Refer to Web version on PubMed Central for supplementary material. (a) At any given point in the project, every pair of proteins is assigned an interaction probability based on its experimental history (initially these probabilities are set to background or informed by predictions). The interaction probabilities and experimental history are used to design a 96-well plate Y2H experiment according to one of the strategies. The result of this experiment is simulated based on the detectability of the tested interactions (given the assay type) and the pooling sensitivity. The new experimental results are recorded in the history and also (b) used to update the interaction probabilities of the relevant protein pairs. The pyramid represents the ordered list of protein pairs ranked by probability. It is wider at the bottom than at the top to reflect that most pairs are negative-i.e., most pairs will have low probability and only a few pairs will percolate to the top of the list with high probability. Interactions with probability above an upper threshold are added to the mapped interactome, which is compared to the simulated "True Network" at intervals of 1,000 plates for reporting coverage and FDR. The false discovery rate (FDR) of interactions that are observed exactly once (orange), twice (purple), thrice (green), four times (yellow), and five times (cyan) as a function of the number of times they are tested with independent assays. To achieve FDR < 5% interactions should be observed at least twice when tested with < 5 independent assays, and at least three times when tested with 5-17 assays. (c) The effective coverage level at FDR < 5% is shown (red curve) by embedding the observation threshold from (b) into the curves of (a). While saturation is achieved after 8 screens, 21 screens are required for 95% coverage at FDR < 5%. * Interaction costs are given in units of total number of plates (K = Thousands, M = Millions) required for 50% or 95% coverage. When 95% coverage is achieved more than once, the greatest cost is presented. Augmented Lung Inflammation Protects against Influenza A Pneumonia BACKGROUND: Influenza pneumonia causes high mortality every year, and pandemic episodes kill millions of people. Influenza-related mortality has been variously ascribed to an ineffective host response that fails to limit viral replication, an excessive host inflammatory response that results in lung injury and impairment of gas exchange, or to bacterial superinfection. We sought to determine whether lung inflammation promoted or impaired host survival in influenza pneumonia. METHODS AND FINDINGS: To distinguish among these possible causes of influenza-related death, we induced robust lung inflammation by exposing mice to an aerosolized bacterial lysate prior to challenge with live virus. The treatment induced expression of the inflammatory cytokines IL-6 and TNF in bronchoalveolar lavage fluid 8- and 40-fold greater, respectively, than that caused by lethal influenza infection. Yet, this augmented inflammation was associated with striking resistance to host mortality (0% vs 90% survival, p = 0.0001) and reduced viral titers (p = 0.004). Bacterial superinfection of virus infected lungs was not observed. When mice were repeatedly exposed to the bacterial lysate, as would be clinically desirable during an influenza epidemic, there was no tachyphylaxis of the induced viral resistance. When the bacterial lysate was administered after the viral challenge, there was still some mortality benefit, and when ribavirin was added to the aerosolized bacterial lysate, host survival was synergistically improved (0% vs 93.3% survival, p<0.0001). CONCLUSIONS: Together, these data indicate that innate immune resistance to influenza can be effectively stimulated, and suggest that ineffective rather than excessive inflammation is the major cause of mortality in influenza pneumonia. The annual worldwide mortality associated with pneumonia exceeds that of any other infection [1, 2, 3] . In particular, influenza pneumonia annually causes more than 40,000 deaths in the United States alone [4, 5] . Beyond the impact of seasonal influenza, episodes of pandemic influenza have accounted for as many as 50 million deaths [6] . H5N1 avian influenza has already caused more than 240 human deaths worldwide (http://www. who.int/csr/disease/avian_influenza/), and increased globalization since 1918 suggests that eventual human-to-human transmission of avian influenza may cause even greater lethality than the infamous ''Spanish flu'' [7] . Further, viral pathogens, including influenza, are considered potential agents of bioterror [8] .