PBSoft took part in the Third SysPatho annual Workshop that was held in Cyprus, 2013. Nikita Ivanisenko presented the work «A Mathematical Model of Subgenomic Hepatitis C Virus Replication in Huh-7 Cells» done at ICG SB RAS in the context of SysPatho in collaboration with PBSoft, St. Petersburg State Polytechnical University and TU Dresden.
The group has developed a stochastic model of a subgenomic HCV replicon replication, in which the existence of the drug resistant mutant viral RNAs in replicon cells is taken into account. Nikita showed results simulations on long term dynamics of the viral RNA suppression for various inhibitor concentrations, indicating that the observable difference between the viral RNA kinetics for different inhibitor concentrations can be explained by the differences in the replication rate and inhibitor sensitivity of the mutant RNAs. Future work in SysPatho in the field of HCV mathematical modeling will focus on (1) simulation of NS5A and NS5B inhibitors action; (2) incorporation of intravesicular processes and interferon response; (3) HCV model on organism level with incorporation of intracellular processes. The work will be done in collaborations with PBSoft, TU Dresden, SPBSPU, UHEI and Bartenschlager group (UKL-HD).
Dr. Vladimir Ivanisenko presented the work «Hepatitis C associome» done at PBSoft in the context of SysPatho task «Text mining for interactions in HCV-host molecular-genetic systems».
The group has developed the relational database containing integrated literature network with Y2H data describing virus-host interactions called as Human-HCV Associome Database. The Human-HCV Associome Database containing virus-host, host-host and virus-virus molecular-genetic interactions. It was shown that proteins associated with HCV are more connected to each other than random proteins, indicating that HCV proteins regulate host biological pathways. The pathways in which host proteins associated with HCV are involved localized mostly in single GO cell components. Future work in SysPatho will focus on an evaluation of the completeness, comprehensiveness and statistical features of literature networks. The work will be done in collaborations with ICG, TU Dresden, SPBSPU, UHEI and UKL-HD.
