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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)

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)

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)

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)

Age-related variations in DNA methylation have been reported; however, the functional relevance of these differentially methylated sites (age-dMS) are unclear. Here we report potentially functional age-dMS, defined as age- and cis-gene expression-associated methylation sites (age-eMS), identified by integrating genome-wide CpG methylation and gene… (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)

The joint action of multiple genes is an important source of variation for complex traits and human diseases. However, mapping genes with epistatic effects and gene-environment interactions is a difficult problem because of relatively small sample sizes and very large parameter spaces for quantitative trait locus models that include such interactions. Here… (More)

A method for multiple-trait genetic evaluation for categorical and continuous traits was generalized to a polychotomous rather than a binary trait and to several continuous traits rather than one. Any missing data pattern was allowed. Breeding values were estimated based on an animal model with fixed and random effects differing among traits. Equations in… (More)

A Bayesian method for mapping linked quantitative trait loci (QTL) using multiple linked genetic markers is presented. Parameter estimation and hypothesis testing was implemented via Markov chain Monte Carlo (MCMC) algorithms. Parameters included were allele frequencies and substitution effects for two biallelic QTL, map positions of the QTL, and markers,… (More)

A residual maximum likelihood method, implemented with a derivative-free algorithm, was derived for estimating position and variance contribution of a single QTL together with additive polygenic and residual variance components. The method is based on a mixed linear model including random polygenic effects and random QTL effects, assumed to be normally… (More)