Molecular Recognition in Biological Systems and Bioinformatics

Genetics; complex traits; statistical genetics; software development.

Development of Web-based software to support the Collaborative Cross. This is a large cross of eight inbred mouse lines intended to yield several hundred to one thousand recombinant inbred lines. These lines will constitute a unique genetic reference population for finding disease-related genes, for defining networks of interacting gene products, and for defining environmental interactions with genetic variation.

• Quantitative trait locus mapping
• Web-based computer application development

Mouse

The ability to study interactions of disease-related genes in model organisms, either interactions among genes or with environmental factors, will have long-term benefits for all common diseases.

• Statistical association
• Gene mapping
• Complex trait mapping

Obesity, diabetes, cancer

Any

Gatti, D., Maki, A., Chesler, E. J., Kirova, R., Kosyk, O., Lu, L., Manly, K. F., Williams, R. W., Perkins, A., Langston, M. A., Threadgill, D. W., and Rusyn, I.: Genome-level analysis of genetic regulation of liver gene expression networks. Hepatology 46: 548-57, 2007

Lan, H., Chen, M., Flowers, J. B., Yandell, B. S., Stapleton, D. S., Mata, C. M., Mui, E. T., Flowers, M. T., Schueler, K. L., Manly, K. F., Williams, R. W., Kendziorski, C., and Attie, A. D.: Combined Expression Trait Correlations and Expression Quantitative Trait Locus Mapping. PLoS Genet 2: e6, 2006

Li, H., Chen, H., Bao, L., Manly, K. F., Chesler, E. J., Lu, L., Wang, J., Zhou, M., Williams, R. W., and Cui, Y.: Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits. Hum Mol Genet 15: 481-92, 2006

Peirce, J. L., Li, H., Wang, J., Manly, K. F., Hitzemann, R. J., Belknap, J. K., Rosen, G. D., Goodwin, S., Sutter, T. R., Williams, R. W., and Lu, L.: How replicable are mRNA expression QTL? Mamm Genome 17: 643-56, 2006

Manly, K. F.: Conventional P-values fail to assure reproducibility for genetic association tests. Trends in Genetics 21: 268-269, 2005

Manly, K. F.: Reliability of statistical associations between genes and disease. Immunogenetics 57: 549-58, 2005

Manly, K. F., Wang, J., and Williams, R. W.: Weighting by heritability for detection of quantitative trait loci with microarray estimates of gene expression. Genome Biology 6: R27, 2005