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Accession
No.		NameSource /
Entry Date		Species /
Tissue		Cell CompartmentMethodology /
Model 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
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
    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
    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
    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
    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
    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
    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
    93CaMKIV_submodelPeer-reviewed publication /
     2014-06-10 00:00:00    		General Mammalian /
    Neuronal    		Cytosol, NucleusQuantitative match to experiments /
    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
    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
    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
    11NOS_IwanagaIn-house. /
     2001-11-12 00:00:00    		Rat; Mammalian /
    Neuronal; Expression in E.coli    		CytosolQuantitative 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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    20
  • NOS_Phosph_
    regulation
    		• In-house /
     2001-12-25 00:00:00    		rat; Mammalian /
    Brain - Neuronal; expressed in E.coli    		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
    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
    26PKC_turnoverIn-house  /
     2002-01-22 00:00:00    		Generic mammalian /
    Brain - Neuronal    		Cell membrane +CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    28
  • CO_activation_
    of_GC
    		• In-house  /
     2002-01-22 00:00:00    		Bovine /
    Lungs    		CytosolQuantitative match to experiments, Qualitative /
    Exact GENESIS implementation
    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
    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
    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
    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
    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
    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
    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
    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
    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