Resources for Systems Genetics -- Heterogeneous Stock Populations for Analysis of Complex Traits -- Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research -- GeneNetwork: A Toolbox for Systems Genetics -- Complex Trait Analyses of the Collaborative Cross: Tools and Databases -- Integrative Functional Genomics for Systems Genetics in GeneWeaver.org -- A Suite of Tools for Biologists that Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel -- Expression QTLs Mapping and Analysis: A Bayesian Perspective -- Epigenetics and Control of RNAs -- Integrating Multidimensional Data Sources to Identify Genes Regulating Complex Phenotypes -- RNA-Seq in the Collaborative Cross -- QTL Mapping and Identification of Candidate Genes in DO Mice: A Use Case Model Derived from a Benzene Toxicity Experiment -- Visualization of Results from System Genetics Studies in Chromosomal Context -- Genomic Control of Retinal Cell Number: Challenges, Protocols, and Results -- Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene -- Genetic Dissection of Variation in Hippocampal Intra-and Infrapyramidal Mossy Fibers in the Mouse -- Complex Genetics of Cardiovascular Traits in Mice: F2-Mapping of QTLs and their Underlying Genes -- Systems Genetics of Live Fibrosis -- Systems Genetic Analysis of Iron and its Regulation in Brain and Periphery -- Systems Genetics of Obesity -- Social Interactions and Indirect Genetic Effects on Complex Juvenile and Adult Traits -- Complex Genetics of Behaior: BXDs in the Automated Home-Cage -- Integrative Analysis of Genetic, Genomic and Phenotypic Data for Ethanol Behaviors: A Network-Based Pipeline for Identifying Mechanisms and Potential Drug Targets -- Dissection of Host Susceptibility to Bacterial Infections and its Toxins -- The Collaborative Cross Resource for Systems Genetics Research of Infectious Diseases -- Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease -- Using Baseline Transcriptional Connectomes in Rat to Identify Genetic Pathways Associated with Predisposition to Complex Traits -- Precise Network Modeling of Systems Genetic Data Using the Bayesian Network Webserver -- Using Systems Genetics to Understanding the Etiology of Complex Disease. .

This volume focuses on the use of system genetic methods and the use of murine models to study the role of gene variants and environmental factors on human health and disease-what is now often called personalized or precision health care. The protocols in this book will help readers analyze genetic causes of heritable variation across a wide range of systems and traits using rodent models. The chapters in this book are separated into three sections that cover: 1) resources for systems genetics; 2) tools for analysis and integration in systems genetics; and 3) systems genetics use cases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and tools, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and thorough, Systems Genetics: Methods and Protocols is a valuable resource for anyone who is interested in this diverse field.