PCSC 2008: Dr. Eduardo Mendoza

PCSC 2008
8th Philippine Computing Science Congress
23 - 24 February 2008
University of the Philippines-Diliman, Quezon City, Philippines
Organized by: Computing Society of the Philippines (CSP)
Tel. +63 2 7090907, +63 2 4266125
E-mail: computingsoc@gmail.com
Website: http://www.csp.org.ph/
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"Systems Biology of Viral Infection"

by

Eduardo R. Mendoza, Ph.D.

Abstract:

Traditionally, drugs have targeted virally encoded enzymes that are essential for viral replication. But with the propensity of viruses to develop drug resistance on one hand and the increasing availability of data on virus-host cell interactions on the other, the alternative strategy of host-oriented anti-viral treatment is gaining ground-some authors call this a “paradigm shift” already [1]. The basis of this alternative approach is the emerging field of “systems virology”, which combines both computational and innovative (often high-throughput) experimental techniques to gain an understanding of the dynamics of the infection process in terms of its molecular components and cellular subsystems involved. The talk will discuss some important trends in this field as well as potential applications. It will also introduce some recent projects where Filipino researchers (primarily from UP Diliman) are working with some of the pioneers in the field, including:

• the collaboration on modeling herpesvirus dynamics between J. Haas Lab (LMU/U Edinburgh), U. Reichl (MPI Magdeburg) and J. Bantang (NIP, UP Diliman) [2], [3]

• the establishment of an information system Vir.Lex. (read “Virholex “, short for Virus-host interaction Lexicon) within the MBaRC (Manila Bay Research Corridor) initiative of DLSU-Manila, UP Manila and Mapua. This system can also store information on planned collaborations between various Philippine institutions on dengue virus infections.

• the investigation of “artificial viruses” (which are essentially synthetic delivery systems for DNA or siRNA) by the Rädler Lab (Physics, LMU) [4]

• the implementation of a new modeling tool “brane caculus” as a collaboration between UP Dept of Computer Science (P. David) and Microsoft Research (Cambridge, UK) [5], [6] and its application to stochastically model influenza A virus dynamics in MDCK cells


References:

[1] Tan, S-L., Ganji, G., Paeper, B., Proll, S. and Katze, M.G. (2007) Systems biology and the host response to viral infection, Nature Biotechnology 25, No. 12, 1383-1389
[2] Uetz, P., Dong, Y., Zeretzke, C., Atzler, C., Baiker, A., Berger, B., Rajagopala, S., Roupelieva, M., Rose, D., Fossum, E., and Haas, J. (2006). Herpesviral protein networks and their interaction with the human proteome. Science 311, 239.
[3] Sidorenko, Y., and Reichl, U. (2004). Structured model of influenza virus replication in MDCK cells. Biotechnol Bioeng 88, 1-14.
[4] Schwake, G., David, M.P., Youssef, S., Kuhr, J-T., Kemper, S., Mendoza, E., Frey, E. and Rädler, J.O. Stochasticity in Artificial Gene Delivery (to be submitted to PNAS)
[5] David, M.P. Design and implementation of BCD-a stochastic brane machine, MS Computer Science thesis (March 2008)
[6] David, M.P., Phillips, A., Mendoza, E. and Cardelli, L: Implementing brane calculus (paper accepted at ICMSB 2008)