"A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis" by Janes et al. from the Lauffenburger and Yaffe groups at MIT published in Science December 9, 2005.

This work explores the pathways to cytokine induced apoptosis by perturbing the inputs (in this case TNF, EGF, and insulin) to the well characterized apoptotic pathway. By perturbing the inputs and measuring various outputs they build a predictor of the apoptotic outputs based on partial least squares. They find that this works pretty well and that breaking down the matrices in this using principal component analysis produces a "basis set" of proteins that seems to be most important in predicting apoptotic outputs. Using this approach, they can implicate molecular circuits previously unknown to be involved in this specific signaling network.

Overall it was a good paper, a bit involved, but really showed a good marriage of data mining paired with a (more or less) specific biological question. People would say that this is a systems biology paper, and it is somewhat by its data-driven approach, but I would argue that the cellular modeling that they did was specific to apoptosis and a specific biological question.
If you're interested in cellular modeling, I would highly recommend this paper.