64 Results
for term "sites"
- Sporadic, Global Linkage Disequilibrium Between Unlinked Segregating Sites.... Supporting information is available online at www..org/lookup/suppl/ doi:10.1534/.115.177816/-/DC1. 1Corresponding author: North Carolina State University, 2601 Stinson Dr., Raleigh, NC 27607. E-mail: eric_stone@ncsu.edu Genetics, Vol. 202, 427437 February 2016 427 number of polymorphic sites, exploration ~~~
- Genetic Variant Selection: Learning Across Traits and Sites...prior distributions that facilitate learning the role of each variable site by borrowing evidence across phenotypes and across mutations in the same gene. We illustrate their potential advantages with simulations and reanalyzing a data set of sequencing variants. KEYWORDS Bayesian variant selection; ne ~~~
- A New Mechanism for Mendelian Dominance in Regulatory Genetic Pathways: Competitive Binding by Transcription Factors...) on the cis-regulated promoter site it binds to is determined by binding energy (DG) and TF dosage. Transcription and gene expression proceed when the TF is bound to the promoter. In diploids, individuals may be heterozygous at the cis-site, at the TFs coding region, or at the TFs own promoter, which ~~~
- A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation...the genome while taking into account the distance between CpG sites as a covariate. Our simulation study shows that ABBA has greater power to detect DMRs than existing methods, providing an accurate identication of DMRs in the large majority of simulated cases. To empirically demonstrate the method ~~~
- Choosing Subsamples for Sequencing Studies by Minimizing the Average Distance to the Closest Leaf...a signicant improvement in imputation accuracy, especially for imputation of sites with low-frequency alleles. This improvement in imputation accuracy is robust to changes in reference panel size, marker density, and length of the imputation target region. KEYWORDS algorithms; imputation; polymorphic sites ~~~
- Genotype-Frequency Estimation from High-Throughput Sequencing Data...our ability to draw evolutionary inference in severalways. First, rapidly declining sequencing costs enable researchers to sequence many individuals in a population. One of the major ndings of recent populationgenomic studies is the discovery of polymorphic sites harboring rare alleles ~~~
- Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data...is not an arbitrary choice, but instead represents a formulation that allows us to express the third-moment correlation of gametes produced by individuals. The nal term is the fourth-moment correlation coefcient. This coefcient estimates the fraction of sites where zygosity is guaranteed to be identical ~~~
- A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/dS Estimation...| INVESTIGATION A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specic dN/dS Estimation Stephanie J. Spielman,*,1 Suyang Wan, and Claus O. Wilke* *Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular ~~~
- Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps... hDPjixi;j; (1) where hDPji is the average effect of mutation j across all backgrounds, xi;j is an index that encodes whether or not mutation j is present in genotype i, and L is the number of sites. The dependent variables are the observed phenotypes obs taken from the experimental genotype ~~~
- Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci...RNAs themselves is far less well understood, due to difculties determining the transcription start sites of transient primary transcripts. This challenge can be addressed using expression quantitative trait loci (eQTLs) whose regulatory effects represent a natural source of perturbation of cis ~~~