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Influenza Diallel Analysis
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This respository contains data and code required to reproduce analysis for an infection diallel, using influenza A virus (H1N1) in inbred and F1 mice (n=1,043). The title for this project is: "Bayesian diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice". Our manuscript has been published in G3:

This repository may be updated post-publication. A static version of the data, software, and scripts used to analyze this data is available at DOI: 10.5281/zenodo.293015.


Learn more about this study via slides I presented at the Complex Trait Community Meeting in Memphis, TN (June 16, 2017): CTC-2017-Maurizio.

Data Sets

  1. FluDiData.csv

  2. Flu-preCC-data.csv

  3. Flu-CC-RIX-data.csv


  1. BayesDiallel

  2. Diploffect

  3. treatmentResponseDiallel

More Information

For more information about my research interests, please visit To learn more about research in the Heise and Valdar labs, please visit and and

Key References

Maurizio PL, Ferris MT, Keele GR, Miller DR, Shaw GD, Whitmore AC, West A, Morrison CR, Noll KE, Plante KS, Cockrell AS, Threadgill DW, Pardo-Manuel de Villena F, Baric RS, Heise MT & Valdar W (2018) Bayesian diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice. G3: Genes, Genomes, Genetics 8(2):427-445. 10.1534/g3.117.300438. PMID:29187420.

Maurizio PL & Ferris MT (2017) “Chapter 28: The Collaborative Cross Resource for Systems Genetics Research of Infectious Diseases.” Methods in Molecular Biology: Systems Genetics – Methods and Protocols. Springer Science+Business Media, New York, NY. Klaus Schughart and Robert W. Williams (eds.) 1488:579-596. eBook ISBN: 978-1-4939-6427-7, hardcover ISBN: 978-1-4939-6425-3. doi: 10.1007/978-1-4939-6427-7_28

Zhang Z, Wang W & Valdar W (2014) Bayesian modeling of haplotype effects in multiparent populations. Genetics 198(1):139-56. doi: 10.1534/genetics.114.166249

Crowley JJ, Kim Y, Lenarcic AB, Quackenbush CR, Barrick C, Adkins DE, Shaw GS, Miller DR, Pardo Manuel de Villena F, Sullivan PF & Valdar W (2014) Genetics of adverse reactions to haloperidol in a mouse diallel: A drug-placebo experiment and Bayesian causal analysis. Genetics 196(1):321-47. doi: 10.1534/genetics.113.156901

Ferris MT, Aylor DL, Bottomly D, Whitmore AC, Aicher LD, Bell TA, Bradel-Tretheway B, Bryan JT, Buus RJ, Gralinski LE, Haagmans BL, McMillan L, Miller DR, Rosenzweig E, Valdar W, Wang J, Churchill GA, Threadgill DW, McWeeney SK, Katze MG, Pardo-Manuel de Villena F, Baric RS & Heise MT (2013) Modeling host genetic regulation of influenza pathogenesis in the Collaborative Cross. PLoS Pathogens 9(2):e1003196. doi: 10.1371/journal.ppat.1003196

Lenarcic AB, Svenson KL, Churchill GA & Valdar W (2012) A general Bayesian approach to analyzing diallel crosses of inbred strains. Genetics 190:413-435. doi: 10.1534/genetics.111.132563

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