AIMC Topic: Polymorphism, Single Nucleotide
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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...
Discrimination of driver and passenger mutations in epidermal growth factor receptor in cancer.
Mutation research
Jul 20, 2015
Cancer is one of the most life-threatening diseases and mutations in several genes are the vital cause in tumorigenesis. Protein kinases play essential roles in cancer progression and specifically, epidermal growth factor receptor (EGFR) is an import...
Machine learning approach for pooled DNA sample calibration.
BMC bioinformatics
Jul 9, 2015
BACKGROUND: Despite ongoing reduction in genotyping costs, genomic studies involving large numbers of species with low economic value (such as Black Tiger prawns) remain cost prohibitive. In this scenario DNA pooling is an attractive option to reduce...
Genomics and Machine Learning for Taxonomy Consensus: The Mycobacterium tuberculosis Complex Paradigm.
PloS one
Jul 8, 2015
Infra-species taxonomy is a prerequisite to compare features such as virulence in different pathogen lineages. Mycobacterium tuberculosis complex taxonomy has rapidly evolved in the last 20 years through intensive clinical isolation, advances in sequ...
Cluster Analysis
Machine Learning
Computational Biology
Prevalence
Algorithms
Internet
Polymerase Chain Reaction
DNA, Bacterial
Genomics
Tuberculosis
Molecular Epidemiology
Polymorphism, Single Nucleotide
Databases, Genetic
Mycobacterium tuberculosis
Polymorphism, Restriction Fragment Length
Genotype
Bacterial Typing Techniques
An efficiency analysis of high-order combinations of gene-gene interactions using multifactor-dimensionality reduction.
BMC genomics
Jul 1, 2015
BACKGROUND: Multifactor dimensionality reduction (MDR) is widely used to analyze interactions of genes to determine the complex relationship between diseases and polymorphisms in humans. However, the astronomical number of high-order combinations mak...
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.
Nature methods
May 4, 2015
Protein phosphorylation is important in cellular pathways and altered in disease. We developed MIMP (http://mimp.baderlab.org/), a machine learning method to predict the impact of missense single-nucleotide variants (SNVs) on kinase-substrate interac...
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...
Identification of active transcriptional regulatory elements from GRO-seq data.
Nature methods
Mar 23, 2015
Modifications to the global run-on and sequencing (GRO-seq) protocol that enrich for 5'-capped RNAs can be used to reveal active transcriptional regulatory elements (TREs) with high accuracy. Here, we introduce discriminative regulatory-element detec...
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...
Molecular Sequence Annotation
Gene Ontology
Nucleotide Motifs
Gene Library
Microsatellite Repeats
Physical Chromosome Mapping
Genetic Markers
High-Throughput Nucleotide Sequencing
Phenotype
Gene Frequency
Reproducibility of Results
Citrus
Phylogeny
Transcriptome
Gene Expression Profiling
Polymorphism, Single Nucleotide
Cluster Analysis
Improved feature-based prediction of SNPs in human cytochrome P450 enzymes.
Interdisciplinary sciences, computational life sciences
Mar 21, 2015
Single nucleotide polymorphisms (SNPs) make up the most common form of mutations in human cytochrome P450 enzymes family, and have the potential to bring with different drug responses or specific diseases in individual patients. Here, based on machin...
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