Current Experimental Interests:

- Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription.
- Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance.
- Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism.

Current Computational Interests:

- Systematic analysis of genetic interacton to reveal redundant systems and order of action in genetic pathways.
- Using knockout, knockdown, overexpression or other genetic perturbations of combinations of genes in S. cerevisiae, C. elegans or mouse.
- Using genome-scale genotyping of natural polymorphisms in S. cerevisiae and human populations.
- Integrating large-scale studies – including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns – to quantitatively assign function to genes and guide experimentation and disease association studies.
- Alternative splicing and its relationship to protein interaction networks.

Selected Publications:

R.P. St. Onge, R. Mani, J. Oh, M. Proctor, E. Fung, R.W. Davis, C. Nislow, F.P. Roth and G. Giaever (2007). Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nature Genetics, 39(2): 199-206.

L. Pena-Castillo, M. Tasan, C.L. Myers, H. Lee, T. Joshi, C. Zhang, Y. Guan, M. Leone, A. Pagnani, W.K. Kim, C. Krumpelman, W. Tian, G. Obozinski, Y. Qi, S. Mostafavi, G.N. Lin, G.F. Berriz, F.D. Gibbons, G. Lanckriet, J. Qiu, C. Grant, Z. Barutcuoglu, D.P. Hill, D. Warde-Farley, C. Grouios, D. Ray, J.A. Blake, M. Deng, M. Jordan, W.S. Noble, Q. Morris, J. Klein-Seetharaman, Z. Bar-Joseph, T. Chen, F. Sun, O.G. Troyanskaya, E.M. Marcotte, D. Xu, T.R. Hughes. and F.P. Roth (2008). A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology 9 Suppl 1:S2.

R. Mani, R.P. St. Onge., J.L. Hartman IV, G. Giaever and F.P. Roth (2008). Defining genetic interaction. Proceedings of the National Academy of Sciences 105(9): 3461-3466.