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MOTIVATION A major challenge of systems biology is to infer biochemical interactions from large-scale observations, such as transcriptomics, proteomics and metabolomics. We propose to use a partial correlation analysis to construct approximate Undirected Dependency Graphs from such large-scale biochemical data. This approach enables a distinction between(More)
Quantitative trait loci (QTL) affecting milk production and health of dairy cattle were mapped in a very large Holstein granddaughter design. The analysis included 1794 sons of 14 sires and 206 genetic markers distributed across all 29 autosomes and flanking an estimated 2497 autosomal cM using Kosambi's mapping function. All families were analyzed jointly(More)
Additive and nonadditive genetic variances were estimated for cow fertility of Holsteins. Measures of fertility were first lactation days open and service period as recorded and with upper bounds of 150 and 91 d, respectively. Six million inseminations from the Raleigh, North Carolina Processing Center were used to form fertility records of 379,009 cows.(More)
The conditional probability of an observation in a subpopulation i (a combination of levels of explanatory variables) falling into one of 2" mutually exclusive and exhaustive categories is modelled using a normal integral in n-dimensions. The mean of subpopulation i is written as a linear combination of an unknown vector 8 which can include « fixed >>(More)
Genetic analysis of gene expression in a segregating population, which is expression profiled and genotyped at DNA markers throughout the genome, can reveal regulatory networks of polymorphic genes. We propose an analysis strategy with several steps: (1) genome-wide QTL analysis of all expression profiles to identify eQTL confidence regions, followed by(More)
Our goal is gene network inference in genetical genomics or systems genetics experiments. For species where sequence information is available, we first perform expression quantitative trait locus (eQTL) mapping by jointly utilizing cis-, cis-trans-, and trans-regulation. After using local structural models to identify regulator-target pairs for each eQTL,(More)
For estimation of dominance effects and dominance variance, the inverse of a dominance relationship matrix is required. Dominance effects can be partitioned into sire x dam or sire x maternal grandsire subclass effects that are inherited and residuals within subclass that are not inherited. The subclass effects have immediate use in predicting performance(More)
A Gibbs sampling scheme for Bayesian analysis of binary threshold data was derived. A simulation study was conducted to evaluate the accuracy of 3 variance component estimators, deterministic approximate marginal maximum likelihood (AMML), Monte-Carlo marginal posterior mode (MCMML), and Monte-Carlo marginal posterior mean (MCMPM). Several designs with(More)
Information on multiple linked genetic markers was used in a Bayesian method for the statistical mapping of quantitative trait loci (QTL). Bayesian parameter estimation and hypothesis testing were implemented via Markov chain Monte Carlo algorithms. Variables sampled were the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable(More)
Statistical methods to map quantitative trait loci (QTL) in outbred populations are reviewed, extensions and applications to human and plant genetic data are indicated, and areas for further research are identified. Simple and computationally inexpensive methods include (multiple) linear regression of phenotype on marker genotypes and regression of squared(More)