Publications 

Hippocampus
  • Chay A., Zamparo I., Koschinski A., Zaccolo M.Z., BLackwell K.T. (2016) Control of beta-AR and NMDAR dependent cAMP dynamics in hippocampal neurons. PLoS Comp Biol.12:e1004735 abstract, Model Files (XML, software, output processing), uses NeuroRD v2.1.9
  • Kim M, Park AJ, Havekes R, Chay A, Guercio LA, Oliveira RF, Abel T, BlackwellKT (2011) Colocalization of protein kinase A with adenylyl cyclase enhances protein kinase A activity during induction of long-lasting long-term-potentiation, PLoS Comp Biol. 7:e1002084, abstract,NeuroRD XML (model) files, uses NeuroRD v2.0.3

  • Kim M, Huang T, Abel T, BlackwellKT (2010) Temporal sensitivity of protein kinase A activation in late-phase long term potentiation. PLoS Comp Biol 6:e100691 ODE model file for XPP, Abstract


Hermissenda Learning
  • Blackwell and Farley (2008) Hermissenda. Scholarpedia 3(7):4090

  • Blackwell (2006) Subcellular, cellular, and circuit mechanisms underlying classical conditioning in Hermissenda. Anat Rec B New Anat 289: 25-37 Abstract

  • Blackwell (2006) Ionic currents underlying difference in light response between photoreceptors. J Neurophys 95: 3060-7 Abstract, simulation files in modelDB, or download the tar file

  • Blackwell (2004) Paired Turbulence and Light do not Produce a Supralinear Calcium Increase in Hermissenda. J Comput Neurosci 17: 79-97 Abstract, simulation files in ModelDB

  • Mo and Blackwell (2003) Comparison of Hermissenda type A and type B photoreceptor's response to light. J Neurosci 23: 8020-8. Abstract

  • Blackwell (2002) The effect of intensity and duration on the light induced currents in Hermissenda type B photoreceptor. J Neurosci 22: 4217-4228 Abstract

  • Blackwell (2002) Calcium waves and closure of leak potassium currents caused by GABA stimulation of the type B photoreceptor of Hermissenda. J Neurophys 87: 776-792 Abstract

  • Blackwell (2000) Evidence for a distinct light-induced caclium-dependent potassium current in Hermissenda. J Comput Neurosci 9: 149-170 Abstract

  • Blackwell and Alkon (1999) Ryanodine receptor modulation of in vitro associative learning in Hermissenda. Brain Res 822: 114-125 Abstract

Basal Ganglia
  • Hawes SL, Evans RC, Unruh BA, Benkert EE, Gillani F, Dumas TC, Blackwell KT (2015) Multimodal Plasticity in Dorsal Striatum While Learning a Lateralized Navigation Task. J Neurosci. 2015 35(29):10535-49 abstract

  • Damodaran S, Cressman JR, Jedrzejewski-Szmek Z, Blackwell KT (2015) Desynchronization of Fast-Spiking Interneurons Reduces-Band Oscillations and Imbalance in Firing in the Dopamine-Depleted Striatum. J Neurosci. 35:1149-59 abstract simulation files in modelDB

  • Evans RC, Herin GA, Hawes SL, Blackwell KT (2015) Calcium-dependent inactivation of calcium channels in the medial striatum increases at eye opening. J Neurophysiol. 113(7):2979-86 abstract, Data available on request

  • Nair AG, Gutierrez-Arenas O, Eriksson O, Jauhiainen A, Blackwell KT, Kotaleski JH (2014) Modeling intracellular signaling underlying striatal function in health and disease. Prog Mol Biol Transl Sci. 123:277-304 abstract

  • Damodaran S, Evans RC, Blackwell KT (2014) Synchronized firing of fast-spiking interneurons is critical to maintain balanced firing between direct and indirect pathway neurons of the striatum. J Neurophysiol. 111(4):836-48 abstract simulation files in modelDB

  • Hawes SL, Gillani F, Evans RC, Benkert EA, Blackwell KT. (2013) Sensitivity to theta-burst timing permits LTP in dorsal striatal adult brain slice. J Neurophysiol. 110(9):2027-36. abstract

  • Evans RC, Maniar YM, Blackwell KT. (2013) Dynamic modulation of spike timing-dependent calcium influx during corticostriatal upstates. J Neurophysiol. 110(7):1631-45 abstract, simulation files in modelDB

  • Kim B, Hawes SL, Gillani F, Wallace L, Blackwell KT (2013) Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity. PLoS Comput Biol 9(3):e1002953. abstract, Simulation files: main sims, Long Morphology, Robustness, NeuroRD version, Guide to files, PostProcessing programs

  • Evans RC, Morera-Herreras T, Cui Y, Du K, Sheehan T, Kotaleski JH, Venance L, Blackwell (2012) The Effects of NMDA Subunit Composition on Calcium Influx and Spike Timing-Dependent Plasticity in Striatal Medium Spiny Neurons.PLoS Comput Biol 8: e1002493 article, simulation files in ModelDB

  • Oliveira R.F., Kim M., Blackwell K.T. (2012) Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites. PLoS Comput Biol 8: e1002383 article, simulation files, uses NeuroRD v2.0.3

  • Hjorth, Blackwell, Kotaleski (2009) Gap junctions between striatal fast-spiking interneurons regulate spiking activity and synchronization as a function of cortical activity. J Neurosci 29: 5276-86 Abstract , simulation files in ModelDB

  • Lindskog, Kim, Wikstrom, Blackwell, Kotaleski (2006) Transient calcium and dopamine increase PKA activity and DARPP-32 phosphorylation. PLoS Comput Biol. 2:e119.Abstract ODE model file for XPP

  • Gustafson, Gireesh-Dharmaraj, Czubayko, Blackwell, Plenz (2006) A comparative voltage and current-clamp analysis of feedback and feedforward synaptic transmission in the striatal microcircuit in vitro. J Neurophys 95: 737-52 Abstract

  • Kotaleski, Plenz, Blackwell (2006) Using potassium currents to solve signal-to-noise problems in inhibitory feedforward networks of the striatum. J Neurophys 95: 331-41Abstract, simulation files in ModelDB

  • Blackwell, Plenz (2003) Quantitative estimate of synaptic inputs to striatal neurons during up and down states in vitro. J Neurosci 23: 9123-32 Abstract

Modeling/Software/Reviews
  • Jedrzejewski-Szmek Z, Blackwell KT (2016) Asynchronous tau-leaping. J Chem Phys. In Press.

  • Evans RC, Blackwell KT (2015) Calcium: amplitude, duration, or location? Biol Bull. 228(1):75-83 abstract

  • Blackwell KT, Jedrzejewska-Szmek J. (2013) Molecular mechanisms underlying neuronal synaptic plasticity: systems biology meets computational neuroscience in the wilds of synaptic plasticity. Wiley Interdiscip Rev Syst Biol Med. 5(6):717-31 abstract

  • Blackwell (2013) Approaches and tools for modeling signaling pathways and calcium dynamics in neurons. J Neurosci Methods 2013 Nov 15;220(2):131-40 abstract

  • Blackwell, Wallace, Kim, Oliveira, Koh (2013) Modeling spatial aspects of intracellular dopamine signaling. Methods Mol Biol 964:61 abstract

  • Koh, Blackwell (2012) Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations. J Chem Phys 137:154111 abstract

  • Koh, Blackwell (2011) An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping. J Chem Phys. 134(15):154103 abstract, simulation files

  • Oliveira, Terrin, Di Bennedetto, Koh, Kim, Zaccolo, Blackwell (2010) NeuroRD: novel software for stochastic modeling of microdomains of signaling molecules. PLoS ONE 5:e11725 abstract, simulation files, uses NeuroRD version 2.0.3

  • Manninen T, Hituri K, Kotaleski JH, Blackwell KT, Linne ML. (2010) Postsynaptic signal transduction models for long-term potentiation and depression.Front Comput Neurosci. 4:152 abstract

  • Kotaleski JH, Blackwell KT (2010) Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches. Nat Rev Neurosci. 11:239 Abstract

  • Ferrante M, Blackwell KT, Migliore M, Ascoli GA. (2008) Computational models of neuronal biophysics and the characterization of potential neuropharmacological targets. Curr Med Chem. 15:2456-71 Abstract, simulation files in ModelDB

  • Blackwell K.T. (2006) An efficient stochastic diffusion algorithm for modeling second messengers in dendrites and spines. J Neurosci Methods 157: 142-53 Abstract

  • Blackwell (2005) A New Era in Computational Neuroscience. Neuroinformatics 3: 163-166

  • Kotaleski, J.H., Lester D., Blackwell K.T. (2002) Subcellular interactions between parallel fibre and climbing fibre signals in Purkinje cells predict sensitivity of classical conditioning to interstimulus interval. Integrative Physiol and Behav Sci 37: 265-292 Abstract

  • Blackwell K.T., Hellgren Kotaleski J (2002) Modeling the dynamics of second messenger pathways. In Neuroscience Databases: A Practical Guide, Ed. R. Kotter. Kluwer Academic Publishers, Norwell, MA PDF file

  • Yang, Blackwell (2000) Analog pattern matching in a dendritic spine model based on phosphorylation of potassium channels. Network: Comput Neural Systems 11: 281-297 Abstract



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Blackwell

Revised: 6/2014 - Avrama Blackwell