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Accession
No.		NameSource /
Entry Date		Species /
Tissue		Cell CompartmentMethodology /
Model Implementation
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
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
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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    96BCMBhalla PLoS Comput Biol 2021 (peer reviewed publication) /
     2022-05-19 00:00:00    		General Mammalian /
    Neuronal    		Cell membrane/cytosolQualitative /
    Reduced ODE model
    108bcm_bistableBhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.  /
     2022-09-30 23:49:58    		Generic /
    		cytosolAbstract phenomenological model /
    HillTau 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
    106bistableBhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
     2022-09-30 22:20:03    		Generic /
    		cytosolAbstract phenomenological model /
    HillTau 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
    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
    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
    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
    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
    93CaMKIV_submodelPeer-reviewed publication /
     2014-06-10 00:00:00    		General Mammalian /
    Neuronal    		Cytosol, NucleusQuantitative match to experiments /
    Exact GENESIS implementation
    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
    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
    34cGMP_regulationIn-house  /
     2002-08-27 00:00:00    		Bovine and Sprague-Dawley rats; mammalian /
    Pulmonary, cardiac and expressed in Baculovirus infected Sf21(Spodoptera frugiperda) insect cells    		CytosolQuantitative match to experiments, Qualitative /
    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
    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
    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
    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
    28
  • CO_activation_
    of_GC
    		• In-house  /
     2002-01-22 00:00:00    		Bovine /
    Lungs    		CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    95
  • Differential syn
    thesis of mRNA
    		• Peer-reviewed publication,Book /
     2014-06-10 00:00:00    		General Mammalian/Neuronal /
    Neuronal    		Surface,Cytosol, NucleusQuantitative match to experiments,Approximate implementation,Qualitative,Qualitative /
    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