Short Course on Graphical Models

Monday, June 19, 2017 - 8:30am to Friday, June 23, 2017 - 12:00pm
Event Type: 

Instructors:     Dr. Guilherme J. M. Rosa           University of Wisconsin-Madison      (

Dr. Francisco Peñagaricano    University of Florida-Gainesville            (


Registration for this course is now open at: .   Space is limited, so register early (by May 31).

Limited shared on-campus housing is available on a first-come basis at $125 per week (book through the registration website by May 15). 

A room block is available at the Best Western Plus University Park Inn & Suites at $109 /$119 single/double/day.; book directly with hotel at (515) 296-2500. Be sure to mention you are with the Animal Breeding & Genetics Short Course.

For transportation to and from the Des Moines airport, see: 


Course Content

The course will provide an introduction to graphical models, including correlation networks, structural equation models, and Bayesian networks. Topics to be discussed include the concept of d-separation, causal sufficiency, and Markov blanket. The material will be illustrated with applications in quantitative genetics and genomics, including the prediction of phenotypes using earlier expressed traits, and genome-enabled prediction. Other examples of application of graphical modeling will include genome-wide association analysis (GWAS) and quantitative trait loci (QTL) mapping for multiple traits, structural equation models with latent variables, and the combination of multiple layers of omics information. Additional topics will include the concept of Mendelian randomization, direct and indirect genetic effects, and the analysis of field data in livestock production.


Target audience and prerequisites

The course targets graduate students and researchers interested on the analysis of genetics and genomics data, including complex traits, molecular markers and gene expression. Some basic knowledge of quantitative and molecular genetics, linear mixed models, and elementary probability and statistics is expected. However, a brief overview of matrix algebra, probability distributions, and statistical inference will be provided at the beginning of the course. In addition, a working knowledge of R is desirable but an introduction will be offered prior to the use of specific R packages for graphical modeling.




Correlation and Causation

Sewall Wright and path analysis

Observational and experimental data

Confounding and selection bias



Basics of Matrix Algebra

Definitions and matrix operations

Systems of equations

Linear regression and least squares


Aspects of Multivariate Distributions

Density function or mass function

Marginal and conditional distributions

Expectation and variance

Covariance and independence

The multivariate normal distribution


Inference with Multivariate Models

Likelihood principle

Parameter estimation, Hypothesis test

Independence tests (Discrete, Continuous, and Mixed cases)


Introduction to Graphical Models

Basic concepts; network topology features

Correlation networks

Marginal and partial correlations

Conditional independence and the concept of d-separation


Structural Equation Models in Quantitative Genetics

Traditional multi-trait mixed effects model (MTM)

Genetic and phenotypic correlation

Basics of structural equation models (SEM)

SEM with latent variables

SEM embedded in MTM; direct and indirect genetic effects


Bayesian Networks


Structure learning (constraint- and score-based algorithms)

Parameter learning

The concept of Markov blanket

Causal inference


Applications in Genetics and Genomics

Building parsimonious models

Genome-enabled prediction

Instrumental variable and Mendelian randomization

Multiple-trait QTL mapping

Combining multiple layers of omics information


R packages: Rgraphviz, pcalg, bnlearn, qtlnet, sem, lavaan, among others


Dr. Jack C. M. Dekkers

C.F. Curtiss Distinguished Professor

Section Leader of Animal Breeding and Genetics

239D Kildee Hall

Department of Animal Science

Iowa State University

Ames, IA, 50011

515-294-7509  Fax: 515-294-9150