Part I Resources for Systems Genetics 1. Resources for Systems Genetics Robert W. Williams and Evan G. Williams 2. Heterogeneous Stock Populations for Analysis of Complex Traits Leah Solberg Woods and Richard Mott Part II Tools for Analysis and Integration in Systems Genetics 3. Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research Janan T. Eppig, Cynthia L. Smith, Judith A. Blake, Martin Ringwald, James A. Kadin, Joel E. Richardson, and Carol J. Bult 4. GeneNetwork: A Toolbox for Systems Genetics Megan K. Mulligan, Khyobeni Mozhui, Pjotr Prins, and Robert W. Williams 5. Complex Trait Analyses of the Collaborative Cross: Tools and Databases Ramesh Ram and Grant Morahan 6. Integrative Functional Genomics for Systems Genetics in GeneWeaver.org Jason A. Bubier, Michael A. Langston, Erich J. Baker, and Elissa J. Chesler 7. A Suite of Tools for Biologists that Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel Christoph D. Rau, Mete Civelek, Calvin Pan, and Aldons J. Lusis 8. Expression QTLs Mapping and Analysis: A Bayesian Perspective Martha Imprialou, Leonardo Bottolo, and Enrico Petretto 9. Epigenetics and Control of RNAs Henrike Maatz, Sebastiaan van Heesch, Allison Faber, Franziska Kreuchwig, Eleonora Adami, Norbert Hubner, and Matthias Heinig 10. Integrating Multidimensional Data Sources to Identify Genes Regulating Complex Phenotypes <integrating multidimensional=" data=" sources=" to=" identify=" genes=" regulating=" complex=" phenotypesRupert W. Overall 11. RNA-Seq in the Collaborative Cross Richard Green, Courtney Wilkins, Martin T. Ferris, and Michael Gale, Jr. 12. QTL Mapping and Identification of Candidate Genes in DO Mice: A Use Case Model Derived from a Benzene Toxicity Experiment Dan Gatti, John E. French, and Klaus Schughart 13. Visualization of Results from System Genetics Studies in Chromosomal Context Karen Y. Orostica and Ricardo A. Verdugo Part III Systems Genetics Use Cases: Mapping and Combining Multiple Phenotypic Traits in Mouse Genetic Reference Populations Organ Systems 14. Genomic Control of Retinal Cell Number: Challenges, Protocols, and Results Patrick W. Keeley, Irene E. Whitney, and Benjamin E. Reese 15. Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene Sumana R. Chintalapudi and Monica M. Jablonski 16. Genetic Dissection of Variation in Hippocampal Intra-and Infrapyramidal Mossy Fibers in the Mouse Anna Delprato and Wim E. Crusio 17. Complex Genetics of Cardiovascular Traits in Mice: F2-Mapping of QTLs and their Underlying Genes Svitlana Podliesna, Connie R. Bezzina, and Elisabeth M. Lodder 18. Systems Genetics of Live Fibrosis Rabea A. Hall and Frank Lammert Metabolism 19. Systems Genetic Analysis of Iron and its Regulation in Brain and Periphery Byron C. Jones and Leslie C. Jellen 20. Systems Genetics of Obesity Sebastian Heise, Danny Arends, Ayca Dogan, and Gudrun A. Brockmann Behavior 21. Social Interactions and Indirect Genetic Effects on Complex Juvenile and Adult Traits David G. Ashbrook and Reinmar Hager 22. Complex Genetics of Behaior: BXDs in the Automated Home-Cage Maarten Loos, NeuroBsik Mouse Phenomics Consortium, Matthijs Verhage, Sabine Spijker, and August B Smit 23. Integrative Analysis of Genetic, Genomic and Phenotypic Data for Ethanol Behaviors: A Network-Based Pipeline for Identifying Mechanisms and Potential Drug Targets James W. Bogenpohl, Kristin M. Mignogna, Maren L. Smith, and Michael F. Miles Infectious Diseases 24. Dissection of Host Susceptibility to Bacterial Infections and its Toxins Aysar Nashef, Mahmoud Agbaria, Ariel Shusterman, Nicole Ivan Lore, Alessandra Bragonzi, Ervin Wiess, Yael Houri-Haddad, and Fuad A. Iraqi 25. The Collaborative Cross Resource for Systems Genetics Research of Infectious Diseases Paul L. Maurizio and Martin T. Ferris From Traits to Networks 26. Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease Aida Moreno-Moral, Francesco Pesce, Jacques Behmoaras, and Enrico Petretto 27. Using Baseline Transcriptional Connectomes in Rat to Identify Genetic Pathways Associated with Predisposition to Complex Traits Laura Saba, Paula Hoffman, and Boris Tabakoff 28. Precise Network Modeling of Systems Genetic Data Using the Bayesian Network Webserver Jesse D. Ziebarth and Yan Cui Translation to Human 29. Using Systems Genetics to Understanding the Etiology of Complex Disease Ramesh Ram and Grant Morahan
