Department of Computer Science
Office: PGH 230
Contact: email@example.com - (713) 743-8553
Education: Ph.D., Kuibyshev (Samara) State University, USSR
Bioinformatics. Computer Science. Applied statistics. Mathematical modeling. Information theory.
Yuriy Fofanov received his M.S. in Physics in 1977 and his Ph.D. in Physics and Mathematics in 1988 from Kuibyshev (Samara) State University, USSR. Since joining the Computer Science Department at the University of Houston, he has been the director of the departments Bioinformatics Lab and an adjunct assistant professor both in the Department of Biology and Biochemistry at UH and in the Department of Health Informatics at the School of Health Information Science at the University of Texas. In 2002 Fofanov also became a faculty member for the W.M. Keck Center for Computational and Structural Biology.
The focus of the Bioinformatics Lab is two-fold: gene expression and genomic sequence analysis, each of which has many on-going projects. The gene expression projects consist of approaches in micro-array data normalization, using local invariants for genetic regulatory networks reconstruction, and a mutual information approach to identify nonlinear patterns in gene expressions. Genomic sequence analysis projects include studies of the statistical properties of short subsequences in microbial and viral genomes and the design of ultra-specific host/background blind probes and primers for microbial and viral identification. The latter project was recently awarded funding through the Department of Homeland Securitys Advanced Research Projects Agency, Science and Technology Directorate. The successes of the laboratory are made possible due to our many collaborations with faculty members at UH in the Biology and Biochemistry, Chemical Engineering, and Chemistry Departments as well as collaborations with the University of Texas Medical Branch in Galveston, the University of Texas at Houston, the University of Arizona, the University of Guadalajara, Mexico, and Genomics USA in Houston, Texas.
- Reed C, Fofanov V, Putonti C, Chumakov S, Slezak T, Fofanov Y. (2007). Effect of the mutation rate and background size on the quality of pathogen identification. Bioinformatics, 23(20):2665-71.
- Putonti C, Luo Y, Katili C, Chumakov S, Fox GE, Graur D, Fofanov Y. (2006). A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Molecular Biology and Evolution, 23(10):1863-8.
- Fofanov, Y., Luo, Y., Katili, C., Wang, J., Belostudsev, Y., Powdrill, T., Belapurkar, C., Fofanov, V., Li, T-B, Chumakov, S., and Pettitt, B.M. (2004) How independent are appearances of n-mers in different genomes? Bioinformatics 20:2421-2428.
- Webb, M.S., Miller, A.L., Johnson, B.H., Fofanov, Y., Li, T-B., Wood, T.G., Thompson, E.B. (2003) Gene networks in glucocorticoid-evoked apoptosis of leukemic cells. The Journal of Steroid Biochemistry and Molecular Biology 85:183-193.
- Medh R.D., Webb, M.S., Miller, A.L., Johnson, B.H., Fofanov, Y., Li, T, Wood, T.G., Luxon, B.A., Thompson, E.B. (2003) Gene expression profile of human lymphoid CEM cells sensitive and resistant to glucocorticoid-evoked apoptosis. Genomics 81: 543-55.
- Vainrub, A., Li, T-B., Fofanov, Y., Pettitt, B.M. (2003) Theoretical considerations for the efficient design of DNA arrays. In: Moore, J. Zouridakis, G. (eds) Biomedical Technology and Device Handbook. CRC Press.
- Fofanov, Y., Pettitt, B.M. (2002) Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: Local Invariants approach. Journal of Biomedical Informatics 35: 343-351.