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Accession
No.		NameSource /
Entry Date		Species /
Tissue		Cell CompartmentMethodology /
Model 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
    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
    11NOS_IwanagaIn-house. /
     2001-11-12 00:00:00    		Rat; Mammalian /
    Neuronal; Expression in E.coli    		CytosolQuantitative match to experiments /
    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
    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
    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
    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
    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
    93CaMKIV_submodelPeer-reviewed publication /
     2014-06-10 00:00:00    		General Mammalian /
    Neuronal    		Cytosol, 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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    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
    94mRNA synthesisPeer-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
    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
    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