Lin, W. W., and M. Karin. 2007. A cytokine-mediated link between innate immunity, inflammation, and cancer. J. Clin. Invest. 117:1175-1183. (Pubitemid 46718402)
Gnecchi, M., H. M. He,..., V. J. Dzau. 2005. Paracrine action accounts for marked protection of ischemic heart by Akt-modified mesenchymal stem cells. Nat. Med. 11:367-368. (Pubitemid 40562318)
Croci, D. O., M. F. Z. Fluck,..., O. G. Scharovsky. 2007. Dynamic cross-talk between tumor and immune cells in orchestrating the immunosuppressive network at the tumor microenvironment. Cancer Immunol. Immunother. 56:1687-1700. (Pubitemid 47313090)
Seruga, B., H. B. Zhang,..., I. F. Tannock. 2008. Cytokines and their relationship to the symptoms and outcome of cancer. Nat. Rev. Cancer. 8:887-899.
Polyak, K., and R. A. Weinberg. 2009. Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits. Nat. Rev. Cancer. 9:265-273.
Ariztia, E. V., C. J. Lee,..., D. A. Fishman. 2006. The tumor microenvironment: key to early detection. Crit. Rev. Clin. Lab. Sci. 43:393-425. (Pubitemid 44596061)
Sachs, K., O. Perez,..., G. P. Nolan. 2005. Causal protein-signaling networks derived from multiparameter single-cell data. Science. 308:523-529. (Pubitemid 40570578)
Nomura, L., V. C. Maino, and H. T. Maecker. 2008. Standardization and optimization of multiparameter intracellular cytokine staining. Cytometry A. 73 A: 984-991.
Lamoreaux, L., M. Roederer, and R. Koup. 2006. Intracellular cytokine optimization and standard operating procedure. Nat. Protoc. 1:1507-1516.
Cox, J. H., G. Ferrari, and S. Janetzki. 2006. Measurement of cytokine release at the single cell level using the ELISPOT assay. Methods. 38:274-282.
Deforge, L. E., and D. G. Remick. 1991. Kinetics of TNF, IL-1, IL-6, and IL-8 gene expression in LPS-stimulated human whole blood. Biochem. Biophys. Res. Commun. 174:18-24.
Song, M. C., and D. S. Phelps. 2000. Comparison of SP-A and LPS effects on the THP-1 monocytic cell line. Am. J. Physiol. Lung Cell. Mol. Physiol. 279:L110-L117. (Pubitemid 30619530)
Quake, S. R., and A. Scherer. 2000. From micro-to nanofabrication with soft materials. Science. 290:1536-1540.
Shin, Y. S., H. Ahmad,..., J. R. Heath. 2010. Chemistries for patterning robust DNA microbarcodes enable multiplex assays of cytoplasm proteins from single cancer cells. Chemphyschem. 11:3063-3069.
Bailey, R. C., G. A. Kwong,..., J. R. Heath. 2007. DNA-encoded antibody libraries: a unified platform for multiplexed cell sorting and detection of genes and proteins. J. Am. Chem. Soc. 129:1959-1967.
Wacker, R., and C. M. Niemeyer. 2004. DDI-microFIA-a readily configurable microarray-fluorescence immunoassay based on DNA-directed immobilization of proteins. Chembiochem. 5:453-459. (Pubitemid 39257101)
Aderem, A., and R. J. Ulevitch. 2000. Toll-like receptors in the induction of the innate immune response. Nature. 406:782-787.
Fan, J., and A. B. Malik. 2003. Toll-like receptor-4 (TLR4) signaling augments chemokine-induced neutrophil migration by modulating cell surface expression of chemokine receptors. Nat. Med. 9:315-321. (Pubitemid 36362787)
Millet, L. J., M. E. Stewart,..., M. U. Gillette. 2007. Microfluidic devices for culturing primary mammalian neurons at low densities. Lab Chip. 7:987-994. (Pubitemid 47101747)
Altschuler, S. J., and L. F. Wu. 2010. Cellular heterogeneity: do differences make a difference? Cell. 141:559-563.
Wang, J., H. Ahmad,..., J. Heath. 2010. A self-powered, one-step chip for rapid, quantitative and multiplexed detection of proteins from pinpricks of whole blood. Lab Chip. 10:3157-3162.
Findlay, J. W., and R. F. Dillard. 2007. Appropriate calibration curve fitting in ligand binding assays. AAPS J. 9:E260-E267.
Levine, R. D., and M. Tribus, editors. 1979. The Maximum Entropy Formalism. MIT Press, Cambridge, MA.
Nemenman, I. 2005. Fluctuation-dissipation theorem and models of learning. Neural Comput. 17:2006-2033. (Pubitemid 41053632)
Varshavsky, R., A. Gottlieb,..., D. Horn. 2006. Novel unsupervised feature filtering of biological data. Bioinformatics. 22:e507-e513. (Pubitemid 44288322)
Lezon, T. R., J. R. Banavar,..., N. V. Fedoroff. 2006. Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc. Natl. Acad. Sci. USA. 103:19033-19038. (Pubitemid 350002823)
Slonim, N., G. S. Atwal,..., W. Bialek. 2005. Information-based clustering. Proc. Natl. Acad. Sci. USA. 102:18297-18302. (Pubitemid 43011220)
Ziv, E., M. Middendorf, and C. H. Wiggins. 2005. Information-theoretic approach to network modularity. Phys. Rev. E. 71:046117.
Schneidman, E., M. J. Berry,..., W. Bialek. 2006. Weak pairwise correlations imply strongly correlated network states in a neural population. Nature. 440:1007-1012.
Mora, T., A. M. Walczak,..., C. G. Callan. 2010. Maximum entropy models for antibody diversity. Proc. Natl. Acad. Sci. USA. 107:5405-5410.
Remacle, F., N. Kravchenko-Balasha,..., R. D. Levine. 2010. Information-theoretic analysis of phenotype changes in early stages of carcinogenesis. Proc. Natl. Acad. Sci. USA. 107:10324-10329.
Margolin, A. A., K. Wang,..., I. Nemenman. 2010. Multivariate dependence and genetic networks inference. IET Syst. Biol. 4:428-440.
Graeber, T. G., J. R. Heath,..., R. D. Levine. 2010. Maximal entropy inference of oncogenicity from phosphorylation signaling. Proc. Natl. Acad. Sci. USA. 107:6112-6117.
Levine, R. D., and R. B. Bernstein. 1974. Energy disposal and energy consumption in elementary chemical-reactions - information theoretic approach. Acc. Chem. Res. 7:393-400.
Levine, R. D. 1985. Statistical dynamics. In Theory of Reactive Collisions. M. Baer, editor. CRC, Boca Raton, FL.
Levine, R. D. 2005. Molecular Reaction Dynamics. The University Press, Cambridge, UK.
Callen, H. B. 1985. Thermodynamics and an Introduction to Thermostatics. Wiley, New York.
Alter, O., P. O. Brown, and D. Botstein. 2000. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. USA. 97:10101-10106.
Yeung, M. K. S. J., J. J. Tegner, and Collins. 2002. Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl. Acad. Sci. USA. 99:6163-6168. (Pubitemid 34493283)
Alter, O. 2007. Genomic signal processing: from matrix algebra to genetic networks. In Microarray Data Analysis: Methods and Applications. M. J. Korenberg, editor. Humana Press, Totowa, NJ. 17-59. (Pubitemid 350183364)
Janes, K. A., J. G. Albeck,..., M. B. Yaffe. 2005. A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science. 310:1646-1653. (Pubitemid 41780781)
Janes, K. A., S. Gaudet,..., P. K. Sorger. 2006. The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell. 124:1225-1239.
Detwiler, P. B., S. Ramanathan,..., B. I. Shraiman. 2000. Engineering aspects of enzymatic signal transduction: photoreceptors in the retina. Biophys. J. 79:2801-2817.
Tabach, Y., M. Milyavsky, I. Shats, R. Brosh, O. Zuk, A. Yitzhaky, R. Mantovani, E. Domany, V. Rotter, and Y. Pilpel. 2005. The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol. Syst. Biol. 1, 2005 0022.
Alon, U. 2006. An Introduction to Systems Biology. Chapman & Hall, London.
Shmulevich, I., and J. D. Aitchison. 2009. Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol. 467:335-356.
Koller, D., and N. Friedman. 2009. Probabilistic Graphical Models: Principles and Techniques. MIT Press, Cambridge, MA.
Pe'er, D. 2005. Bayesian network analysis of signaling networks: a primer. Sci. STKE. 281:14.
Reference deleted in proof.
Levine, R. D. 1978. Information theory approach to molecular reaction dynamics. Annu. Rev. Phys. Chem. 29:59-92.
Levine, R. D. 1980. Information theoretical approach to inversion problems. J. Physics A. 13:91-108.
Remacle, F., and R. D. Levine. 2009. The elimination of redundant constraints in surprisal analysis of unimolecular dissociation and other endothermic processes. J. Phys. Chem. A. 113:4658-4664.
Jaynes, E. T. 2004. Probability Theory: The Logic of Science. Cambridge University Press, Cambridge, UK.
Mayer, J. E., and M. G. Mayer. 1966. Statistical Mechanics. Wiley, New York.
Lotka, A. J. 1921. Noteon moving equilibra. Proc. Natl. Acad. Sci. USA. 7:168-172.
Bellman, R. 1970. Introduction to Matrix Analysis. McGraw-Hill, New York.
Wall, M. E., A. Rechtsteiner, and L. M. Rochas. 2003. Singular value decomposition and principal component analysis. In A Practical Approach to Microarray Data Analysis. D. P. Berrar, W. Dubitzky, and M. Granzow, editors. Kluwer, Norwell, MA. 91-109.
Jolliffe, I. T. 2002. Principal Component Analysis. Springer, New York.
Roger, T., J. David,..., T. Calandra. 2001. MIF regulates innate immune responses through modulation of Toll-like receptor 4. Nature. 414:920-924. (Pubitemid 34024744)
Calandra, T., J. Bernhagen,..., R. Bucala. 1994. Macrophage is an important and previously unrecognized source of macrophage-migration inhibitory factor. J. Exp. Med. 179:1895-1902. (Pubitemid 24155670)
Janeway, C., K. P. Murphy,..., M. Walport. 2008. Janeway's Immunobiology. Garland Science, New York.
