Modeling formalisms in Systems Biology
暂无分享,去创建一个
Miguel Rocha | Isabel Rocha | Rafael S. Costa | Bruce Tidor | Daniel Machado | Rafael S Costa | Eugénio C Ferreira | B. Tidor | D. Machado | E. Ferreira | I. Rocha | Miguel Rocha | R. Costa
[1] Jeremy S. Edwards,et al. Coupled Stochastic Spatial and Non-Spatial Simulations of ErbB1 Signaling Pathways Demonstrate the Importance of Spatial Organization in Signal Transduction , 2009, PloS one.
[2] G. Church,et al. Analysis of optimality in natural and perturbed metabolic networks , 2002 .
[3] William S. Hlavacek,et al. Simulation of large-scale rule-based models , 2009, Bioinform..
[4] R. Albert,et al. Discrete dynamic modeling of cellular signaling networks. , 2009, Methods in enzymology.
[5] T. Jaakkola,et al. Bayesian Network Approach to Cell Signaling Pathway Modeling , 2002, Science's STKE.
[6] Luca Cardelli,et al. Brane Calculi , 2004, CMSB.
[7] Monika Heiner,et al. Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber , 2005, Bioinform..
[8] G. T. Tsao,et al. A cybernetic view of microbial growth: Modeling of cells as optimal strategists , 1985, Biotechnology and bioengineering.
[9] Onami,et al. Bio-calculus: Its Concept and Molecular Interaction. , 1999, Genome informatics. Workshop on Genome Informatics.
[10] Glen E. P. Ropella,et al. Essential operating principles for tumor spheroid growth , 2008, BMC Systems Biology.
[11] Satoru Miyano,et al. Inferring gene networks from time series microarray data using dynamic Bayesian networks , 2003, Briefings Bioinform..
[12] Eugénio C. Ferreira,et al. Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations , 2010, Biosyst..
[13] J. Vohradský. Neural network model of gene expression , 2001, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[14] A. Hasman,et al. Probabilistic reasoning in intelligent systems: Networks of plausible inference , 1991 .
[15] Peter K. Sorger,et al. Logic-Based Models for the Analysis of Cell Signaling Networks† , 2010, Biochemistry.
[16] H. Kitano. Systems Biology: A Brief Overview , 2002, Science.
[17] Hitoshi Iba,et al. Inference of differential equation models by genetic programming , 2002, Inf. Sci..
[18] J. Heijnen. Approximative kinetic formats used in metabolic network modeling , 2005, Biotechnology and bioengineering.
[19] Jörg R. Weimar. Cellular Automata Approaches to Enzymatic Reaction Networks , 2002, ACRI.
[20] Erwin P. Gianchandani,et al. Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks , 2008, PLoS Comput. Biol..
[21] D. Broomhead,et al. Something from nothing − bridging the gap between constraint‐based and kinetic modelling , 2007, The FEBS journal.
[22] G. T. Tsao,et al. Cybernetic modeling of microbial growth on multiple substrates , 1984, Biotechnology and bioengineering.
[23] T. Deisboeck,et al. Development of a three-dimensional multiscale agent-based tumor model: simulating gene-protein interaction profiles, cell phenotypes and multicellular patterns in brain cancer. , 2006, Journal of theoretical biology.
[24] Eberhard O. Voit,et al. Hybrid Modeling in Biochemical Systems Theory by Means of Functional Petri Nets , 2009, J. Bioinform. Comput. Biol..
[25] Alvis Brazma,et al. Current approaches to gene regulatory network modelling , 2007, BMC Bioinformatics.
[26] S. Brahmachari,et al. Boolean network analysis of a neurotransmitter signaling pathway. , 2007, Journal of theoretical biology.
[27] Jason A. Papin,et al. Genome-scale microbial in silico models: the constraints-based approach. , 2003, Trends in biotechnology.
[28] H. D. Jong,et al. Qualitative simulation of genetic regulatory networks using piecewise-linear models , 2004, Bulletin of mathematical biology.
[29] Katherine C. Chen,et al. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. , 2003, Current opinion in cell biology.
[30] Kim G. Larsen,et al. On Modal Refinement and Consistency , 2007, CONCUR.
[31] C. Chassagnole,et al. Dynamic modeling of the central carbon metabolism of Escherichia coli. , 2002, Biotechnology and bioengineering.
[32] W. Wiechert. 13C metabolic flux analysis. , 2001, Metabolic engineering.
[33] Bernhard O. Palsson,et al. Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems , 2006, PLoS Comput. Biol..
[34] Steffen Klamt,et al. A Logical Model Provides Insights into T Cell Receptor Signaling , 2007, PLoS Comput. Biol..
[35] A. Burgard,et al. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization , 2003, Biotechnology and bioengineering.
[36] Jose L. Segovia-Juarez,et al. Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model. , 2004, Journal of theoretical biology.
[37] Satoru Miyano,et al. Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model , 1998, Pacific Symposium on Biocomputing.
[38] T. Henzinger,et al. Executable cell biology , 2007, Nature Biotechnology.
[39] D. Fell,et al. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.
[40] Mathias John,et al. A Spatial Extension to the π Calculus , 2007 .
[41] D. Kaiser,et al. A three-dimensional model of myxobacterial aggregation by contact-mediated interactions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[42] Michael L. Mavrovouniotis,et al. Petri Net Representations in Metabolic Pathways , 1993, ISMB.
[43] Jason A. Papin,et al. Reconstruction of cellular signalling networks and analysis of their properties , 2005, Nature Reviews Molecular Cell Biology.
[44] Gheorghe Paun,et al. Computing with Membranes , 2000, J. Comput. Syst. Sci..
[45] Corrado Priami,et al. Beta Binders for Biological Interactions , 2004, CMSB.
[46] Shayn M. Peirce,et al. Combining experiments with multi-cell agent-based modeling to study biological tissue patterning , 2007, Briefings Bioinform..
[47] Monika Heiner,et al. Application of Petri net based analysis techniques to signal transduction pathways , 2006, BMC Bioinformatics.
[48] Peter Tang,et al. Dynamic cellular automata: an alternative approach to cellular simulation. , 2005, In silico biology.
[49] Radu Mateescu,et al. Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli , 2005, ISMB.
[50] J. Heijnen,et al. Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. , 2003, Metabolic engineering.
[51] C. Tomlin,et al. Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling. , 2004, Systems biology.
[52] Dipak Barua,et al. Computational Models of Tandem Src Homology 2 Domain Interactions and Application to Phosphoinositide 3-Kinase* , 2008, Journal of Biological Chemistry.
[53] Gary An,et al. A model of TLR4 signaling and tolerance using a qualitative, particle-event-based method: introduction of spatially configured stochastic reaction chambers (SCSRC). , 2009, Mathematical biosciences.
[54] Thomas Pfeiffer,et al. Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae , 2002, Bioinform..
[55] Jens Nielsen,et al. Evolutionary programming as a platform for in silico metabolic engineering , 2005, BMC Bioinformatics.
[56] Thomas Lengauer,et al. Pathway analysis in metabolic databases via differetial metabolic display (DMD) , 2000, German Conference on Bioinformatics.
[57] James R Faeder,et al. The complexity of complexes in signal transduction , 2003, Biotechnology and bioengineering.
[58] Michael J. North,et al. AgentCell: a digital single-cell assay for bacterial chemotaxis , 2005, Bioinform..
[59] Sarala M. Wimalaratne,et al. The Systems Biology Graphical Notation , 2009, Nature Biotechnology.
[60] Dirk Husmeier,et al. Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks , 2003, Bioinform..
[61] Gilles Clermont,et al. A Patient-Specific in silico Model of Inflammation and Healing Tested in Acute Vocal Fold Injury , 2008, PloS one.
[62] Yuh-Jyh Hu,et al. Extracting the abstraction pyramid from complex networks , 2010, BMC Bioinformatics.
[63] Michael Hucka,et al. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core , 2010 .
[64] E. Voit,et al. Recasting nonlinear differential equations as S-systems: a canonical nonlinear form , 1987 .
[65] Ting Chen,et al. Modeling Gene Expression with Differential Equations , 1998, Pacific Symposium on Biocomputing.
[66] S. Gilmore,et al. Automatically deriving ODEs from process algebra models of signalling pathways , 2005 .
[67] R. Jackson,et al. General mass action kinetics , 1972 .
[68] E. Klipp,et al. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints , 2006, Theoretical Biology and Medical Modelling.
[69] Steffen Klamt,et al. Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling , 2009, BMC Systems Biology.
[70] David S Wishart,et al. Computational systems biology in drug discovery and development: methods and applications. , 2007, Drug discovery today.
[71] Li Chen,et al. Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets , 2007, Journal of Biosciences.
[72] Bernhard O. Palsson,et al. Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System , 2009, PLoS Comput. Biol..
[73] Neema Jamshidi,et al. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. , 2010, Biophysical journal.
[74] B. Palsson,et al. Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use , 1994, Bio/Technology.
[75] KonagayaAkihiko,et al. Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm , 2005 .
[76] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[77] David Harel,et al. Statecharts: A Visual Formalism for Complex Systems , 1987, Sci. Comput. Program..
[78] Kevin Burrage,et al. Stochastic approaches for modelling in vivo reactions , 2004, Comput. Biol. Chem..
[79] Matthias Reuss,et al. Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants , 2011, BMC Systems Biology.
[80] Mario J. Pérez-Jiménez,et al. P Systems, a New Computational Modelling Tool for Systems Biology , 2006, Trans. Comp. Sys. Biology.
[81] François Fages,et al. BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge , 2006, Bioinform..
[82] Jane Hillston,et al. Bio-PEPA: A framework for the modelling and analysis of biological systems , 2009, Theor. Comput. Sci..
[83] Dawn C. Walker,et al. The virtual cell - a candidate co-ordinator for 'middle-out' modelling of biological systems , 2009, Briefings Bioinform..
[84] Mike Holcombe,et al. Formal agent-based modelling of intracellular chemical interactions. , 2006, Bio Systems.
[85] T. Marshall,et al. Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b , 2006, Theoretical Biology and Medical Modelling.
[86] Stefan Schuster,et al. Topological analysis of metabolic networks based on Petri net theory , 2003, Silico Biol..
[87] Cosimo Laneve,et al. Formal molecular biology , 2004, Theor. Comput. Sci..
[88] R. M. Zorzenon dos Santos,et al. Dynamics of HIV infection: a cellular automata approach. , 2001, Physical review letters.
[89] P. S. Thiagarajan,et al. Petri Nets and Other Models of Concurrency - ICATPN 2006, 27th International Conference on Applications and Theory of Petri Nets and Other Models of Concurrency, Turku, Finland, June 26-30, 2006, Proceedings , 2006, ICATPN.
[90] Pierre N. Robillard,et al. Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways , 2008, Bioinform..
[91] Q. Ouyang,et al. The yeast cell-cycle network is robustly designed. , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[92] Patrik D'haeseleer,et al. Genetic network inference: from co-expression clustering to reverse engineering , 2000, Bioinform..
[93] Peter Dittrich,et al. Chemical Organisation Theory , 2007, Bulletin of mathematical biology.
[94] W. S. Hlavacek,et al. A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. , 2006, Bio Systems.
[95] Goldenfeld,et al. Simple lessons from complexity , 1999, Science.
[96] Eberhard O. Voit,et al. Integrative biological systems modeling: challenges and opportunities , 2009, Frontiers of Computer Science in China.
[97] Judea Pearl,et al. Probabilistic reasoning in intelligent systems - networks of plausible inference , 1991, Morgan Kaufmann series in representation and reasoning.
[98] Fidel Ramírez,et al. Computing topological parameters of biological networks , 2008, Bioinform..
[99] Monika Heiner,et al. From Petri Nets to Differential Equations - An Integrative Approach for Biochemical Network Analysis , 2006, ICATPN.
[100] Yun Soo Bae,et al. Cellular Signal Transduction , 2001 .
[101] Shuhei Kimura,et al. Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm , 2005, Bioinform..
[102] Luca Cardelli,et al. BioAmbients: an abstraction for biological compartments , 2004, Theor. Comput. Sci..
[103] Yukiko Matsuoka,et al. Using process diagrams for the graphical representation of biological networks , 2005, Nature Biotechnology.
[104] Christoph Kaleta,et al. Using chemical organization theory for model checking , 2009, Bioinform..
[105] Thomas A. Henzinger,et al. Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development , 2007, PLoS Comput. Biol..
[106] Vincent Danos,et al. Formal Molecular Biology Done in CCS-R , 2007, Electron. Notes Theor. Comput. Sci..
[107] Denis Thieffry,et al. Petri net modelling of biological regulatory networks , 2008, J. Discrete Algorithms.
[108] B. Palsson,et al. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. , 2000, Journal of theoretical biology.
[109] E. Ruppin,et al. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[110] B. Palsson. Systems Biology: Properties of Reconstructed Networks , 2006 .
[111] Vincent Frouin,et al. Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset , 2008, BMC Bioinformatics.
[112] Michael Luck,et al. Agents in bioinformatics, computational and systems biology , 2006, Briefings Bioinform..
[113] Jesper Tegnér,et al. Growing Bayesian network models of gene networks from seed genes , 2005, ECCB/JBI.
[114] L. Wackett. An annotated selection of World Wide Web sites relevant to the topics in Microbial Biotechnology , 2013, Microbial biotechnology.
[115] Min Zou,et al. A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data , 2005, Bioinform..
[116] B. Palsson,et al. Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli , 2003, Journal of bacteriology.
[117] K. Sachs,et al. Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data , 2005, Science.
[118] Reinhard Schneider,et al. A survey of visualization tools for biological network analysis , 2008, BioData Mining.
[119] Edward R. Dougherty,et al. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks , 2002, Bioinform..
[120] Vincent Danos,et al. Rule-Based Modelling of Cellular Signalling , 2007, CONCUR.
[121] J. Hopfield,et al. From molecular to modular cell biology , 1999, Nature.
[122] Claire J. Tomlin,et al. Lateral Inhibition through Delta-Notch Signaling: A Piecewise Affine Hybrid Model , 2001, HSCC.
[123] Natalio Krasnogor,et al. Evolving cell models for systems and synthetic biology , 2010, Systems and Synthetic Biology.
[124] Annegret Wagler,et al. Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks , 2011, BMC Systems Biology.
[125] David Harel,et al. Four-dimensional realistic modeling of pancreatic organogenesis , 2008, Proceedings of the National Academy of Sciences.
[126] Denis Noble,et al. The rise of computational biology , 2002, Nature Reviews Molecular Cell Biology.
[127] Bernhard O. Palsson,et al. Dynamic simulation of the human red blood cell metabolic network , 2001, Bioinform..
[128] A Finney,et al. Systems biology markup language: Level 2 and beyond. , 2003, Biochemical Society transactions.
[129] Denis Thieffry,et al. Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets , 2004, ICATPN.
[130] Jamey D. Young,et al. Integrating cybernetic modeling with pathway analysis provides a dynamic, systems‐level description of metabolic control , 2008, Biotechnology and bioengineering.
[131] B. Palsson,et al. Transcriptional regulation in constraints-based metabolic models of Escherichia coli Covert , 2002 .
[132] Christoph Kaleta,et al. Phenotype prediction in regulated metabolic networks , 2008, BMC Systems Biology.
[133] Marco Grzegorczyk,et al. Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler , 2008, Bioinform..
[134] C. Petri. Kommunikation mit Automaten , 1962 .
[135] Satoru Miyano,et al. Inferring qualitative relations in genetic networks and metabolic pathways , 2000, Bioinform..
[136] Neil Swainston,et al. Towards a genome-scale kinetic model of cellular metabolism , 2010, BMC Systems Biology.
[137] A. Turing. The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.
[138] Bryant A. Julstrom,et al. Evolving petri nets to represent metabolic pathways , 2005, GECCO '05.
[139] Jens U. Wurthner,et al. A cellular automaton model of cellular signal transduction , 2000, Comput. Biol. Medicine.
[140] Danail Bonchev,et al. Modeling Biochemical Networks: A Cellular‐Automata Approach , 2005, Chemistry & biodiversity.
[141] S. Kauffman. Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.
[142] John von Neumann,et al. Theory Of Self Reproducing Automata , 1967 .
[143] Christoph Kaleta,et al. Computing chemical organizations in biological networks , 2008, Bioinform..
[144] David Harel,et al. Computational insights into Caenorhabditis elegans vulval development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[145] Adam M. Feist,et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011 , 2011, Molecular systems biology.
[146] Mike Holcombe,et al. Introducing Spatial Information into Predictive NF-κB Modelling – An Agent-Based Approach , 2008, PloS one.
[147] C. Clevenger. Signal transduction. , 2003, Breast disease.
[148] Ruth Nussinov,et al. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method , 2011, BMC Bioinformatics.
[149] Adam M. Feist,et al. Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.
[150] Francesco Pappalardo,et al. Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator , 2006, BMC Bioinformatics.
[151] Denis Thieffry,et al. Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli , 2005, ECCB/JBI.
[152] Barbara M. Bakker,et al. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. , 2000, European journal of biochemistry.
[153] Nir Friedman,et al. Inferring Cellular Networks Using Probabilistic Graphical Models , 2004, Science.
[154] J. Weinstein,et al. Depicting combinatorial complexity with the molecular interaction map notation , 2006, Molecular systems biology.
[155] Corrado Priami,et al. BlenX4Bio - BlenX for Biologists , 2009, CMSB.
[156] Corrado Priami,et al. Application of a stochastic name-passing calculus to representation and simulation of molecular processes , 2001, Inf. Process. Lett..
[157] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[158] Guy Karlebach,et al. Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.
[159] Peter Dittrich,et al. Chemical Organizations in the Central Sugar Metabolism of Escherichia coli , 2007 .
[160] ROBIN MILNER,et al. Edinburgh Research Explorer A Calculus of Mobile Processes, I , 2003 .
[161] David Harel,et al. LSCs: Breathing Life into Message Sequence Charts , 1999, Formal Methods Syst. Des..
[162] A. Barabasi,et al. Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.
[163] Vincent Danos,et al. Internal coarse-graining of molecular systems , 2009, Proceedings of the National Academy of Sciences.
[164] A. M. Turing,et al. The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.
[165] C. Anthony Hunt,et al. Simulating Properties of In Vitro Epithelial Cell Morphogenesis , 2006, PLoS Comput. Biol..
[166] David Harel,et al. The immune system as a reactive system: modeling T cell activation with statecharts , 2001, Proceedings IEEE Symposia on Human-Centric Computing Languages and Environments (Cat. No.01TH8587).
[167] Richard Banks,et al. Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach , 2007, Bioinform..
[168] D. Harel,et al. Toward rigorous comprehension of biological complexity: modeling, execution, and visualization of thymic T-cell maturation. , 2003, Genome research.
[169] J. Massagué. TGF-beta signal transduction. , 1998, Annual review of biochemistry.
[170] Mark M. Meerschaert,et al. Mathematical Modeling , 2014, Encyclopedia of Social Network Analysis and Mining.
[171] Corrado Priami,et al. Evolving BlenX programs to simulate the evolution of biological networks , 2008, Theor. Comput. Sci..
[172] Jane Hillston,et al. Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks , 2007, FBTC@CONCUR.
[173] Robin Milner,et al. A Calculus of Communicating Systems , 1980, Lecture Notes in Computer Science.
[174] Raymond R. Devillers,et al. Incremental and unifying modelling formalism for biological interaction networks , 2007, BMC Bioinformatics.
[175] Sunwoo Park,et al. Dichotomies between computational and mathematical models , 2008, Nature Biotechnology.
[176] Masaru Tomita,et al. Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico , 2005, FEBS letters.
[177] G B Ermentrout,et al. Cellular automata approaches to biological modeling. , 1993, Journal of theoretical biology.
[178] Dipak Barua,et al. A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases , 2009, PLoS Comput. Biol..
[179] Nan Xiao,et al. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli , 2008, Bioinform..
[180] Steffen Klamt,et al. A methodology for the structural and functional analysis of signaling and regulatory networks , 2006, BMC Bioinformatics.
[181] Hiroaki Kitano,et al. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .
[182] David Camacho,et al. Cellulat: an agent-based intracellular signalling model. , 2003, Bio Systems.
[183] Thomas A. Henzinger,et al. Reactive Modules , 1996, Proceedings 11th Annual IEEE Symposium on Logic in Computer Science.
[184] Aviv Regev,et al. Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra , 2000, Pacific Symposium on Biocomputing.
[185] R. Sharan,et al. A genome-scale computational study of the interplay between transcriptional regulation and metabolism , 2007, Molecular systems biology.
[186] Robin Milner,et al. A Calculus of Mobile Processes, II , 1992, Inf. Comput..
[187] E. Andrianantoandro,et al. Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.
[188] Gordon D. Plotkin,et al. A Language for Biochemical Systems: Design and Formal Specification , 2010, Trans. Comp. Sys. Biology.
[189] Catherine M Lloyd,et al. CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.
[190] D. Ramkrishna,et al. A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variables , 2008, Biotechnology progress.
[191] Björn H. Junker,et al. Computational Models of Metabolism: Stability and Regulation in Metabolic Networks , 2008 .
[192] David W. Corne,et al. Dynamics of HIV infection studied with cellular automata and conformon-P systems , 2008, Biosyst..
[193] K. Kohn. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. , 1999, Molecular biology of the cell.
[194] Monika Heiner,et al. A structured approach for the engineering of biochemical network models, illustrated for signalling pathways , 2008, Briefings Bioinform..
[195] William S. Hlavacek,et al. BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains , 2004, Bioinform..
[196] William S. Hlavacek,et al. RuleMonkey: software for stochastic simulation of rule-based models , 2010, BMC Bioinformatics.
[197] Dipak Barua,et al. Structure-based kinetic models of modular signaling protein function: focus on Shp2. , 2007, Biophysical journal.
[198] D. Lauffenburger,et al. Physicochemical modelling of cell signalling pathways , 2006, Nature Cell Biology.
[199] Vincent Danos,et al. Rule-Based Modelling and Model Perturbation , 2009, Trans. Comp. Sys. Biology.
[200] Bartek Wilczynski,et al. Applying dynamic Bayesian networks to perturbed gene expression data , 2006, BMC Bioinformatics.
[201] Kenneth J. Kauffman,et al. Advances in flux balance analysis. , 2003, Current opinion in biotechnology.
[202] Thomas Hinze,et al. Rule-based spatial modeling with diffusing, geometrically constrained molecules , 2010, BMC Bioinformatics.
[203] M. Reuss,et al. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. , 1997, Biotechnology and bioengineering.
[204] R. Albert,et al. The large-scale organization of metabolic networks , 2000, Nature.
[205] Ian Stark,et al. The Continuous pi-Calculus: A Process Algebra for Biochemical Modelling , 2008, CMSB.