Armidale Animal Breeding Summer Course 2019

Venue: University of New England, Armidale, NSW Australia

Course Audience: Postgraduate students and other professionals




Introduction to Graphical Models with Applications to Quantitative Genetics and Genomics 



Dr Guilherme J. M. Rosa        University of Wisconsin-Madison

Dr Francisco Peñagaricano    University of Florida-Gainesville


Dates:     Tuesday 29 January 2019 (9am) – Friday 1 February 2019 (4pm)


Program 2019


Course Materials 2019


Day 1

Correlation and causation

Matrix basics

Probability, random variables

Path Analysis

Estimation, Independence test


R examples Rosa


Day 2

Correlation networks

Correlation networks (lab 1)

Mixed Models

Structural Equation Models


Mixed model examples



Latent variables

SEM (lab 2)

Bayesian Networks

Examples: prediction and causal inference



Bayes Nets (lab 3)

Instrumental variable

GWAS and QTL analysis

GWAS and QTL analysis (lab 4)





Photos (click on image to download higher resolution photo)




Material of previous years:


Armidale Genetics Summer Course 2018    Materials

·         Mathematical modeling of infection dynamics in genetically diverse livestock populations: Andrea Doeschl-Wilson and Osvaldo Anacleto          


Armidale Genetics Summer Course 2017    Materials

·         Genotype by environment interaction in breeding programs: Piter Bijma and Han Mulder           


Armidale Genetics Summer Course 2016    Materials


Investigating the Genetic Architecture of Complex Traits  & Prediction of Phenotype

from Genome-wide SNPs - Doug Speed and David Balding


Armidale Animal Breeding Summer Course 2015   Materials

                    Primer to genomic analysis using R:    Cedric Gondro

                    From Sequence Data to Genomic Prediction:   Ben Hayes and Hans Daetwyler


Armidale Animal Breeding Summer Course 2014    Materials

Breeding Program Design with Genomic Selection: Jack Dekkers, Julius van der Werf


Armidale Animal Breeding Summer Course 2012    Materials

Statistical Methods for Genome-Enabled Selection: Daniel Gianola, Gustavo de los Campos 


Armidale Animal Breeding Summer Course 2011    Materials

·         Statistical methods and design in plant breeding and genomics: Ian Mackay

·        IBD inference in genome association studies: Elizabeth Thompson


Armidale Animal Breeding Summer Course 2010    Materials

·         Application of evolutionary algorithms to solve complex problems in quantitative genetics

and bioinformatics:   Brian Kinghorn, Cedric Gondro

·         Bayesian methods in genome association studies:  Dorian Garrick,  Rohan Fernando


Armidale Animal Breeding Summer Course 2009    Materials

·        Quantitative Genetic Theory and Analysis- Selection Theory:    Bruce Walsh

·         Quantitative Genetic Models for social interaction and inherited variability: Piter Bijma


Armidale Animal Breeding Summer Course 2008      Materials 

·         Genomic Selection:       Ben Hayes


Armidale Animal Breeding Summer Course 2007      Materials

·         Generalized Linear Mixed Models:        Steve Kachman


Armidale Animal Breeding Summer Course 2006    Materials

·         Gene Expression:          Toni Reverter

·         Breeding Program Design:         Graser, James, Van der Werf

Armidale Animal Breeding Summer Course 2005    Materials
·         Breeding Objectives: Gibson, Van der Werf, Kinghorn
·         Scientific Writing:          David Lindsay
·         ASReml:           Arthur Gilmour
Armidale Animal Breeding Summer Course 2004    Materials
·         Bayesian for Beginners               Kerrie Mengersen
·         Bayesian Models for QTL analysis        Michel Perez-Enciso
·         Bioinformatics   John McEwan

Armidale Animal Breeding Summer Course 2003    Materials

·         Scientific Writing:  David Lindsay
·         Linear Models for animal breeding:   Julius van der Werf, Mike Goddard
·         QTL mapping for practitioners, from linkage to gene: Ben Hayes, Julius van der Werf
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