16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets.

PloS one Feb 3, 2015
The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome sequencing technologies, the focus has shifted towards the sequencing of hypervariable regions of 16S...
Machine Learning Time Factors RNA, Ribosomal, 16S Databases, Genetic Metagenomics Classification Genetic Variation
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Types and effects of protein variations.

Human genetics Jan 24, 2015
Variations in proteins have very large number of diverse effects affecting sequence, structure, stability, interactions, activity, abundance and other properties. Although protein-coding exons cover just over 1 % of the human genome they harbor an di...
Models, Molecular Protein Processing, Post-Translational Molecular Dynamics Simulation Proteins Amino Acid Sequence Databases, Protein Humans Gene Ontology Genetic Variation Structure-Activity Relationship Animals Protein Structure, Secondary Protein Folding Protein Structure, Quaternary
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RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Science (New York, N.Y.) Dec 18, 2014
To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intron...
Exons Genetic Code MutL Protein Homolog 1 RNA Splice Sites RNA Splicing Child Development Disorders, Pervasive Colorectal Neoplasms, Hereditary Nonpolyposis Muscular Atrophy, Spinal Adaptor Proteins, Signal Transducing DNA Genetic Markers Genetic Variation Molecular Sequence Annotation Introns Mutation, Missense Quantitative Trait Loci Polymorphism, Single Nucleotide RNA-Binding Proteins Models, Genetic Nuclear Proteins Humans Artificial Intelligence Computer Simulation Genome-Wide Association Study
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