Agarwal D, Dange RB, Raizada MK, Francis J. (2013). Angiotensin II causes imbalance between pro- and anti-inflammatory cytokines by modulating GSK-3ß in neuronal culture. British journal of pharmacology. 169 [PubMed]
Ajmone-Cat MA, Nicolini A, Minghetti L. (2003). Prolonged exposure of microglia to lipopolysaccharide modifies the intracellular signaling pathways and selectively promotes prostaglandin E2 synthesis. Journal of neurochemistry. 87 [PubMed]
Amor S, Puentes F, Baker D, van der Valk P. (2010). Inflammation in neurodegenerative diseases. Immunology. 129 [PubMed]
An GC, Faeder JR. (2009). Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning. Mathematical biosciences. 217 [PubMed]
Anastasio TJ. (2015). Temporal-logic analysis of microglial phenotypic conversion with exposure to amyloid-ß. Molecular bioSystems. 11 [PubMed]
Anastasio TJ. (2015). Computational identification of potential multi-drug combinations for reduction of microglial inflammation in Alzheimer disease. Frontiers in pharmacology. 6 [PubMed]
Azhar N et al. (2013). Analysis of serum inflammatory mediators identifies unique dynamic networks associated with death and spontaneous survival in pediatric acute liver failure. PloS one. 8 [PubMed]
Barone FC, Feuerstein GZ. (1999). Inflammatory mediators and stroke: new opportunities for novel therapeutics. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism. 19 [PubMed]
Barzel B, Barabási AL. (2013). Universality in network dynamics. Nature physics. 9 [PubMed]
Becker W, Tarantola S, Zeitz D. (2012). On the Performance of quasi-Monte Carlo and Latin Supercube sampling in global sensitivity analysis Computer Physics Communications. 183
Behar M, Hao N, Dohlman HG, Elston TC. (2007). Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways. Biophysical journal. 93 [PubMed]
Bell MT et al. (2013). Toll-like receptor 4-dependent microglial activation mediates spinal cord ischemia-reperfusion injury. Circulation. 128 [PubMed]
Bezbradica JS, Rosenstein RK, DeMarco RA, Brodsky I, Medzhitov R. (2014). A role for the ITAM signaling module in specifying cytokine-receptor functions. Nature immunology. 15 [PubMed]
Bilbo SD et al. (2005). Neonatal infection-induced memory impairment after lipopolysaccharide in adulthood is prevented via caspase-1 inhibition. The Journal of neuroscience : the official journal of the Society for Neuroscience. 25 [PubMed]
Bogdan C, Nathan C. (1993). Modulation of macrophage function by transforming growth factor beta, interleukin-4, and interleukin-10. Annals of the New York Academy of Sciences. 685 [PubMed]
Bogdan C, Paik J, Vodovotz Y, Nathan C. (1992). Contrasting mechanisms for suppression of macrophage cytokine release by transforming growth factor-beta and interleukin-10. The Journal of biological chemistry. 267 [PubMed]
Butovsky O et al. (2014). Identification of a unique TGF-ß-dependent molecular and functional signature in microglia. Nature neuroscience. 17 [PubMed]
Cai S, Zhou P, Liu Z. (2013). Functional characteristics of a double negative feedback loop mediated by microRNAs. Cognitive neurodynamics. 7 [PubMed]
Caldwell AB, Cheng Z, Vargas JD, Birnbaum HA, Hoffmann A. (2014). Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes & development. 28 [PubMed]
Cambier S et al. (2005). Integrin alpha(v)beta8-mediated activation of transforming growth factor-beta by perivascular astrocytes: an angiogenic control switch. The American journal of pathology. 166 [PubMed]
Caso JR et al. (2007). Toll-like receptor 4 is involved in brain damage and inflammation after experimental stroke. Circulation. 115 [PubMed]
Chao CC et al. (1992). Cytokine release from microglia: differential inhibition by pentoxifylline and dexamethasone. The Journal of infectious diseases. 166 [PubMed]
Chao CC, Hu S, Sheng WS, Peterson PK. (1995). Tumor necrosis factor-alpha production by human fetal microglial cells: regulation by other cytokines. Developmental neuroscience. 17 [PubMed]
Chao CC, Hu S, Sheng WS, Tsang M, Peterson PK. (1995). Tumor necrosis factor-alpha mediates the release of bioactive transforming growth factor-beta in murine microglial cell cultures. Clinical immunology and immunopathology. 77 [PubMed]
Chen CJ et al. (2012). Glutamate released by Japanese encephalitis virus-infected microglia involves TNF-a signaling and contributes to neuronal death. Glia. 60 [PubMed]
Chen Z et al. (2014). Microglial displacement of inhibitory synapses provides neuroprotection in the adult brain. Nature communications. 5 [PubMed]
Cheng CS et al. (2011). The specificity of innate immune responses is enforced by repression of interferon response elements by NF-?B p50. Science signaling. 4 [PubMed]
Cilfone NA, Perry CR, Kirschner DE, Linderman JJ. (2013). Multi-scale modeling predicts a balance of tumor necrosis factor-a and interleukin-10 controls the granuloma environment during Mycobacterium tuberculosis infection. PloS one. 8 [PubMed]
Correnti JM et al. (2015). Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling. The Journal of physiology. 593 [PubMed]
Daun S et al. (2008). An ensemble of models of the acute inflammatory response to bacterial lipopolysaccharide in rats: results from parameter space reduction. Journal of theoretical biology. 253 [PubMed]
David S, Kroner A. (2011). Repertoire of microglial and macrophage responses after spinal cord injury. Nature reviews. Neuroscience. 12 [PubMed]
Dean CB, Nielsen JD. (2007). Generalized linear mixed models: a review and some extensions. Lifetime data analysis. 13 [PubMed]
Dong Y, Benveniste EN. (2001). Immune function of astrocytes. Glia. 36 [PubMed]
Engl HW, Flamm C, Kugler P, Lu J, Muller S, Schuster P. (2009). Inverse problems in systems biology Inverse Problems. 25
Furchtgott LA, Chow CC, Periwal V. (2009). A model of liver regeneration. Biophysical journal. 96 [PubMed]
Greenhalgh AD, David S. (2014). Differences in the phagocytic response of microglia and peripheral macrophages after spinal cord injury and its effects on cell death. The Journal of neuroscience : the official journal of the Society for Neuroscience. 34 [PubMed]
Gregory AP et al. (2012). TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis. Nature. 488 [PubMed]
Gutenkunst RN et al. (2007). Universally sloppy parameter sensitivities in systems biology models. PLoS computational biology. 3 [PubMed]
Hahn J, Dai W, Bansal L, Word D. (2014). Parameter set selection for dynamic systems under uncertainty via dynamic optimization and hierarchical clustering AIChE Journal. 60
Hahn J, Jayaraman A, Maiti S, Dai W, Alaniz R. (2015). S. Maiti, W. Dai, R. Alaniz, J. Hahn, and A. Jayaraman. Mathematical Modeling of Pro- and Anti-Inflammatory Signaling in Macrophages Processes. 3(1)
Hanisch UK. (2002). Microglia as a source and target of cytokines. Glia. 40 [PubMed]
Heneka MT, Kummer MP, Latz E. (2014). Innate immune activation in neurodegenerative disease. Nature reviews. Immunology. 14 [PubMed]
Hickman SE et al. (2013). The microglial sensome revealed by direct RNA sequencing. Nature neuroscience. 16 [PubMed]
Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM. (2004). ModelDB: A Database to Support Computational Neuroscience. Journal of computational neuroscience. 17 [PubMed]
Hoffmann A, Levchenko A, Scott ML, Baltimore D. (2002). The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science (New York, N.Y.). 298 [PubMed]
Hopp SC et al. (2014). Age-associated alterations in the time-dependent profile of pro- and anti-inflammatory proteins within the hippocampus in response to acute exposure to interleukin-1ß. Journal of neuroimmunology. 267 [PubMed]
Hornig M, Weissenböck H, Horscroft N, Lipkin WI. (1999). An infection-based model of neurodevelopmental damage. Proceedings of the National Academy of Sciences of the United States of America. 96 [PubMed]
Janes KA, Lauffenburger DA. (2006). A biological approach to computational models of proteomic networks. Current opinion in chemical biology. 10 [PubMed]
Joyce ME, Roberts AB, Sporn MB, Bolander ME. (1990). Transforming growth factor-beta and the initiation of chondrogenesis and osteogenesis in the rat femur. The Journal of cell biology. 110 [PubMed]
Kettenmann H, Hanisch UK, Noda M, Verkhratsky A. (2011). Physiology of microglia. Physiological reviews. 91 [PubMed]
Kholodenko BN et al. (2002). Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proceedings of the National Academy of Sciences of the United States of America. 99 [PubMed]
Kigerl KA et al. (2007). Toll-like receptor (TLR)-2 and TLR-4 regulate inflammation, gliosis, and myelin sparing after spinal cord injury. Journal of neurochemistry. 102 [PubMed]
Kilic U, Kilic E, Matter CM, Bassetti CL, Hermann DM. (2008). TLR-4 deficiency protects against focal cerebral ischemia and axotomy-induced neurodegeneration. Neurobiology of disease. 31 [PubMed]
Kroner A et al. (2014). TNF and increased intracellular iron alter macrophage polarization to a detrimental M1 phenotype in the injured spinal cord. Neuron. 83 [PubMed]
Le Y et al. (2004). TGF-beta1 disrupts endotoxin signaling in microglial cells through Smad3 and MAPK pathways. Journal of immunology (Baltimore, Md. : 1950). 173 [PubMed]
Liebermeister W, Lehrach H, Klipp EW, Wierling CKowald A, Herwig R. (2011). Systems biology Systems Biology.
Livak KJ, Schmittgen TD. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods (San Diego, Calif.). 25 [PubMed]
Lodge PA, Sriram S. (1996). Regulation of microglial activation by TGF-beta, IL-10, and CSF-1. Journal of leukocyte biology. 60 [PubMed]
Longbrake EE, Lai W, Ankeny DP, Popovich PG. (2007). Characterization and modeling of monocyte-derived macrophages after spinal cord injury. Journal of neurochemistry. 102 [PubMed]
Ma W, Trusina A, El-Samad H, Lim WA, Tang C. (2009). Defining network topologies that can achieve biochemical adaptation. Cell. 138 [PubMed]
Machta BB, Chachra R, Transtrum MK, Sethna JP. (2013). Parameter space compression underlies emergent theories and predictive models. Science (New York, N.Y.). 342 [PubMed]
Marino S et al. (2015). Macrophage polarization drives granuloma outcome during Mycobacterium tuberculosis infection. Infection and immunity. 83 [PubMed]
McCoy MK, Tansey MG. (2008). TNF signaling inhibition in the CNS: implications for normal brain function and neurodegenerative disease. Journal of neuroinflammation. 5 [PubMed]
Meyer-Hermann M, Figge MT, Straub RH. (2009). Mathematical modeling of the circadian rhythm of key neuroendocrine-immune system players in rheumatoid arthritis: a systems biology approach. Arthritis and rheumatism. 60 [PubMed]
Miller GM, Ogunnaike BA, Schwaber JS, Vadigepalli R. (2010). Robust dynamic balance of AP-1 transcription factors in a neuronal gene regulatory network. BMC systems biology. 4 [PubMed]
Minogue AM, Barrett JP, Lynch MA. (2012). LPS-induced release of IL-6 from glia modulates production of IL-1ß in a JAK2-dependent manner. Journal of neuroinflammation. 9 [PubMed]
Mocellin S, Panelli MC, Wang E, Nagorsen D, Marincola FM. (2003). The dual role of IL-10. Trends in immunology. 24 [PubMed]
Morgan TE et al. (2000). Transforming growth factor-beta1 induces transforming growth factor-beta1 and transforming growth factor-beta receptor messenger RNAs and reduces complement C1qB messenger RNA in rat brain microglia. Neuroscience. 101 [PubMed]
Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA. (2011). Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS computational biology. 7 [PubMed]
Moya C, Huang Z, Cheng P, Jayaraman A, Hahn J. (2011). Investigation of IL-6 and IL-10 signalling via mathematical modelling. IET systems biology. 5 [PubMed]
Naiki Y et al. (2005). Transforming growth factor-beta differentially inhibits MyD88-dependent, but not TRAM- and TRIF-dependent, lipopolysaccharide-induced TLR4 signaling. The Journal of biological chemistry. 280 [PubMed]
Neher JJ, Brown GC. (2007). Neurodegeneration in models of Gram-positive bacterial infections of the central nervous system. Biochemical Society transactions. 35 [PubMed]
Nguyen TT, Calvano SE, Lowry SF, Androulakis IP. (2013). An agent-based model of cellular dynamics and circadian variability in human endotoxemia. PloS one. 8 [PubMed]
Nimmerjahn A, Kirchhoff F, Helmchen F. (2005). Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo. Science (New York, N.Y.). 308 [PubMed]
Nørgaard P, Spang-Thomsen M, Poulsen HS. (1996). Expression and autoregulation of transforming growth factor beta receptor mRNA in small-cell lung cancer cell lines. British journal of cancer. 73 [PubMed]
Olson JK, Miller SD. (2004). Microglia initiate central nervous system innate and adaptive immune responses through multiple TLRs. Journal of immunology (Baltimore, Md. : 1950). 173 [PubMed]
Pan H et al. (2010). SMAD4 is required for development of maximal endotoxin tolerance. Journal of immunology (Baltimore, Md. : 1950). 184 [PubMed]
Paolicelli RC et al. (2011). Synaptic pruning by microglia is necessary for normal brain development. Science (New York, N.Y.). 333 [PubMed]
Parakalan R et al. (2012). Transcriptome analysis of amoeboid and ramified microglia isolated from the corpus callosum of rat brain. BMC neuroscience. 13 [PubMed]
Park KM, Bowers WJ. (2010). Tumor necrosis factor-alpha mediated signaling in neuronal homeostasis and dysfunction. Cellular signalling. 22 [PubMed]
Parkhurst CN et al. (2013). Microglia promote learning-dependent synapse formation through brain-derived neurotrophic factor. Cell. 155 [PubMed]
Perry VH, Cunningham C, Holmes C. (2007). Systemic infections and inflammation affect chronic neurodegeneration. Nature reviews. Immunology. 7 [PubMed]
Pickering M, Cumiskey D, O'Connor JJ. (2005). Actions of TNF-alpha on glutamatergic synaptic transmission in the central nervous system. Experimental physiology. 90 [PubMed]
Pribiag H, Stellwagen D. (2013). TNF-a downregulates inhibitory neurotransmission through protein phosphatase 1-dependent trafficking of GABA(A) receptors. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33 [PubMed]
Puri IK, Li L. (2010). Mathematical modeling for the pathogenesis of Alzheimer's disease. PloS one. 5 [PubMed]
Raue A, Karlsson J, Saccomani MP, Jirstrand M, Timmer J. (2014). Comparison of approaches for parameter identifiability analysis of biological systems. Bioinformatics (Oxford, England). 30 [PubMed]
Ray JC, Wang J, Chan J, Kirschner DE. (2008). The timing of TNF and IFN-gamma signaling affects macrophage activation strategies during Mycobacterium tuberculosis infection. Journal of theoretical biology. 252 [PubMed]
Reynolds A et al. (2006). A reduced mathematical model of the acute inflammatory response: I. Derivation of model and analysis of anti-inflammation. Journal of theoretical biology. 242 [PubMed]
Riazi K et al. (2008). Microglial activation and TNFalpha production mediate altered CNS excitability following peripheral inflammation. Proceedings of the National Academy of Sciences of the United States of America. 105 [PubMed]
Rock RB et al. (2004). Role of microglia in central nervous system infections. Clinical microbiology reviews. 17 [PubMed]
Rodriguez-Fernandez M et al. (2013). Modeling the intra- and extracellular cytokine signaling pathway under heat stroke in the liver. PloS one. 8 [PubMed]
Saez-Rodriguez J et al. (2009). Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular systems biology. 5 [PubMed]
Saijo K, Glass CK. (2011). Microglial cell origin and phenotypes in health and disease. Nature reviews. Immunology. 11 [PubMed]
Saltelli A. (). Global Sensitivity Analysis: The Primer.
Savageau MA. (1969). Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. Journal of theoretical biology. 25 [PubMed]
Schafer DP, Lehrman EK, Stevens B. (2013). The "quad-partite" synapse: microglia-synapse interactions in the developing and mature CNS. Glia. 61 [PubMed]
Shao H, He Y, Li KC, Zhou X. (2013). A system mathematical model of a cell-cell communication network in amyotrophic lateral sclerosis. Molecular bioSystems. 9 [PubMed]
Sheng WS, Hu S, Kravitz FH, Peterson PK, Chao CC. (1995). Tumor necrosis factor alpha upregulates human microglial cell production of interleukin-10 in vitro. Clinical and diagnostic laboratory immunology. 2 [PubMed]
Sheppard PW, Sun X, Emery JF, Giffard RG, Khammash M. (2011). Quantitative characterization and analysis of the dynamic NF-?B response in microglia. BMC bioinformatics. 12 [PubMed]
Sheppard PW, Sun X, Khammash M, Giffard RG. (2014). Overexpression of heat shock protein 72 attenuates NF-?B activation using a combination of regulatory mechanisms in microglia. PLoS computational biology. 10 [PubMed]
Stellwagen D, Malenka RC. (2006). Synaptic scaling mediated by glial TNF-alpha. Nature. 440 [PubMed]
Szretter KJ et al. (2009). The immune adaptor molecule SARM modulates tumor necrosis factor alpha production and microglia activation in the brainstem and restricts West Nile Virus pathogenesis. Journal of virology. 83 [PubMed]
Tang SC et al. (2007). Pivotal role for neuronal Toll-like receptors in ischemic brain injury and functional deficits. Proceedings of the National Academy of Sciences of the United States of America. 104 [PubMed]
Tarantola A. (2006). Popper, Bayes and the inverse problem Nature Physics. 2
Tellinghuisen J. (2008). Chapter 23. Stupid Statistics! Methods in Cell Biology. 84
Trapp BD et al. (2007). Evidence for synaptic stripping by cortical microglia. Glia. 55 [PubMed]
Valeyev NV et al. (2010). A systems model for immune cell interactions unravels the mechanism of inflammation in human skin. PLoS computational biology. 6 [PubMed]
Van Obberghen-Schilling E, Roche NS, Flanders KC, Sporn MB, Roberts AB. (1988). Transforming growth factor beta 1 positively regulates its own expression in normal and transformed cells. The Journal of biological chemistry. 263 [PubMed]
Vereyken EJ et al. (2011). Classically and alternatively activated bone marrow derived macrophages differ in cytoskeletal functions and migration towards specific CNS cell types. Journal of neuroinflammation. 8 [PubMed]
Villiger PM, Kusari AB, ten Dijke P, Lotz M. (1993). IL-1 beta and IL-6 selectively induce transforming growth factor-beta isoforms in human articular chondrocytes. Journal of immunology (Baltimore, Md. : 1950). 151 [PubMed]
Vincent VA, Tilders FJ, Van Dam AM. (1998). Production, regulation and role of nitric oxide in glial cells. Mediators of inflammation. 7 [PubMed]
Vitkovic L et al. (2000). Cytokine signals propagate through the brain. Molecular psychiatry. 5 [PubMed]
Vodovotz Y, Bogdan C, Paik J, Xie QW, Nathan C. (1993). Mechanisms of suppression of macrophage nitric oxide release by transforming growth factor beta. The Journal of experimental medicine. 178 [PubMed]
Vodovotz Y et al. (1999). Regulation of transforming growth factor beta1 by nitric oxide. Cancer research. 59 [PubMed]
Wang W, Hu D, Xiong H. (2008). Macrophage attenuation of neuronal excitability: implications for pathogenesis of neurodegenerative disorders. Glia. 56 [PubMed]
Welser-Alves JV, Milner R. (2013). Microglia are the major source of TNF-a and TGF-ß1 in postnatal glial cultures; regulation by cytokines, lipopolysaccharide, and vitronectin. Neurochemistry international. 63 [PubMed]
Werner SL, Barken D, Hoffmann A. (2005). Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science (New York, N.Y.). 309 [PubMed]
Whitney NP, Eidem TM, Peng H, Huang Y, Zheng JC. (2009). Inflammation mediates varying effects in neurogenesis: relevance to the pathogenesis of brain injury and neurodegenerative disorders. Journal of neurochemistry. 108 [PubMed]
Williamson LL, Sholar PW, Mistry RS, Smith SH, Bilbo SD. (2011). Microglia and memory: modulation by early-life infection. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31 [PubMed]
Wu KL, Chan SH, Chan JY. (2012). Neuroinflammation and oxidative stress in rostral ventrolateral medulla contribute to neurogenic hypertension induced by systemic inflammation. Journal of neuroinflammation. 9 [PubMed]
Xue J et al. (2014). Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity. 40 [PubMed]
Yang . (2011). Convergence and uncertainty analyses in Monte-Carlo based sensitivity analysis Environ. Modell. Softw.. 26
Yiu HH, Graham AL, Stengel RF. (2012). Dynamics of a cytokine storm. PloS one. 7 [PubMed]
Zhang Y et al. (2014). An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 34 [PubMed]
Ziraldo C, Mi Q, An G, Vodovotz Y. (2013). Computational Modeling of Inflammation and Wound Healing. Advances in wound care. 2 [PubMed]
Zoppoli P, Morganella S, Ceccarelli M. (2010). TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC bioinformatics. 11 [PubMed]
Zubcevic J, Waki H, Raizada MK, Paton JF. (2011). Autonomic-immune-vascular interaction: an emerging concept for neurogenic hypertension. Hypertension (Dallas, Tex. : 1979). 57 [PubMed]