Research publications using GENESIS

The following list contains the 312 research publications that we know of (as of April, 2009), originating from outside of the Bower laboratory.

We have listed only peer-reviewed papers in journals, books, and published conference proceedings. This does not include the many conference abstracts or unpublished proceedings, talks, and poster presentations. If you know of others, please let us know through the forums and mailing list.


Yearsort iconTitleAuthor(s)Journal/Book Reference
(2008)Calcium, synaptic plasticity and intrinsic homeostasis in Purkinje neuron models.Achard, P. and De Schutter, EFrontiers in Computational Neuroscience 2:8.
(2006)Complex parameter landscape for a complex neuron model.Achard, P. and De Schutter, E. PLoS Comput Biol. 2:94.
(2007)A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity. Ajay, S. M. and Bhalla, U. S. HFSP Journal, 1:49-66
(2004)A role for ERKII in synaptic pattern selectivity on the time-scale of minutes. Ajay, S. M. and Bhalla, U. S. Eur. J. Neurosci. 20: 2671-2680
(2007)A propagating ERKII switch forms zones of elevated dendritic activation correlated with plasticity.Ajay, S.M. and Bhalla, U.SHFSP Journal 1:49-66.
(1999)Role of Multiple Calcium and Calcium-Dependent Conductances in Regulation of Hippocampal Dentate Granule Cell Excitability.Aradi, I. and Holmes, W. R.J. Comput. Neurosci. 6: 215-235.
(1999)Active dendrites regulate spatio-temporal synaptic integration in hippocampal dentate granule cells.Aradi, I. and Holmes, W. R.Neurocomputing 26-27: 45-51.
(2003)Sensitivity of AMPA receptor channel to calcium oscillations: a computational study.Atunes, G., Simoes-de-Souza, F.M. and Roque, A.CNeurocomputing 52-54: 341-346.
(1995)Information maintenance by retinal ganglion cell spikes.August, D. A. and Levy, W. B.Proceedings of the Third Annual Computation and Neural Systems Meeting, J. M. Bower (Ed.), Kluwer Academic Publishers, Boston, 41-46.
(2005)A coherent framework for multiresolution analysis of biological networks with "memory": Ras pathway, cell cycle, and immune systBarbano, P. E., Spivak, M., Feng, J., Antoniotti, M,. and Mishra, B.Proc. Natl. Acad. Sci. USA 102:6245-6250.
(1994)Modulation of the input/output function of rat piriform cortex pyramidal cells.Barkai E. and Hasselmo M.E.J. Neurophysiol. 72:644-658.
(1994)Modulation of associative memory function in a biophysical simulation of rat piriform cortex.Barkai E., Bergman, R.E., Horwitz, G. and Hasselmo M.E. J. Neurophysiol. 72:659-677.
(1999)Single cell and population activities in cortical-like systems.Bazso, F., Kepecs, A., Lengyel, M., Payrits, S., Szalisznyo, K., Zalanyi, L. and Erdi, P. Rev. Neurosci.10(3-4):201-212.
(2005)Introduction to Realistic Neural Modeling. Beeman, D. Brains, Minds, and Media. 1: bmm218 ( urn:nbn:de:0009-3-2189).
(2005)GENESIS Modeling Tutorial. Beeman, D. Brains, Minds, and Media. 1: bmm220 (urn:nbn:de:0009-3-2206).
(1994)Simulation-based tutorials for neuroscience education.Beeman, D.Computation in Neurons and Neural Systems, F. Eeckman, Ed., Kluwer Academic Publishers, pp. 65-70.
(2004)A detailed three-dimensional model of the cerebellar granular layer.Berends, M., Maex, R. and De Schutter, E. Neurocomputing 58-60:587-592.
(2004)Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways.Bhalla, U. S.Biophys. J. 87:733-44.
(2004)Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties. Bhalla, U. S. Biophys. J. 87:745-753.
(2003)Managing models of signalling networks.Bhalla, U. S. Neurocomputing, 52-54: 215-220.
(2002)Biochemical signaling networks decode temporal patterns of synaptic input.Bhalla, U. S.J. Comput. Neurosci. 13: 49-62.
(2000)Modeling Networks of Signaling Pathways.Bhalla, U. S.Computational Neuroscience: Realistic Modeling for Experimentalists, E. De Schutter (ed.)
(2008)How to Record a Million Synaptic Weights in a Hippocampal Slice.Bhalla, U.S.PLoS Comput. Biol. 4(6).
(2003)Temporal computation by synaptic signaling pathways.Bhalla, U.S. J. Chem. Neuroanat. 26:81-86.
(2002)Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways.Bhalla, U.S.Biophys. J. 83:740-752.
(2002)The chemical organization of signaling interactions.Bhalla, U.S. Bioinformatics 18:855-863.
(2002)Use of Kinetikit and GENESIS for modeling signaling pathways. Bhalla, U.S.Methods in Enzymology. 345:3-23 Ed. J.D. Hildebrandt and R. Iyengar.
(2001)Robustness of the bistable behavior of a biological signaling feedback loop. Bhalla, U.S. and Iyengar, R.Chaos 11:221-226.
(1999)Emergent properties of networks of biological signaling pathways.Bhalla, U.S. and Iyengar, R.Science 283: 381-387.
(2002)MAP kinase phosphatase as a locus of flexibility in a mitogen- activated protein kinase signaling network.Bhalla, U.S., Ram, P. and Iyengar, R.Science 297:1018-1023.
(2002)Calcium waves and closure of leak potassium currents caused by GABA stimulation of the type B photoreceptor of Hermissenda crassBlackwell K.T.J. Neurophysiol. 87: 776-792.
(2000)Evidence for a distinct light-induced calcium-dependent potassium current in Hermissenda crassicornis.Blackwell K.T.J. Comput. Neurosci. 9: 147-170.
(2000)Characterization of the light-induced currents in Hermissenda.Blackwell K.T. Neurocomputing 32-33: 45-49.
(1999)Dynamics of light-induced current in Hermissenda.Blackwell K.T.Neurocomputing 26-27: 61-67.
(2006)Subcellular, cellular, and circuit mechanisms underlying classical conditioning in Hermissenda.Blackwell, K. T.Anat. Rec. B New Anat. 289:25-37
(2006)Ionic currents underlying difference in light response between photoreceptors. Blackwell, K. T.J. Neurophys. 95:3060-3067.
(2005)Modeling Calcium Concentration and Biochemical Reactions. Blackwell, K. T. Brains, Minds, and Media. 1:bmm224 (urn:nbn:de:0009-3-2245).
(2004)Paired turbulence and light do not produce a supralinear calcium increase in Hermissenda.Blackwell, K. T.J. Comput. Neurosci. 17:79-97.
(2001)Propagation of calcium waves i the Hermissenda Type B photoreceptor.Blackwell, K. T. Neurocomputing 38-40: 1-7.
(1996)Channel model of second messenger mediated transformation of GABA induced currents. Blackwell, K. T., Vogl, T. P., Alkon, D. L. J. M. Bower (Ed.), Computational Neuroscience: Trends in Research 1995, Academic Press, NY, 3-8.
(1998)Cellular mechanisms of calcium elevation involved in long term memory.Blackwell, K.T., Vogl, T.P., and Alkon, D.L.Computational Neuroscience: Trends in Research 1998 J. M. Bower, (Ed.), Plenum Publishing Co., NY pp. 137-142.
(1993)A Neural Network Model of Inhibitory Information Processing in Aplysia.Blazis, D. E.J., Fischer, T. M. and Carew, T. J.Neural Computation 5: 213.
(2001)Modeling molecular diffusion.Bormann G., Brosens F., and De Schutter, E.Computational Methods in Molecular and Cellular Biology: from Genotype to Phenotype. J.M. Bower and H. Bolouri editors MIT Press, Boston.
(2000)Realistic modeling of small neuronal circuits.Calabrese, R., Hill, A. A. V. and van Hooser, S. D. Computational Neuroscience: Realistic Modeling for Experimentalists, E. De Schutter ed. CRC Press, Boca Raton, Chapter 10,259-288.
(2007)Interoperability of Neuroscience Modeling Software: Current Status and Future Directions.Cannon, R. C., Gewaltig, M-O., Gleeson, P., Bhalla, U. S., Cornelis, H., Hines, M. L., Howell, F. W., Muller, E., Stiles, J. R., Wils, S. and De Schutter, E.Neuroinformatics in press.
(1993) A model of the peristaltic reflex.Coop, A. and Redman, S.J.Computation and Neural Systems, F. H. Eeckman and J. M. Bower (eds.), Kluwer Academic Publishers pp. 313-320.
(2005)Signal compression in the sensory periphery.Copelli, M., Oliveira, R. F., Roque, A. C. and Kinouchi, O.Neurocomputing 65-66:691-696.
(2003)Phase response of model sinoatrial node cells. Coster, A. C. F. and Celler, B. G.Annals of Biomedical Engineering 31:271-283.
(2007) MorphML: Level 1 of the NeuroML standards for neuronal morphology data and model specification.Crook, S., Gleeson, P., Howell, F., Svitak, J. and Silver, R. A.Neuroinformatics (in press).
(1997)Identification of synaptic connections in neural ensembles by graphical models.Dahlhaus, R., Eichler, M. and Sandkuhler, J. J. Neurosci. Methods 77: 93-107.