cal trials using agent-based modeling. Crit Care Med 32: 20502060. 33. An G Agent-based computer simulation and sirs: building a bridge between basic science and clinical trials. Shock 16: 266273. 34. An G A model of TLR4 signaling and tolerance using a qualitative, particle-event-based method: introduction of spatially configured stochastic reaction chambers. Math Biosci 217: 4352. 35. An GC, Faeder JR Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Math Biosci 217: 5363. 36. Folcik VA, An GC, Orosz CG The Basic Immune Simulator: an agentbased model to study the interactions between innate and adaptive immunity. Theor Biol Med Model 4: 39. 37. Baldazzi V, Castiglione F, Bernaschi M An enhanced agent based model of the immune system response. Cell Immunol 244: 7779. 38. Celada F, Seiden PE A computer model of cellular interactions in the immune system. Immunol Today 13: 5662. 39. Meier-Schellersheim M, Xu X, Angermann B, Kunkel EJ, Jin T, et al. Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PLoS Comput Biol 2: e82. 40. Warrender C, Forrest S, Koster F Modeling intercellular interactions in early Mycobacterium infection. Bull Math Biol 68: 22332261. 41. Kaern M, Elston TC, Blake WJ, Collins JJ Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451464. 42. Kilfoil ML, Lasko P, Abouheif E Stochastic variation: from single cells to superorganisms. Hfsp J 3: 379385. 43. Niepel M, Spencer SL, Sorger PK Non-genetic cell-to-cell variability and the consequences for pharmacology. Curr Opin Chem Biol 25279926 13: 556561. 44. Raser JM, O’Shea EK Noise in gene expression: origins, consequences, and control. Science 309: 20102013. 45. Mager DE, Wyska E, Jusko WJ Diversity of mechanism-based pharmacodynamic models. Drug Metab Dispos 31: 510518. 46. Nguyen TT, Nowakowski RS, Androulakis IP Unsupervised selection of highly coexpressed and noncoexpressed genes using a consensus clustering approach. Omics 13: 219237. 47. Prabhakar U, Conway TM, 
Murdock P, Mooney JL, Clark S, et al. Correlation of protein and gene expression profiles of inflammatory proteins after endotoxin challenge in human subjects. DNA Cell Biol 24: 410431. 48. Li Q, Verma IM NF-kappaB regulation in the immune system. Nat Rev Immunol 2: 725734. 49. Vallabhapurapu S, Karin M Regulation and function of NF-kappaB transcription factors in the immune system. Annu Rev Immunol 27: 693733. 50. NVP BGJ398 site Ihekwaba AE, Broomhead DS, Grimley 25395428 RL, Benson N, Kell DB Sensitivity analysis of parameters controlling oscillatory signalling in the NFkappaB pathway: the roles of IKK and IkappaBalpha. Syst Biol 1: 93103. 51. Natarajan M, Lin KM, Hsueh RC, Sternweis PC, Ranganathan R A global analysis of cross-talk in a mammalian cellular signalling network. Nat Cell Biol 8: 571580. 52. Hu X, Chen J, Wang L, Ivashkiv LB Crosstalk among Jak-STAT, Tolllike receptor, and ITAM-dependent pathways in macrophage activation. J Leukoc Biol 82: 237243. 53. Akira S, Takeda K Toll-like receptor signalling. Nat Rev Immunol 4: 499511. 54. O’Neill LA When signaling pathways collide: positive and negative regulation of toll-like receptor signal transduction. Immunity 29: 1220. 55. Croker BA, Kiu H, Nicholson SE SOCS regulation of the JAK/STAT signalling pathway. Semin Cell Dev Biol 19: 414422. 56. Shuai K, Liu B Regulation of JAK-STAT signalling in the immune system. Nat Rev Immunol 3