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The dynamics of acute malaria infections. I. Effect of the parasite's red blood cell preference
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Antia, R.1
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Sparse production but preferential incorporation of recently produced naive T cells in the human peripheral pool
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Vrisekoop N., den Braber I., de Boer A.B., Ruiter A.F., Ackermans M.T., van der Crabben S.N., Schrijver E.H., Spierenburg G., Sauerwein H.P., Hazenberg M.D., et al. Sparse production but preferential incorporation of recently produced naive T cells in the human peripheral pool. Proc Natl Acad Sci USA 105 (2008) 6115-6120
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Estimation of the rate of killing by cytotoxic T lymphocytes in vivo
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Regoes R.R., Barber D.L., Ahmed R., and Antia R. Estimation of the rate of killing by cytotoxic T lymphocytes in vivo. Proc Natl Acad Sci USA 104 (2007) 1599-1603
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Regoes, R.R.1
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Dynamic pathway modeling of signal transduction networks: a domain-oriented approach
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Conzelmann H., and Gilles E.D. Dynamic pathway modeling of signal transduction networks: a domain-oriented approach. Methods Mol Biol 484 (2008) 559-578
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Conzelmann, H.1
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Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks
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Christensen C., Thakar J., and Albert R. Systems-level insights into cellular regulation: inferring, analysing, and modelling intracellular networks. IET Syst Biol 1 (2007) 61-77
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Christensen, C.1
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8
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Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction
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Franke R., Muller M., Wundrack N., Gilles E.D., Klamt S., Kahne T., and Naumann M. Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Syst Biol 2 (2008) 4
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Franke, R.1
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Naumann, M.7
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Modeling systems-level regulation of host immune responses
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Thakar J., Pilione M., Kirimanjeswara G., Harvill E.T., and Albert R. Modeling systems-level regulation of host immune responses. PLoS Comput Biol 3 (2007) e109
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Thakar, J.1
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10
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Constraint based network model of pathogen-immune system interactions
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This article demonstrates the success of hybrid Boolean modeling at the inter-cellular level.
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Thakar J., Saadatpour A., Harvill E.T., and Albert R. Constraint based network model of pathogen-immune system interactions. J R Soc Interface 6 (2009) 599-612. This article demonstrates the success of hybrid Boolean modeling at the inter-cellular level.
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Thakar, J.1
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Harvill, E.T.3
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55849100058
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Network model of survival signaling in large granular lymphocyte leukemia
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The Boolean model developed in this article predicts the minimal cause and several therapeutic targets for of T-LGL leukemia.
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Zhang R., Shah M.V., Yang J., Nyland S.B., Liu X., Yun J.K., Albert R., and Loughran Jr. T.P. Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci USA 105 (2008) 16308-16313. The Boolean model developed in this article predicts the minimal cause and several therapeutic targets for of T-LGL leukemia.
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Proc Natl Acad Sci USA
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Zhang, R.1
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Nyland, S.B.4
Liu, X.5
Yun, J.K.6
Albert, R.7
Loughran Jr., T.P.8
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12
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Pathway databases and tools for their exploitation: benefits, current limitations and challenges
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Bauer-Mehren A., Furlong L.I., and Sanz F. Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol 5 (2009) 290
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Robustness and fragility of Boolean models for genetic regulatory networks
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Chaves M., Albert R., and Sontag E.D. Robustness and fragility of Boolean models for genetic regulatory networks. J Theor Biol 235 (2005) 431-449
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Chaves, M.1
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Sontag, E.D.3
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A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles
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Espinosa-Soto C., Padilla-Longoria P., and Alvarez-Buylla E.R. A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. Plant Cell 16 (2004) 2923-2939
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Espinosa-Soto, C.1
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A logical analysis of the Drosophila gap-gene system
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Sanchez L., and Thieffry D. A logical analysis of the Drosophila gap-gene system. J Theor Biol 211 (2001) 115-141
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Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module
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Sanchez L., and Thieffry D. Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. J Theor Biol 224 (2003) 517-537
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Zadeh H. Fuzzy logic=computing with words. IEEE Trans Fuzzy Syst 4 (1996) 103-111
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Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks
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Huang S., and Ingber D.E. Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Exp Cell Res 261 (2000) 91-103
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Shmulevich I., Kauffman S.A., and Aldana M. Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc Natl Acad Sci USA 102 (2005) 13439-13444
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Topology of biological networks and reliability of information processing
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Klemm K., and Bornholdt S. Topology of biological networks and reliability of information processing. Proc Natl Acad Sci USA 102 (2005) 18414-18419
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The crosstalk between EGF, IGF, and insulin cell signaling pathways-computational and experimental analysis
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Zielinski R., Przytycki P.F., Zheng J., Zhang D., Przytycka T.M., and Capala J. The crosstalk between EGF, IGF, and insulin cell signaling pathways-computational and experimental analysis. BMC Syst Biol 3 (2009) 88
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Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling
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This article applies a fuzzy logic framework and uncovers novel signaling crosstalk and regulation.
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Aldridge B.B., Saez-Rodriguez J., Muhlich J.L., Sorger P.K., and Lauffenburger D.A. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol 5 (2009) e1000340. This article applies a fuzzy logic framework and uncovers novel signaling crosstalk and regulation.
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Aldridge, B.B.1
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62549162241
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Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance
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Sahin O., Frohlich H., Lobke C., Korf U., Burmester S., Majety M., Mattern J., Schupp I., Chaouiya C., Thieffry D., et al. Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst Biol 3 (2009) 1
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Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
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This paper develops an interpolation based hybrid Boolean model and applies is to T cell receptor signaling.
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Wittmann D.M., Krumsiek J., Saez-Rodriguez J., Lauffenburger D.A., Klamt S., and Theis F.J. Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst Biol 3 (2009) 98. This paper develops an interpolation based hybrid Boolean model and applies is to T cell receptor signaling.
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Wittmann, D.M.1
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27
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Boolean network simulations for life scientists
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Albert I., Thakar J., Li S., Zhang R., and Albert R. Boolean network simulations for life scientists. Source Code Biol Med 3 (2008) 16. This article describes an easy to use software for Boolean modeling.
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Source Code Biol Med
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Albert, I.1
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