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Accession
No.		NameSource /
Entry Date		Species /
Tissue		Cell CompartmentMethodology /
Model Implementation
19CondorelliGCCondorelli P, George SC. Biophys J. (2001) 80(5):2110-9). ( peer-reviewed publication  /
 2001-12-25 00:00:00		Generic mammalian /
Pulmonary and vascular smooth muscle		CytosolQuantitative match to experiments /
Mathematically equivalent
18Kuroda_GCKuroda S. et al. J Neurosci. (2001) 21(15):5693-702. ( peer-reviewed publication ) /
 2001-12-24 00:00:00		Generic mammalian /
Neuronal		SynapseQuantitative match to experiments /
Exact GENESIS implementation
43
  • CDK2-CyclinA_
    activation_
    improved
    		• 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    		CytosolQuantitative match to experiments /
    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
    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
    30
  • Huang_Ferrell_
    MAPK
    		• Huang CY and Ferrell JE Jr. Proc Natl Acad Sci U S A. (1996) 93(19):10078-83 ( peer-reviewed publication ) /
     2002-01-31 00:00:00    		Xenopus /
    Oocytes extract    		CytosolQuantitative match to experiments /
    Approximate implementation
    75NOHArginineAbu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
     2006-08-07 00:00:00    		human /
    Kidney cell expressing the rat brain nNOS    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    74NMArginineAbu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
     2006-08-07 00:00:00    		human /
    Kidney cell expressing the rat brain nNOS    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    73HomoArginineAbu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
     2006-08-07 00:00:00    		human /
    Kidney cell expressing the rat brain nNOS    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    72L-ArginineAbu-Soud HM et al. Biochemistry. 1999 Sep 21;38(38):12446-51. ( Peer-reviewed publication ) /
     2006-08-07 00:00:00    		Human /
    Kidney cell expressing the rat brain nNOS    		CytosolQuantitative match to experiments /
    Exact GENESIS implementation
    85
  • Mammalian_cell_
    cycle
    		• Novak B,Tyson JJ. J Theor Biol. 2004 Oct 21;230(4):563-79. ( Peer-reviewed publication ) /
     2006-12-21 00:00:00    		General Mammalian /
    -    		NucleusQuantitative match to experiments /
    Approximate implementation
    77
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning
    		• Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80 ( Peer-reviewed publication ) /
     2006-12-12 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    78
  • Ajay_Bhalla_
    2004_Feedback_
    Tuning
    		• Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication ) /
     2006-12-12 00:00:00    		Rat /
    Hippocampal CA1    		DendritesSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    76
  • Ajay_Bhalla_
    2004_PKM_Tuning
    		• Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication ) /
     2006-12-12 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi -Quantitative match to experiments /
    Exact GENESIS implementation
    82
  • Ajay_Bhalla_
    2007_ReacDiff1_
    1e-13
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    83
  • Ajay_Bhalla_
    2007_ReacDiff2
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    84
  • Ajay_Bhalla_
    2007_ReacDiff3
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    81
  • Ajay_bhalla_
    2007_ReacDiff1_
    1e-12
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    80
  • Ajay_Bhalla_
    2007_PKM
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    79
  • Ajay_Bhalla_
    2007_Bistable
    		• Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87 /
     2006-12-08 00:00:00    		Rat /
    Hippocampal CA1    		DendriteSemi-Quantitative match to experiments /
    Exact GENESIS implementation
    2fig3_CaMKIIBhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-11-07 00:00:00    		Generic mammalian /
    Neuronal    		SynapseQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    3fig4_synapseBhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) /
     2001-11-07 00:00:00    		Generic mammalian /
    Neuronal    		SynapseQuantitative match to experiments, Qualitative, Hypothetical /
    Exact GENESIS implementation
    92mTOR_pathwayJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-13 00:00:00    		General Mammalian /
    Neuronal    		DendriticQuantitative match to experiments /
    Approximate implementation
    91
  • Protein_
    synthesis
    		• Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    -    		Cell membrane, CytosolQuantitative match to experiments, Hypothetical /
    Exact GENESIS implementation
    90CaMKIIIJain 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, Cytosol, NucleusQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation,Approximate implementation
    894EBPJain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) /
     2009-02-12 00:00:00    		General Mammalian /
    E.coli Expression    		Surface, CytosolQuantitative match to experiments, Qualitative /
    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
    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
    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
    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
    108bcm_bistableBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-09-30 23:49:58    		Generic /
    		cytosolAbstract phenomenological model /
    HillTau implementation
    110aut6Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:02:13    		Rodent /
    Brain    		SynapseQuantitative fit to experiments /
    HillTau implementation
    111oscBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:05:03    		Generic /
    		cytosolAbstract phenomenological 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
    113
  • syn_prot_
    minimal
    		• Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-10-01 00:09:57    		Rodent /
    Brain    		SynapseReduced quantitative fit to experiments /
    HillTau 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
    104fb_inhibBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 22:16:21    		Generic /
    		cytosolAbstract phenomenological 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