Koene, R.A. and Hasselmo, M.E. (2008). Consequences of parameter differences in a model of short-term persistent spiking buffers provided by pyramidal cells in entorhinal cortex. Brain Research. Vol.1202C, pp.54-67. Brain Research Advanced Access published on July 17, 2007, doi:10.1016/j.brainres.2007.06.067.
electronic reprint: PDF (984K)
reference to the published article at Brain Research
Koene, R.A. and Hasselmo, M.E. (2007). First-in-first-out item replacement in a model of short-term memory based on persistent spiking. Cerebral Cortex.. Vol.17(8), pp.1766-1781. Cerebral Cortex Advanced Access published on October 9, 2006, doi: 10.1093/cercor/bhl088.
electronic reprint: preprint PDF (1305K), free-access URL at Cerebral Cortex
reference to the published article at Cerebral Cortex
McGaughy, J., Koene, R.A., Eichenbaum, H. and Hasselmo, M.E. (2005). Cholinergic deafferentation of the entorhinal cortex in rats impairs encoding of novel but not familiar stimuli in a delayed nonmatch-to-sample task.
Journal of Neuroscience. Vol.25(44), pp.10273-10281.
electronic reprint: PDF (532K)
reference to the published article at the Journal of Neuroscience
Koene, R.A. and Hasselmo, M.E. (2005). An integrate and fire model of prefrontal cortex neuronal activity during performance of goal-directed decision making. Cerebral Cortex. Vol.15:12, pp.1964-1981. (Cerebral Cortex Advanced Access published April 27, 2005.)
electronic reprint: preprint PDF (875K)
reference to the published article at the journal Cerebral Cortex
Koene, R.A., Gorchetchnikov, A., Cannon, R.C. and Hasselmo, M.E. (2003). Modeling goal-directed spatial navigation in the rat based on physiological data from the hippocampal formation. Neural Networks. Vol. 16:5-6, pp. 577-584.
electronic reprint: PDF (575K), preprint PDF (580K)
reference to the published article at the journal Neural Networks
Cannon, R.C., Hasselmo, M.E. and Koene, R.A. (2003). From biophysics to behavior: Catacomb2 and the Design of Biologically Plausable Models for Spatial Navigation. Neuroinformatics. Vol. 1:1, pp. 3-42.
electronic reprint: PDF (842K)
reference to the published article at the journal Neuroinformatics
Koene, R. and Takane, Y. (1999). Discriminant component pruning. Regularization and interpretation of multi-layered back-propagation networks. Neural Computation. Vol. 11, pp. 783-802.
electronic reprint: PDF (346K), compressed postscript (99K)
reference to the published article at the journal Neural Computation
Koene, R.A. and Hasselmo, M.E. (2007). Connectionist Memory Models of Hippocampal Function. In the Learning and Memory: A Comprehensive Reference. (In press). Elsevier.
electronic reprint: (pending)
reference page at Elsevier (pending)
Koene, R.A. and Hasselmo, M.E. (2006). Hippocampus: Computational models. In the New Encyclopedia of Neuroscience. (In press). Elsevier.
electronic reprint: (pending)
reference to the encyclopedia authors' page at Elsevier
Koene, R.A. (2006). Scope and Resolution in Neural Prosthetics and Special Concerns for the Emulation of a Whole Brain. Journal of Geoethical Nanotechnology.1(4).
electronic reprint: PDF (?K)
Koene, R.A. (2006). Short-term memory based on intrinsic neuronal dynamics during on-line acquisition of context dependent memory.
(Neurocomputing, In Review).
electronic reprint: compressed postscript (-pending-K)
Koene, R.A. and Hasselmo, M.E. (2005). An integrate and fire model of prefrontal cortex provides a biological implementation of action selection in reinforcement learning theory that reuses known representations. In Proceedings of the International Joint Conference on Neural Networks (IJCNN2005).
electronic reprint: preprint PDF (601K), Powerpoint (1116K), presentation notes PDF (129K), AVI movie (102K), AVI movie (121K)
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2003). Goal-directed spatial navigation of the rat depends on phases of theta oscillation in hippocampal circuitry. In Proceedings of the International Joint Conference on Neural Networks (IJCNN2003).
electronic reprint: PDF (372K)
Hasselmo, M.E., Cannon, R.C. and Koene, R.A. (2002). A simulation of parahippocampal and hippocampal structures guiding spatial navigation of a virtual rat in a virtual environment: A functional framework for theta theory. In: Witter, M P.and Wouterlood, F.G. (eds.) The Parahippocampal Region: Organization and Role of Cognitive Functions. Oxford University Press: Oxford. pp.139-161.
electronic reprint: compressed postscript (246K)
Koene, R.A. (1995). Extracting Knowledge in Terms of Rules from Trained Neural Networks. M.Sc. thesis, Delft University of Technology, Delft, The Netherlands.
electronic reprint: compressed postscript (315K)
Koene, R.A., van Pelt, J. and van Ooyen, A. (2008). NETMORPH DEMO at INCF booth FENS 2008. Presented at the 6th FENS Forum of European Neuroscience. Geneva, Switzerland.
electronic reprint: compressed archive (4735K)
reference to the web site of the 2008 FENS Forum of European Neuroscience
Koene, R.A. and Hasselmo, M.E. and Stern, C. and Kahana, M. and Eichenbaum, H.B. (2008). Learning and Episodic Memory: Encoding and Retrieval. Presented at the CELEST EASRB Meeting. February, 2008. Center of Excellence for Learning in Education, Science, and Technology. Boston, MA.
electronic reprint: Powerpoint (9742K)
reference to the web site of the Center of Excellence for Learning in Education, Science, and Technology (CELEST)
Koene, R.A. (2008). Cognitive Facilitation and Memory Access. Presented at the Medical Center of the University of Navarrre (CIMA). January, 2008. Fatronik. San Sebastian, Spain.
electronic reprint: Powerpoint (192660K)
reference to the web site of Fatronik
Koene, R.A. (2007). Accessing Memory by Serial Reconstruction. Presented at the InnerSpace Foundation Neuroengineering Meeting. Boston, MA.
electronic reprint: directory (315296K)
reference to the web site of the InnerSpace Foundation
Koene, R.A. (2007). Spike timing dependent mechanisms in cortical function and the involvement of specific neuron morphology in large scale neuronal networks. Presented at the Laboratory of Theoretical Neurobiology of the University of Antwerp. Antwerp, Belgium.
electronic reprint: Powerpoint (15469K), PDF (2979K)
reference to the web site of the Laboratory of Theoretical Neurobiology of the University of Antwerp
Koene, R.A. (2007). Three challenges in whole brain neuroscience. Verifying automated reconstruction methods by generating virtual known network data. Presented at the University of Oxford Future of Humanity Institute Whole Brain Emulation Workshop 2007. Faculty of Philosophy and James Martin 21st Century School at Oxford. Oxford, U.K.
electronic reprint: Powerpoint (12584K)
reference to the web site of the Future of Humanity Institute at the University of Oxford, Oxford, U.K.
Koene, R.A. (2006). Scope and Resolution in Neural Prosthetics and Special Concerns for the Emulation of a Whole Brain. Presented at the 2nd Annual Workshop on Geoethical Nanotechnology. Lincoln, Vermont.
electronic reprint: compressed Powerpoint (4568K), compressed narrated Powerpoint (8276K), PDF (4814K), presentation text RTF (55K)
reference to the web site of the 2nd Annual Workshop on Geoethical Nanotechnology at the Terasem Green Mountain Center Retreat, Lincoln, Vermont
Koene, R.A. (2004). Short-term memory. Presented at the 2004 Annual Meeting of the Group on Action and Perception (GAP). London, Ontario.
electronic reprint: presentation PDF (K), compressed presentation postscript (K), Powerpoint (4157K), notes PDF (K)
reference to the web site of the Group on Action and Perception (GAP)
Koene, R.A. (2004). Design-based modeling of neurophysiology and environment gives insight into neuronal functions of goal-directed behavior. Presented at the Netherlands Institute for Brain Research (NIBR). Amsterdam, Netherlands.
electronic reprint: presentation PDF (10898K), compressed presentation postscript (3504K), Powerpoint (1475K), movie 1 MPG (304K), movie 2 AVI (236K), notes plain text (1K)
reference to the web site of the Netherlands Institute for Brain Research (NIBR)
Koene, R.A. (1996). The Extraction of Rules from Neural Networks with the Knowledgetron Algorithm. Presented at the Biophysics Meeting of the University of Nijmegen. Nijmegen, Netherlands.
Koene, R.A. (2007). Computational Modeling: Neural Morphogenesis and Network Development. Lecture given at the NEURoVERS-it Workshop on Computational Modeling. Amsterdam, Netherlands.
electronic reprint:
reference to the web site of
Koene, R.A. (2007). Large scale high resolution network generation: Producing known validation sets for serial reconstruction methods that use histological images of neural tissue. Presented at the International Conference on Complex Systems 2007. Boston, MA.
electronic reprint: Powerpoint (?K), PDF (32K)
reference to the web site of the International Conference on Complex Systems 2007.
Koene, R.A. (2007). NETMORPH. Presented at the May 2007 Meeting of the Center for Neurogenomics and Cognitive Research (CNCR). Amsterdam, Netherlands.
electronic reprint: Powerpoint (5676K), PDF (4060K), notes PDF (496K)
reference to the web site of the Center for Neurogenomics and Cognitive Researh
Koene, R.A. and Hasselmo, M.E. (2007). A reversing buffer mechanism that enables instances of retrospective activity in hippocampal regions CA3 and CA1. Presented at the 2007 International Joint Conference on Neural Networks (IJCNN2007). Orlando, FL.
electronic reprint: Powerpoint (952K), PDF (1039K), preprint PDF (642K)
reference to the web site of the 2007 International Joint Conference on Neural Networks.
Koene, R.A. (2007). NETMORPH: Technical. Presented at the Center for Neurogenomics and Cognitive Research (CNCR). Amsterdam, Netherlands.
electronic reprint: Powerpoint (121K)
reference to the web site of the Center for Neurogenomics and Cognitive Researh
Koene, R.A. and Hasselmo, M.E. (2006). Short-term buffers sustained by intrinsic spiking in the entorhinal cortex. Presented at the Computational Cognitive Neuroscience Conference 2006. Houston, TX.
electronic reprint: Powerpoint (???K), abstract PDF (???K), poster PDF (???K)
reference to the web site of the Computational Cognitive Neuroscience Conference
Koene, R.A. (2006). The network generator: NETMORPH present and future. Presented at the October 2006 Meeting of the Computational Analysis of Spatiotemporal Patterns of Activity (CASPAN) Group. Amsterdam, Netherlands.
electronic reprint: Powerpoint (2380K), PDF (3413K)
reference to the web site of the Computational Analysis of Spatiotemporal Patterns of Activity in Neuronal Networks (CASPAN) Group
van Pelt, J., Koene, R.A., van Ooyen, A., Vajda, I., Uylings, H. and Ramakers, G. (2006). Modeling the development of neurons and neuronal networks. Presented at the Modeling the Brain's Labyrinth Meeting (MoBL2006). Fodele Beach (Crete), Greece.
electronic reprint: abstract RTF (18K)
reference to the web site of the 2006 Modeling the Brain's Labyrinth Meeting
van Ooyen, A. and Koene, R.A. (2006). Models of neuronal network development. Presented at the Workshop on Mathematical Models of Development and Learning in the Nervous System. University of Edinburgh, UK.
electronic reprint: [...abstract PDF (?K)...], [...presentation PDF (?K)...], [...Powerpoint (?K)...]
reference to the web site of the 2006 Workshop on Mathematical Models of Development and Learning in the Nervous System
Koene, R.A. and Hasselmo, M.E. (2006). Encoding episodes in a specific temporal context depends on the reduction of interference by extending representations in dentate gyrus. Presented at the Tenth International Conference on Cognitive and Neural Systems (ICCNS2006). Boston, Massachusetts.
electronic reprint: abstract PDF (48K), presentation PDF (301K), Powerpoint (755K), presentation text PDF (87K), explanation PDF (75K)
reference to the web site of the 2006 International Conference on Cognitive and Neural Systems
Koene, R.A. (2005). Simulating fiber direction in culture and cortical layers. Presented at the December 2005 Meeting of the Computational Analysis of Spatiotemporal Patterns of Activity (CASPAN) Group. Amsterdam, Netherlands.
electronic reprint: Powerpoint (9314K), PDF (4168K)
reference to the web site of the Computational Analysis of Spatiotemporal Patterns of Activity in Neuronal Networks (CASPAN) Group
Koene, R.A. and Hasselmo, M.E. (2005). Decision making with an integrate-and-fire model that encodes and retrieves temporal context in hippocampus and dentate gyrus. Presented at the 2005 Annual Meeting of the Society for Neuroscience (author was unable to present).
electronic reprint: abstract PDF (40K) Society for Neuroscience Abstracts, Powerpoint (501K), PDF (1876K)
reference to the web site of the 2005 Annual Meeting of the Society for Neuroscience
Koene, R.A. (2005). Fibre to synapses to connectivity. Presented at the September 2005 Meeting of the Computational Analysis of Spatiotemporal Patterns of Activity (CASPAN) Group. Amsterdam, Netherlands.
electronic reprint: Powerpoint (3703K), PDF (1222K)
reference to the web site of the Computational Analysis of Spatiotemporal Patterns of Activity in Neuronal Networks (CASPAN) Group
Koene, R.A. (2005). Improving Network Generation to Produce Structure that Resembles Data from Culture. Presented at the May 2005 Meeting of the Computational Analysis of Spatiotemporal Patterns of Activity (CASPAN) Group. Amsterdam, Netherlands.
electronic reprint: Powerpoint (8141K)
reference to the web site of the Computational Analysis of Spatiotemporal Patterns of Activity in Neuronal Networks (CASPAN) Group
Koene, R.A. (2005). Simulating Activity in Large Scale Neural Networks with Spatial Detail: A Network Generation Framework. Presented at the February 2005 Meeting of the Computational Analysis of Spatiotemporal Patterns of Activity in Neuronal Networks (CASPAN) Group. Amsterdam, Netherlands.
electronic reprint: compressed presentation PDF (3166K), Powerpoint (4786K)
reference to the web site of the Computational Analysis of Spatiotemporal Patterns of Activity in Neuronal Networks (CASPAN) Group
Koene, R.A. and Hasselmo, M.E. (2004). An integrate and fire model of minicolumns in prefrontal cortex explains selective firing of neurons during goal-directed behavior. Presented at the 2004 Annual Meeting of the Society for Neuroscience.
electronic reprint: abstract PDF (41K) Society for Neuroscience Abstracts, Powerpoint (958K), compressed presentation postscript (1548K), compressed presentation notes postscript (29K), presentation notes PDF (30K)
reference to the web site of the 2004 Annual Meeting of the Society for Neuroscience
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2004). Goal directed behavior guided by the output of a spiking neuron model of prefrontal cortical function. Presented at the Eighth International Conference on Cognitive and Neural Systems (ICCNS2004). Boston, Massachusetts.
electronic reprint: abstract PDF (30K), compressed postscript (-pending-K), Powerpoint (347K)
reference to the web site of the 2004 International Conference on Cognitive and Neural Systems
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2003). Modeling delayed spatial alternation behavior in the rat using a combined model of prefrontal cortex and medial temporal episodic memory function. Presented at the 2003 Annual Meeting of the Society for Neuroscience. 28: 584.9.
electronic reprint: abstract PDF (35K) Society for Neuroscience Abstracts, presentation PDF (269K), compressed presentation postscript (367K), Powerpoint (631K), movie 1 MPG (304K), movie 2 AVI (236K), notes RTF (18K)
reference to the web site of the 2003 Annual Meeting of the Society for Neuroscience
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2003). Goal-directed spatial navigation depends on theta oscillations in hippocampal circuitry. Presented at the International Joint Conference on Neural Networks (IJCNN2003). Portland, Oregon.
electronic reprint: PDF (1014K), Powerpoint file (1012K)
Koene, R.A. (2003). A multi-phase model of relational knowledge acquisition. Presented at the Ph.D. Oral Defense. McGill University, Montreal, Canada.
electronic reprint: Ph.D. Oral Defense Presentation
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2002). Exploring the Virtual Rat I-IV. Presented at Seminars of the Boston University Laboratory of Computational Neurophysiology. Boston, Massachusetts.
electronic reprint: PDF (784K), abstract PDF (342K)
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2002). Simulation of single unit recording data in a neural simulation guiding movement of a virtual rat in a virtual environment. In Proceedings of the 2002 Computational Neuroscience Meeting (CNS*02). Chicago, Illinois.
electronic reprint: PDF (33K), abstract PDF (16K), compressed abstract postscript (12K)
reference to the web site of the 2002 Computational Neuroscience meeting (CNS*02)
Koene, R.A., Takane, Y. and Kiers, H.A.L. (1999). Nonlinear Discriminant Component Pruning of Backpropagation Neural Networks. Presented at the 1999 St.Helene Quantitative Psychology Retreat. St.Helene, QC, Canada.
electronic reprint: compressed postscript (105K)
Koene, R.A. and Takane, Y. (1998). Discriminant Component Pruning: Effective Regularization and Improved Interpretability of Back-propagation Neural Networks. Presented at the Brain, Behavior and Cognitive Science Conference (BBCS1998). Carleton University, Ottawa.
electronic reprint: compressed postscript (90K)
Koene, R.A. (1998). Evaluating the Influence of Implementational Parameters in Networks of Spiking Neurons. Presented at Structural Equation Models. McGill University, Montreal.
electronic reprint: compressed postscript (10K)
Koene, R.A. (1998). Modeling with Spiking Neurons. Presented at the Laboratory for Natural and Simulated Cognition. McGill University, Montreal.
electronic reprint: compressed postscript (18K)
reference to the Laboratory for Natural and Simulated Cognition
Koene, R.A. and Takane, Y. (1997). Disciminant Component Pruning and Network Interpretation. Presented at the Laboratory for Natural and Simulated Cognition. McGill University, Montreal.
electronic reprint: compressed postscript (91K)
reference to the Laboratory for Natural and Simulated Cognition
Koene, R.A. and Takane, Y. (1997). Disciminant Component Pruning. Presented at the Laboratory for Natural and Simulated Cognition. McGill University, Montreal.
electronic reprint: compressed postscript (25K)
reference to the Laboratory for Natural and Simulated Cognition
Koene, R.A. and Hasselmo, M.E. (2007). Biophysical simulation of mechanisms for a persistent firing buffer that is based on intrinsic currents of entorhinal pyramidal cells. Presented at the 2007 Annual Meeting of the Society for Neuroscience.
electronic reprint: abstract PDF (33K) Society for Neuroscience Abstracts, poster PDF (1178K)
reference to the web site of the 2007 Annual Meeting of the Society for Neuroscience
Koene, R.A., van Pelt, J. and van Ooyen, A. (2007). Stochastic neuronal morphogenesis and network development with NETMORPH. Presented at the NWO Computational Life Sciences Meeting 2007. Utrecht, Netherlands.
electronic reprint: poster PDF (3959K), compressed poster PDF (1477K)
reference to the web site of the 2007 Computational Life Sciences (CLS) Meeting of NWO
Koene, R.A and Hasselmo, M.E. (2007). Hippocampal activity may depend on multiple sequence buffers with specific characteristics in layer II of entorhinal cortex. Presented at the Eleventh International Conference on Cognitive and Neural Systems.
electronic reprint: abstract PDF (36K), compressed poster PDF (1477K)
reference to the web site of the 2007 International Conference on Cognitive and Neural Systems
Koene, R.A. and Hasselmo, M.E. (2006). A model of reverse reactivation of episodic activity in the hippocampus during idle awake periods. Presented at the 2006 Annual Meeting of the Society for Neuroscience.
electronic reprint: abstract PDF (33K) Society for Neuroscience Abstracts, poster PDF (1267K), poster references PDF (34K)
reference to the web site of the 2006 Annual Meeting of the Society for Neuroscience
Koene, R.A., Green, N., Ramakers, G., van Pelt, J. and van Ooyen, A. (2006). Scope and resolution, simulating large scale neuronal networks to study the effect of morphological detail on emergent large scale patterns of activity. Presented at the NINDS Neural Interfaces Workshop 2006 (The 37th Annual Neural Prosthesis Workshop). Bethesda, Maryland.
electronic reprint: abstract PDF (38K), poster PDF (365K)
reference to the web site of the 2006 Dutch Endo-Neuro-Psycho Meeting
Koene, R.A and Hasselmo, M.E. (2006). An integrate-and-fire model of temporal context specific episodic encoding and retrieval in the hippocampal formation. Presented at the Computational and Systems Neuroscience (COSYNE) Meeting 2006.
electronic reprint: abstract PDF (55K), compressed poster PDF (667K)
reference to the web site of the 2005 International Conference on Cognitive and Neural Systems
Koene, R.A and Hasselmo, M.E. (2005). An integrate and fire neuron model of short-term memory with ordered replacement of spike patterns. Presented at the Ninth International Conference on Cognitive and Neural Systems.
electronic reprint: abstract PDF (38K), compressed poster PDF (1245K)
reference to the web site of the 2005 International Conference on Cognitive and Neural Systems
Koene, R.A. (2005). An automated method for the generation of connections in a simulated cultured neuronal network with fibre specificity. Presented at the 2005 Computational Life Sciences Meeting of the Netherlands Organization for Scientific Research (NWO). Utrecht, Netherlands.
electronic reprint: poster PDF (619K) compressed flash presentation PDF (306K)
reference to the web site of Computational Life Sciences at NWO
McGaughy, J.A. and Koene, R.A., Eichenbaum, H.B. and Hasselmo, M.E. (2004). Effects of cholinergic deafferentation of prefrontal cortex on working memory: A convergence of behavioral and modeling results. Presented at the 2004 Annual Meeting of the Society for Neuroscience.
electronic reprint: abstract compressed postscript (13K) Society for Neuroscience Abstracts, poster PDF (1828K)
reference to the web site of the 2004 Annual Meeting of the Society for Neuroscience
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2004). Goal directed behavior guided by an integrate and fire model of mechanisms in prefrontal cortex. Presented at the Annual Meeting of the Boston University Center for Memory and Brain.
electronic reprint: poster PDF (525K)
reference to the web site of the 2004 Meeting of the Boston University Center for Memory and Brain
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2003). Three important roles of theta oscillations in a model of goal-directed spatial navigation. Presented at the Seventh International Conference on Cognitive and Neural Systems.
electronic reprint: abstract PDF (36K), compressed poster PDF (426K)
reference to the web site of the 2003 International Conference on Cognitive and Neural Systems
Koene, R.A., Cannon, R.C. and Hasselmo, M.E. (2002). The importance of theta oscillations in rat hippocampal circuitry for goal-directed spatial navigation. Presented at the 2002 Annual Meeting of the Society for Neuroscience.
electronic reprint: abstract PDF (35K) Society for Neuroscience Abstracts, poster PDF (561K)
reference to the web site of the 2002 Annual Meeting of the Society for Neuroscience
Koene, R.A. (2001). Attentional Highlighting and Neuron Recruitment in the Transfer of Memories from Sparse Hippocampal to Dense Neocortical Encoding. Presented at the Fifth International Conference on Cognitive and Neural Systems.
electronic reprint: compressed abstract postscript (12K), compressed poster postscript (88K)
reference to the web site of the 2001 International Conference on Cognitive and Neural Systems
Koene, R.A. (2007). Supplementary materials produced during work on ``NETMORPH: A framework for the stochastic generation of large scale neuronal networks with realistic morphology''. (unpublished supplementary material).
electronic reprint: compressed PDF (331K), [KOE:NETMORPHSUPPLEMENTARY]
source directory: ~/doc/tex/generation-framework
Koene, R.A., Green, N., Ramakers, G., van Pelt, J. and van Ooyen, A. (2007). Reference Paper to: NETMORPH: A framework for the stochastic generation of large scale neuronal networks with realistic morphology. (unpublished).
electronic reprint: reference version (1490K), HTML reference version, [KOE:GENFRAME]
source directory: ~/doc/tex/generation-framework
Koene, R.A. (1998). Meta-Modeling with Structural Equations: Individual Parameter Significance in Spiking Neuron Models. (unpublished manuscript draft).
electronic reprint: compressed postscript (69K)