The Tenth q-bio Summer School - New Mexico: Viral Dynamics

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About the Viral Dynamics focus area

Lead organizer: Ruy Ribeiro

Faculty

• Youfang Cao, Los Alamos National Laboratory, NM
• Fabian Cardozo, Los Alamos National Laboratory, NM
• Mario Castro, Comillas Pontifical University, Madrid, Spain
• Jeremie Guedj, INSERM, Paris, France
• Ruian Ke, North Carolina State University, Raleigh, NC
• Alan S. Perelson, Los Alamos National Laboratory, NM
• Ruy M. Ribeiro, Los Alamos National Laboratory, NM
• Anton Zilman, University of Toronto, Canada

Topics

This series of lectures focus on viral and immune systems dynamics at the cellular population level, that is the modeling of interactions of immune cells and viruses within an individual. There will be a basic introduction to the biology of these systems, followed by lectures on modeling specific issues/processes/immune systems. We will cover both modeling of the healthy immune system, and viral infections such as human immunodeficiency (HIV), hepatitis (B and C), and influenza. Attention will also be given to the evolutionary processes shaping these viruses in vivo, including the topic of phylogenetics. The approach to all these subjects will include discussions of the mathematical framework, the types of available data and how to link models and data to generate new hypotheses, estimate parameters and gain the most biological insight from restricted data sets.

Group projects will include small simulations projects, introduction to data fitting from recent publications and there will be the possibility for research-type projects if enough student interest is manifested.

Projects

This is a tentative list of topics for projects, which will be updated with time and adapted to student interests.

Influenza Replication

Details of this project can be found here: Media:Influenza-replication.pdf‎

Reactivation from HIV Latency

Details of this project can be found here: Media:HIV-latency.pdf‎

Software

Please install the following software to prepare for scheduled computer labs:

• R
• R Studio
• TinkerCell

Recommended Reading

• Ribeiro RM, et al. (2012) Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate. PLoS Pathog 8(8): e1002881. doi:10.1371/journal.ppat.1002881

• Chatterjee A, et al. (2013) Hepatitis C viral kinetics: the past, present, and future. Clin Liver Dis 17(1):13-26.PMC Article

• Perelson AS and Ribeiro RM (2013) Modeling the within-host dynamics of HIV infection. BMC Biology 11: 96 doi:10.1186/1741-7007-11-96

• Rong L and Perelson AS (2009) Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy. PLoS Comp Biol 5: e1000533. doi:10.1371/journal.pcbi.1000533