Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling. - Smita Agrawal; Colin Archer; David V. Schaffer (PLoS Comput. Biol., 2009)

Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles. - Sharon Aviran; Priya S. Shah; David V. Schaffer; Adam P. Arkin (PLoS Comput. Biol., 2010)

HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency. - Ron Skupsky; John C. Burnett; Jonathan E. Foley; David V. Schaffer; Adam P. Arkin (PLoS Comput. Biol., 2010)

Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression. - Kathryn Miller-Jensen; Ron Skupsky; Priya S. Shah; Adam P. Arkin; David V. Schaffer (PLoS Comput. Biol., 2013)