COMPUTATIONAL
NEUROSCIENCE

Papers


Selected papers of general interest to computational neurobiologists.

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Bedard, C., Kroger, H., and Destexhe, A. (2004) Modeling extracellular field potentials and the frequency-filtering properties of extracellular space. Biophysical Journal, 86, 1829-1842.

Beeman, D., Bower, J.M., De Schutter, E., Efthimiadis, E.N., Goddard, N., & Leigh, J. (1997) The GENESIS simulator-based neuronal database. In: Koslow, S.H. and Huerta, M.F. (Eds.) Neuroinformatics: An Overview of the Human Brain Project. Mahwah NJ: Lawrence Erlbaum Associates, pp. 57-81.

[PDF] Blackwell K.T. and Hellgren Kotaleski J. (2003) Modeling the dynamics of second messenger pathways. In: Kotter, R. (Ed.) Neuroscience Databases: A Practical Guide. Norwell, MA: Kluwer Academic Publishers.

[PDF] Cannon, R., Gewaltig, M., Gleeson, P., Bhalla, U., Cornelis, H., Hines, M., Howell, F., Muller, E., Stiles, J., Wils, S., and De Schutter, E. (2007) Interoperability of Neuroscience Modeling Software: Current Status and Future Directions Neuroinformatics, 5

Carnevale, N.T., Tsai, K.Y., Claiborne, B.J., and Brown, T.H. (1995) The electrotonic transformation: a tool for relating neuronal form to function. In: Tesauro, G., Touretzky, D.S., and Leen, T.K. (Eds.) Advances in Neural Information Processing Systems, Vol. 7, Cambridge, MA: MIT Press, pp. 69-76.

[PDF] Cornelis, Hugo and De Schutter, Eric (2003) NeuroSpaces: separating modeling and simulation. Neurocomputing, 52-54, 227-231.

Crook, S., Beeman, D., Gleeson, P., and Howell, F. (2005) XML for Model Specification in Neuroscience: An Introduction and Workshop Summary. Brains, Minds & Media. 1, bmm228 (urn:nbn:de:0009-3-2282).

De Schutter, Eric (1992) A consumer guide to neuronal modeling software. Trends in Neuroscience, 15, 462-464.

Destexhe, A., Mainen, Z.F., and Sejnowski, T.J. (1994) Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism. Journal of Computational Neuroscience, 1, 195-230.

[PDF] Diesmann, Markus and Gewaltig, Marc-Oliver (2002) NEST: An Environment for Neural Systems Simulations. Ges. für Wiss. Datenverarbeitung , Forschung und wisschenschaftliches Rechnen, 58, 43-70.

Eichler-West, Rogene M., De Schutter, E., & Wilcox, G.L. (1999) Using evolutionary algorithms to search for control parameters in a nonlinear partial differential equation. In Evolutionary Algorithms, Vol. 111 of the IMA Volumes in Mathematics and its Applications, Springer-Verlag, 33-64 (1999).

Galan, R.F., Ermentrout, G.B., and Urban, N.N. (2005) Efficient Estimation of Phase-Resetting Curves in Real Neurons and its Significance for Neural-Network Modeling. Physical Review Letters, 94, 158101.

Gleeson, P., Steuber, V., and Silver, R.A. (2007) neuroConstruct: A Tool for Modeling Networks of Neurons in 3D Space Neuron, 54, 219-235.

[PDF] Goddard, N., Hucka, M., Howell, F., Cornelis, H., and Beeman, D. (2001) Towards NeuroML: Model Description Methods for Collaborative Modeling in Neuroscience. Phil. Trans. Royal Society B, 356 (1412), 1209-1228.

Graham, B.P., and van Ooyen, A. (2006) Mathematical modelling and numerical simulation of the morphological development of neurons. BMC Neuroscience, 7 (Suppl 1):S9.

Hines, M.L., and Carnevale, N.T. (1997) The NEURON Simulation Environment. Neural Computation, 9 (6), 1179-1209.

[PDF] Hines, M.L., and Carnevale, N.T. (2000) Expanding NEURON's Repertoire of Mechanisms with NMODL. Neural Computation, 12, 839-851.

[PDF] Hodgkin, A.L., and Huxley, A.F. (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. Journal of Physiology, 117, 500-544.

Izhikevich, E.M. (2004) Which Model to Use for Cortical Spiking Neurons? IEEE Transactions on Neural Networks, 15, 1063-1070.

[PDF] Kotter, R. (2004) Neuroscience databases: tools for exploring brain structure-function relationships. Philos Trans R Soc Lond B Biol Sci, 356(1412), 1111-1120.

Liu, Z., Golowasch, J., Marder, E., and Abbott, L.F. (1998) A Model Neuron with Activity-Dependent Conductances Regulated by Multiple Calcium Sensors. The Journal of Neuroscience, 18(7), 2309-2320.

[PDF] Natschläger, T., Markram, H., and Maass, W. (2002). Computer models and analysis tools for neural microcircuits. In Kötter, R. (Ed.) Neuroscience Databases: A Practical Guide. Norwell, MA: Kluwer Academic Publishers, pp. 121-136.

[PDF] Prinz, A.A., Abbott, L.F., and Marder, E. (2004) The Dynamic Clamp Comes of Age. Trends in Neuroscience, 27:218-224.

Prinz, A.A., Billimoria, C.P., and Marder, E. (2003) Alternative to Hand-Tuning Conductance-Based Models: Construction and Analysis of Databases of Model Neurons. Journal of Neurophysiology, 90, 3998-4015.

[PS] Stainhauser, D., Wyler, L., Müller, L., Senn, W., Kleinle, J., Larkum, M., Lüscher, H.-R., Streit, J., Vogt, K., and Wannier, T. (1995) An Evaluation Aid for Neural Modeling Software. Technical Report IAM-95-013 Institut für Informatik und angewandte Mathematik, Universitaüt Bern.

Shemer, I., Brinne, B., Tegner, J., Grillner, S. (2008) Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus. PLOS Computational Biology, Mar 28;4(3):e1000036.

Strout, J. (1997) A Library for the Compartmental Simulation of Neurons. Neuroscience-Net, Volume 2, Article #10013.

Vetter, P., Roth, A., and Hausser, M. (2001) Propagation of Action Potentials in Dendrites Depends on Dendritic Morphology. Journal of Neurophysiology, 85, 926-937.

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