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Accession
No.		NameSource /
Entry Date		Species /
Tissue		Cell CompartmentMethodology /
Model Implementation
52
  • EGFR_Signaling_
    pathway
    		• Quantification of Short Term Signaling by the EGFR Kholodenko et al, The J Biol Chem. , Vol 274, No. 42, Issue of October 15, pp. 30169 - 30181, 1999. ( peer-reviewed publication ) /
     2003-05-17 00:00:00    		Harlan Sprague Dawley rat; mammalian /
    Hepatocytes    		Cell membrane + cytosolQualitative /
    Mathematically equivalent
    64
  • AMPAR_CaMKII_
    strong_coupling
    		• Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    59
  • AMPAR_traff_
    model0
    		• Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments /
    Exact GENESIS implementation
    60
  • AMPAR_traff_
    model1
    		• Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments /
    Exact GENESIS implementation
    61
  • simple_AMPAR_
    traff_model2
    		• Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Postsynaptic Density, Synaptic SpineIllustrative /
    Exact GENESIS implementation
    63CaMKII_model3Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    65
  • AMPAR_CaMKII_
    weak_coupling
    		• Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-21 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    62
  • CaMKII_noPKA_
    model3
    		• Hayer A, Bhalla US PLoS PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) /
     2005-07-19 00:00:00    		General Mammalian /
    Neuronal    		Synaptic Spine, Postsynaptic DensityQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    44
  • MAPK_Asthagiri_
    no_fb
    		• Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39. ( peer-reviewed publication ). /
     2003-02-22 00:00:00    		Chinese hamster (Cricetulus griseus); mammalian /
    Ovary - CHO cell line    		 Surface, cytosolQuantitative match to experiments, Qualitative /
    Mathematically equivalent
    45
  • MAPK_Asthagiri_
    adapt_fb
    		• Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39. ( peer-reviewed publication ). /
     2003-02-22 00:00:00    		Chinese hamster (Cricetulus griseus); mammalian /
    Ovary - CHO cell line    		 Surface, cytosolQuantitative match to experiments, Qualitative /
    Mathematically equivalent
    46
  • MAPK_Asthagiri_
    enz_fb
    		• Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39. ( peer-reviewed publication ). /
     2003-02-22 00:00:00    		Chinese hamster (Cricetulus griseus); mammalian /
    Ovary - CHO cell line    		 Surface + cytosolQualitative /
    Approximate implementation
    66
  • Jak-Stat_
    Pathway
    		• Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6. ( Peer-reviewed publication ) /
     2006-02-13 00:00:00    		mouse /
    Liver    		Cytosol, NucleusQuantitative match to experiments /
    Exact GENESIS implementation
    67SOCS1_knockoutYamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6. ( Peer-reviewed publication ) /
     2006-02-13 00:00:00    		mouse /
    Liver    		Nucleus , cytoplasmQuantitative match to experiments /
    Exact GENESIS implementation
    12Stuehr_NOS Santolini J. et al. J Biol Chem. (2001) 276(2):1233-43. ( peer-reviewed publication ) /
     2001-11-12 00:00:00    		Generic mammalian /
    Neuronal ; Expressioned in E.coli    		CytosolQuantitative match to experiments /
    Approximate implementation
    29Kierzek_LacZKierzek AM. et al. J Biol Chem. (2001) 276(11):8165-72. ( peer-reviewed publication ) /
     2002-01-28 00:00:00    		E. Coli /
    -    		InternalQualitative /
    Approximate implementation
    35
  • MAPK-bistability
    -fig1c
    		• Bhalla US et al. Science (2002) 297(5583):1018-23 ( peer-reviewed publication ). /
     2002-11-07 00:00:00    		Generic mammalian /
    NIH 3T3 Expression    		Surface - NucleusQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    4
  • mkp1_feedback_
    effects
    		• Bhalla US et al. Science (2002) 297(5583):1018-23. ( peer-reviewed publication ) /
     2001-11-07 00:00:00    		Generic mammalian /
    NIH 3T3 Expression    		Surface - nucleusQuantitative match to experiments /
    Exact GENESIS implementation
    70RanGTPaseGorlich D et al EMBO J. 2003 Mar 3;22(5):1088-100. ( Peer-reviewed publication ) /
     2006-05-12 00:00:00    		Eukaryotic system /
    HeLa Cells    		Cytosol, NucleusQualitative /
    Exact GENESIS implementation
    71RasGTPasePhillips RA et al Biochemistry. 2003 Apr 8;42(13):3956-65. ( Peer-reviewed publication ) /
     2006-05-12 00:00:00    		General Mammalian /
    E.coli Expression system    		CytosolQualitative /
    Exact GENESIS implementation
    69
  • Quorum_
    repressilator
    		•  Garcia-Ojalvo J, Elowitz MB, Strogatz SH. Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10955-60.. ( Peer-reviewed publication ) /
     2006-02-14 00:00:00    		E. Coli /
    E.coli Expression, Transposon Tn10, Lambda phage Expression    		Cytosol, ExtracellularQualitative /
    Exact GENESIS implementation
    48PKC_2003Bhalla US. (2004) Biophys J. 87(2):733-44 .( peer-reviewed publication ) /
     2003-04-28 00:00:00    		Generic mammalian /
    Generic    		Cytosol + Cell membraneQualitative /
    Exact GENESIS implementation
    47PKA_2003Bhalla US. (2004) Biophys J. 87(2):733-44. ( peer-reviewed publication ) /
     2003-04-28 00:00:00    		Generic mammalian /
    Generic    		Cytosol + Cell membraneQualitative /
    Exact GENESIS implementation
    58EGFR_MAPKBhalla US. Biophys J. (2004) 87(2):745-53. ( peer-reviewed publication ) /
     2004-01-14 00:00:00    		Generic mammalian /
    Neuronal    		SynapseQualitative /
    Exact GENESIS implementation
    15
  • sGC_Stone_
    Marletta
    		• Stone JR, Marletta MA. Biochemistry (1996) 35(4):1093-9. ( peer-reviewed publication ) /
     2001-12-12 00:00:00    		Bovine /
    Lungs    		CytosolQuantitative match to experiments /
    Mathematically equivalent
    83d_fold_modelBhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-11-08 00:00:00    		Generic mammalian /
    NIH 3T3 Expression    		Surface - NucleusQuantitative match to experiments /
    Exact GENESIS implementation
    1fig2_egfrBhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-11-07 00:00:00    		Generic mammalian /
    Brain    		Surface - NucleusQuantitative match to experiments, Hypothetical /
    Exact GENESIS implementation
    27MAPK_oscBoris N. Kholodenko Eur J Biochem. (2000) 267(6):1583-8). ( peer-reviewed publication ) /
     2002-01-22 00:00:00    		Xenopus /
    Oocyte extract    		CytosolHypothetical /
    Mathematically equivalent
    25cAMP_pathwayBhalla US Methods Enzymol. 2002;345:3-23). ( peer-reviewed publication ) /
     2002-01-12 00:00:00    		Generic mammalian /
    Brain - Neuronal    		Cell membrane + CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    32
  • Osc_Ca_
    IP3metabolism
    		•  Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) /
     2002-04-03 00:00:00    		Generic mammalian /
    Brain - Neuronal    		CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    23
  • NonOsc_Ca_
    IP3metabolism
    		•  Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) /
     2002-01-07 00:00:00    		Generic mammalian /
    Brain - Neuronal    		CytosolQuantitative match to experiments, Qualitative /
    Approximate implementation
    24
  • Osc_Ca_
    IP3metabolism
    		•  Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) /
     2002-01-08 00:00:00    		Generic mammalian /
    Brain - Neuronal    		CytosolQuantitative match to experiments, Qualitative /
    Approximate implementation
    31
  • NonOsc_Ca_
    IP3metabolism
    		•  Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) /
     2002-04-03 00:00:00    		Generic mammalian /
    Brain - Neuronal    		CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    49CaMKII_2003Bhalla US. Biophys J. 2004 Aug;87(2):733-44. ( peer-reviewed publication ). /
     2003-04-28 00:00:00    		Generic mammalian /
    Brain - Neuronal    		SynapseQualitative /
    Exact GENESIS implementation
    50
  • MAPK_network_
    2003
    		• Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication ) /
     2003-04-28 00:00:00    		Generic mammalian /
    Brain - Neuronal    		SynapseQualitative /
    Exact GENESIS implementation
    55ChemotaxisBray et al. Mol.Biol.Cell (1993) 4(5): 469-482. ( peer-reviewed publication ) /
     2003-06-10 00:00:00    		E. Coli /
    -    		Cell membrane + cytosolQuantitative match to experiments /
    Mathematically equivalent
    57ChemotaxisBray et al. Mol.Biol.Cell (1993) 4(5): 469-482. ( peer-reviewed publication ) /
     2003-06-10 00:00:00    		E. Coli /
    -    		Cell membrane + cytosolQualitative /
    Mathematically equivalent
    16
  • Synaptic_
    Network
    		• Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-12-12 00:00:00    		Generic mammalian /
    Neuronal    		SynapseQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    68RepressilatorElowitz MB, Leibler S., Nature. 2000 Jan 20;403(6767):335-8. ( Peer-reviewed publication ) /
     2006-02-13 00:00:00    		E. Coli /
    E.coli Expression, Transposon, Lambda phage    		CytosolQualitative /
    Exact GENESIS implementation
    37SERCA Mahaney JE. et al. Biophys J. (2000) 78(3) 1306-23. ( peer-reviewed publication ) /
     2002-12-31 00:00:00    		Canine /
    Cardiac; expressed in Baculovirus infected Sf21(Spodoptera frugiperda) insect cells.    		MicrosomesQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    33CaMKIIWilliam R. Holmes J Comput Neurosci. (2000) 8(1):65-85 ( peer-reviewed publication ) /
     2002-08-21 00:00:00    		Generic mammalian /
    Brain - Neuronal    		SynapseQualitative /
    Approximate implementation