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Accession
No.		NameSource /
Entry Date		Species /
Tissue		Cell CompartmentMethodology /
Model Implementation
111oscBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
 2022-10-01 00:05:03		Generic /
cytosolAbstract phenomenological model /
HillTau implementation
108bcm_bistableBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
 2022-09-30 23:49:58		Generic /
cytosolAbstract phenomenological model /
HillTau implementation
106bistableBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 22:20:03		Generic /
cytosolAbstract phenomenological model /
HillTau implementation
104fb_inhibBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 22:16:21		Generic /
cytosolAbstract phenomenological model /
HillTau implementation
97excBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 15:13:55		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
112conv2ndOrderBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
 2022-10-01 00:07:32		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
98exc2ndOrderBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 17:52:22		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
99convBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 17:54:52		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
100inhBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 22:08:48		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
103gainBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 22:14:44		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
102modifierBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
 2022-09-30 22:13:03		Generic /
cytosolFit to elementary ODE model /
HillTau implementation
101
  • exc_tau_
    baseline
    		• Bhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 22:10:56    		Generic /
    		cytosolFit to elementary ODE model /
    HillTau implementation
    107bcmBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 23:36:25    		Generic /
    		SynapseFit to ODE model and experiments /
    HillTau implementation
    105kholodenkoBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 22:18:08    		Xenopus /
    Oocyte extract    		cytosolFit to ODE model and experiments /
    HillTau 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
    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
    36luciferaseL. Yu. Brovko et al 1994, Biochemistry (Moscow) 59(2):195-201, 1994 ( peer-reviewed publication ). /
     2002-12-12 00:00:00    		E. Coli /
    -    		CytosolQualitative /
    Approximate 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
    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
    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
    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
    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
    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
    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
    86BDNF_ReceptorJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    NIH 3T3 Expression    		Surface, CytosolQualitative /
    Exact GENESIS implementation
    42
  • CDK2-CyclinA_
    activation_
    pathway
    		• Morris MC. et al. J Biol Chem. (2002) 277(26):23847-53. ( peer-reviewed publication ) /
     2003-01-11 00:00:00    		Human, Xenopus /
    Expressed in E.coli    		CytosolQualitative /
    Exact GENESIS implementation
    87AKTJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    Brain    		Surface, CytosolQualitative /
    Exact GENESIS implementation
    88S6KJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    HEK293 cells    		Surface, CytosolQualitative /
    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
    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
    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
    96BCMBhalla PLoS Comput Biol 2021 (peer reviewed publication) /
     2022-05-19 00:00:00    		General Mammalian /
    Neuronal    		Cell membrane/cytosolQualitative /
    Reduced ODE model
    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
    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
    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
    9
  • MAPK_MKP1_
    oscillation
    		• Bhalla US, Iyengar R. Chaos (2001) 11(1):221-226. ( peer-reviewed publication ) /
     2001-11-08 00:00:00    		Generic mammalian /
    NIH 3T3 Expression    		Surface - NucleusQualitative /
    Exact GENESIS implementation
    13PLCbeta1In-house  /
     2001-11-12 00:00:00    		Bovine; Mammalian /
    Brain - Neuronal; expressed in E.coli    		Cell MembraneQualitative /
    Exact GENESIS implementation
    109
  • syn_prot_
    composite
    		• Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-09-30 23:58:38    		Rodent /
    Brain    		SynapseQuantitative fit to experiments /
    HillTau implementation
    114syn_CaMKIIIBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:12:23    		Rodent /
    Brain    		SynapseQuantitative fit to experiments /
    HillTau implementation