We are interested in the development of computational tools to facilitate data interpretation and scientific discovery for biologists and clinicians. Researchers now have access to multiple types of genomic-scale data but are left with the daunting challenge of interpreting within and between data sets. This challenge is one shared globally as a number of large-scale projects have been funded to create comprehensive molecular characterizations of processes or diseases of interest, but the data remains largely unexplored for lack of effective analysis approaches. The pervading theme in our work is the integration of heterogeneous data sources, commonly referred to as data fusion, with applications to characterizing genes and their inter-relationships.
Our work also emphasizes graphical network representations of gene interactions and the use of those networks for interpreting and focusing hypothesis generation and validation of datasets contributed by our collaborators. We are especially interested in applications which truly invoke the systems biology mandate of feedback and iteration between data generation and modelling, thereby encouraging strong interplay between researchers with biological/clinical backgrounds and those with a computational background.
Lab Resources and Services
We have access to considerable resources for high-throughput data generation and computational analysis in the Integrated Center for Genes, Environment and Health, including an ABI 3100 capillary sequencer, a Life Technologies Ion Torrent PGM sequencer, and two Life Technologies Ion Proton sequencers. The Center also administers a Dell Linux High Performance Computing cluster with 496 compute cores, accessing 2.4TB of system memory and 300TB of disk storage.
- Sonia Leach, PhD
- Kelsey (K.C.) Anderson, pre-doc Computational Bioscience Program, Univ of CO
- Eitan Halper-Stromberg, PhD (post-doc 2013-2015)
- Job Bacon-Maldonado (summer trainee, 2015)
- Jaime Merlano (rotation student 2011)
O'Connor BP, Danhorn T, De Arras L, Marcus RA, Farias-Hesson E, Leach SM, Alper S. Regulation of Toll-like receptor signaling by the SF3a mRNA splicing complex. PLOS Genetics 2015 Feb 6; 11(2). Abstract
Kim J, Vasu VT, Mishra R, Singleton KR, Yoo M, Leach SM, Farias-Hesson E, Mason RJ, Kang J, Ramamoorthy P, Kern JA, Heasley LE, Finigan JH, Tan AC. Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy. Bioinformatics 2014 Sep 1;30(17):2393-8. Abstract
Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L. Biomedical Discovery Acceleration, with Applications to Craniofacial Development. PLoS Comput Bio, 2009, 5(3):e1000215. Abstract