Publications

Please note: I have not had time to update this page consistently since about mid-2010, so that a number of more recent publications do not yet appear here! I have been adding a few newer ones in a spotty and sporadic manner, which is rather unfortunate. If you are searching for one of my newer publications, check carboncopies.org or please contact me directly. I hope to update this page very soon!
  1. Refereed Journal Articles
  2. Peer Reviewed Articles in Conference Proceedings, Book Chapters and Collections
  3. Dissertations
  4. Invited Talks
  5. Interviews and Appearances
  6. Lectures
  7. Oral Presentations
  8. Poster Presentations
  9. Unpublished Manuscripts

Refereed Journal Articles

Koene, R.A. (2014). Methodical Support for Informational Analysis of Mind: A Review of Igor Aleksander's and Helen Morton's ``Aristotle's Laptop: The Discovery of Our Informational Mind''. International Journal of Machine Consciousness. Vol 6:1, pp.41-43, doi: 10.1142/S179384301440006X
electronic reprint: PDF (68K) 
reference  to the published article at the International Journal of Machine Consciousness

[...SEVERAL MISSING REFERENCES BELONG HERE...]

Koene, R.A. (2012). Fundamentals of Whole Brain Emulation: State, Transition and Update Representations. Special Issue of the International Journal on Machine Consciousness. Vol.4(1), doi: 10.1142/S1793843012500023. 
electronic reprint: PDF (3900K) 
reference to the published article at the International Journal of Machine Consciousness

Koene, R.A. (2012). Experimental Research in Whole Brain Emulation: The Need for Innovative In-Vivo Measurement Techniques. Special Issue of the International Journal on Machine Consciousness. Vol.4(1), doi: 10.1142/S1793843012500047.
electronic reprint: PDF (5700K)
reference to the published article at the International Journal of Machine Consciousness

Koene, R.A., Tijms, B., van Hees, P., Postma, F., de Ridder, S., Ramakers, G., van Pelt, J. and van Ooyen, A. (2009). NETMORPH: A framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics. Vol.7(3), pp.195-210. Neuroinformatics Advanced Access published on August 12, 2009, doi: 10.1007/s12021-009-9052-3.
electronic reprint: PDF (978K)
reference to the published article at the journal Neuroinformatics

Koene, R.A. and Hasselmo, M.E. (2008). Reversed and forward buffering of behavioral spike sequences enables retrospective and prospective retrieval in hippocampal regions CA3 and CA1. Neural Networks. Vol.21(2-3), pp.276-288. Neural Networks Advanced Access published on December 11, 2007, doi:10.1016/j.neunet.2007.12.029.
electronic reprint: PDF (2239K)
DOI reference to the unedited accepted manuscript at Neural Networks

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
Also note Dave Touretsky's reimplementation of our algorithms

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

Peer Reviewed Articles in Conference Proceedings, Book Chapters and Collections

Koene, R.A. (2014). Feasible Mind Uploading. In Intelligence Unbound: The Future of Uploaded and Machine Minds. Eds. Blackford, R. and Broderick, D. Wiley-Blackwell, Oxford, UK. 
electronic reprint: PDF (149K) Original title: System Identification: The foundation of modern science and the core of feasible mind uploading
reference to the carboncopies.org web site of the book Intelligence Unbound: The Future of Uploaded and Machine Minds.

Koene, R.A. (2012). Toward Tractable AGI: Challenges for System Identification in Neural Circuitry. Artificial General Intelligence, Lecture Notes in Computer Science Vol. 7716, pp 136-147. (Proceedings of the 5th International Conference on Artificial General Intelligence (AGI) 2012. Oxford, UK. December 2012.) 
electronic reprint: PDF (934K), presentation slides 
reference to the published article at the journal Lecture Notes in Computer Science
reference to the AGI-12 web site

Koene, R.A. (2012). A Window of Opportunity. In H+ Magazine. May, 2012.
electronic reprint: HTML
reference to the H+ Magazine web site for the article

Koene, R.A. (2012). Embracing competitive balance: The case for substrate-independent minds and whole brain emulation. In The Singularity Hypothesis: A Scientific and Philosophical Assessment. Eds. Eden, A., Søraker, J., Moor, J., and Steinhart, E. Springer, New York, NY. 
electronic reprint: PDF (362K) 
reference to the carboncopies.org web site of the book The Singularity Hypothesis: A Scientific and Philosophical Assessment.

Koene, R.A. (2012). Emulation versus Understanding: A response to Dennis Bray "Brain versus Machine". In The Singularity Hypothesis: A Scientific and Philosophical Assessment. Eds. Eden, A., Søraker, J., Moor, J., and Steinhart, E. Springer, New York, NY.
electronic reprint: PDF (71K)
reference to the carboncopies.org web site of the book The Singularity Hypothesis: A Scientific and Philosophical Assessment.

Koene, R.A. (2011). AGI and Neuroscience: Open Sourcing the Brain. Presented at the Fourth Conference on Artificial General Intelligence (AGI2011). August, 2011. Mountain View, CA.
electronic reprint: PDF (146K)
reference to the web site of the 4th Conference on Artificial General Intelligence (AGI2011).

Koene, R.A. (2011). AGI and Neuroscience: Open Sourcing the Brain. In the Proceedings of the Fourth Conference on Artificial General Intelligence (AGI2011). August, 2011. Mountain View, CA. Reduced version.
electronic reprint: PDF (39K)
reference to the web site of the 4th Conference on Artificial General Intelligence (AGI2011).

Oses, N., Hoffmann, M. and Koene, R.A. (2010). Embodied moving target seeking with prediction and planning. In Proceedings of the 5th International Conference on Hybrid Artificial Intelligence Systems (HAIS2010). June, 2010. San Sebastian, Spain. (submitted)
electronic reprint: (available when accepted) PDF (437K)
reference to the web site of the 5th International Conference on Hybrid Artificial Intelligence Systems (HAIS2010).

Nijboer, F., Hoffmann, U., Morin, F., Carmien, S., Leon, E. and Koene, R.A. (2009). Affective Brain-Computer Interfaces: Psychophysiological Markers of Emotion in Healthy People and People with Amyotrophic Lateral Sclerosis. In Proceedings of the Workshop on Affective Brain-Computer Interfaces & IEEE International Workshop on Social Signal Processing ABCI 2009. Vol.II, pp.1-11.
electronic reprint: PDF (2046K)
reference to the web site of the Workshop on Affective Brain-Computer Interfaces & IEEE International Workshop on Social Signal Processing ABCI 2009.

Carmien, S. and Koene, R.A. (2009). Distributed Intelligence and Scaffolding in Support of Cognitive Health. In Proceedings of the 3rd International Conference on Human-Computer Interaction (HCII 09) in the parallel session 'Cognitive Accessibility and Cognitive Support' in the 5th International Conference on Universal Access in Human-Computer Interaction (UAHCI). Vol.5614, pp.334-343.
electronic reprint: PDF (979K)
reference to the web site of the 3rd International Conference on Human-Computer Interaction (HCII 09).

Carmien, S., Cavallaro, F. and Koene, R.A. (2009). 'Senior Moments': Loss and Context. In Proceedings of the 2nd International Conference on PErvasive Technologies Related to Assistive Environments (PETRA09). Workshop on 'Affect and Behavior Related Assistance in Support for the Elderly'.
electronic reprint: PDF (55K)
reference to the web site of the 2nd International Conference on PErvasive Technologies Related to Assistive Environments (PETRA09).

Koene, R.A. (2009). Assessing the Abstraction Level for Neuroprosthesis: Proposing a Comparison of Functional Simulations in Neuronal Circuitry Generated to Resemble Large-Scale High-Resolution Reconstructions. In NER '09. 4th International IEEE/EMBS Conference on Neural Engineering, pp.92-95, doi: 10.1109/NER.2009.5109242.
electronic reprint: PDF (1069K)
reference to the web site of the NER '09, 4th International IEEE/EMBS Conference on Neural Engineering.

Koene, R.A. and Hasselmo, M.E. (2007). A reversing buffer mechanism that enables instances of retrospective activity in hippocampal regions CA3 and CA1. In Proceedings of the International Joint Conference on Neural Networks (IJCNN2007).
electronic reprint: preprint PDF (642K)
reference to the web site of the 2007 International Joint Conference on Neural Networks.

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)

Dissertations

Koene, R.A. (2001). Functional requirements determine relevant ingredients to model for on-line acquisition of context dependent memory. Ph.D. thesis, McGill Univeristy, Montreal, Canada.
electronic reprint and additional resources: PDF (1879K)

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)

Invited Talks

Koene, R.A. (2012). Machines in Minds to Reverse Engineer the Machine that is Mind. Presented at TEDxTallinn 2012. May, 2012. Tallinn, Estonia.
electronic reprint: Presentation Video + Slides
reference to the web site of TEDxTallinn

Koene, R.A. (2010). Wole Brain Emulation: Issues of scope and resolution, and the need for new methods of in-vivo recording. Presented at the Third Conference on Artificial General Intelligence (AGI2010). March, 2010. Lugano, Switzerland.
electronic reprint: Presentation PDF (1425K)
reference to the web site of the Third Conference on Artificial General Intelligence (AGI2010)

Koene, R.A. (2010). Neural mechanisms of reinforcement learning: How spreading activity in the prefrontal cortex can implement RL for goal-directed tasks. Presented at the Third Conference on Artificial General Intelligence (AGI2010). March, 2010. Lugano, Switzerland.
electronic reprint: Presentation PDF (1281K)
reference to the web site of the Third Conference on Artificial General Intelligence (AGI2010)

Koene, R.A. (2009). The time is now: As a species and as individuals we need whole brain emulation. Presented at the Singularity Summit 2009. October, 2009. New York, NY.
electronic reprint: abstract PDF (64K), Powerpoint (24541K), PDF (8654K), video stream
reference to the web site of the Singularity Summit 2009

Koene, R.A. (2009). From Wheelchairs to Neural Interfaces in a Virtual Brain Laboratory. Presented at the Center for Adaptive Neural Systems Symposium on Co-Adaptive Learning: Adaptive Technology for the Aging (ANS2009). January, 2009. Tempe, AZ.
electronic reprint: Powerpoint presentation (56532K), PDF presentation (3110K)
reference to the web site of the 2009 Symposium of the Center for Adaptive Neural Systems

Koene, R.A. (2008). Assessing the functional significance of errors and omissions by automated network reconstruction in phantom data generated with NETMORPH. Presented at the minisymposium High-Throughput Microscopy and Computational/Theoretical Challenges in the Analysis of Neural Circuit Structure of the 2008 Annual Meeting of the Society for Neuroscience. November, 2008. Washington, D.C.
electronic reprint: lay-language summary PDF (53K), Powerpoint (53390K), PDF (2211K)
reference to the web site of the 2008 Annual Meeting of the Society for Neuroscience
Permanent web site of the SFN2008 minisymposium High-Throughput Microscopy and Computational/Theoretical Challenges in the Analysis of Neural Circuit Structure

Koene, R.A. (2008). 2nd Whole Brain Emulation Social of the Society for Neural Prosthetics and Whole Brain Emulation Science. Presented at the InnerSpace Foundation Satellite Symposium at {SFN2008}. November, 2008. Washington, D.C.
electronic reprint: Powerpoint (2473K), PDF (528K)
reference to the web site of the 2008 Annual Meeting of the Society for Neuroscience

Koene, R.A. (2008). Neuroengineering: An intimate communication with the brain. Presented at the Fatronik - University of Tubingen Research Retreat. July, 2008. Fatronik. San Sebastian, Spain.
electronic reprint: compressed archive (4698K), AVI movie (42142K), AVI movie (1773K), Word File (364K)
reference to the web site of Fatronik, reference to the web site of the University of Tubingen

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 Navarre (CIMA). January, 2008. Pamplona, 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), video stream
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.

Interviews and Appearances


Koene, R.A. interviewed by Kruel, A. (2013). Randal Koene On Cryonics. Kruel.Co, January 16, 2013.
electronic reprint: PDF (316K)
reference to the web site of the article at Kruel.Co.


Koene, R.A. interviewed by Goertzel, B. (2011). Randal Koene on Substrate-Independent Minds. H+ Magazine. August 31, 2011.
electronic reprint: PDF (1251K)
reference to the web site of hplusmagazine.com.

Koene, R.A. (2011). Achieving substrate-independent minds: no, we cannot 'copy' brains. KurzweilAI.net. 24 August, 2011.
electronic reprint: PDF (999K)
reference to the web site of the article at KurzweilAI.net.

Koene, R.A. interviewed by Olson, S. (2011). Are substrate-independent minds possible? NextBigFuture.com. August 22, 2011.
electronic reprint: PDF (2067K)
reference to the web site of NextBigFuture.com

Koene, R.A. (2011). Pattern survival versus Gene survival. KurzweilAI.net. 11 February, 2011.
electronic reprint: PDF (152K)
reference to the web site of the article at KurzweilAI.net.

Koene, R.A. appearance in article by Halpern, D. (2009). About the Singularity. GQ Magazine. New York, NY.
reference to the web site of GQ Magazine

Koene, R.A. interviewed by Loew, J. (2009). All about neural prostheses, mind uploading, and brain emulation. Sunday Evening Update of ImmInst.org. October 25, 2009.
electronic reprint: video stream
reference to the web site of ImmInst.org

Koene, R.A. appearance in article by Rein, L. (2009). Singularity Summit - Anders Sandberg and Randal Koene On Whole Brain Emulation. H+ Magazine, Editor's Blog. San Jose, CA.
electronic reprint: PDF (165K)
reference to the web site of the article in the H+ Magazine Editor's Blog

Koene, R.A. interviewed by Orban, D. (2009). Randal Koene on Whole Brain Emulation. DavidOrban.com.
electronic reprint: video stream
reference to the web site of DavidOrban.com

Koene, R.A. interviewed (2009). About the Department of Neuroengineering in the Health Unit of the Tecnalia Research Centers. La Razon (newspaper, Spanish). Madrid, Spain.
reference to the web site of La Razon

Koene, R.A. interviewed by Zucca, K. (1997). Losing your mind? Upload your brain and gain eternal life. The Link (newspaper). Montreal: Concordia University.
electronic reprint: PDF (88K)
reference to the web site of The Link

Koene, R.A. interviewed by Mesley, W. and Harbron, A. (1996). Wired Flesh. Undercurrents on CBC Television. November 29, 1996. Montreal, Canada.
reference to the web site of Undercurrents on CBC Television

Lectures

Koene, R.A. (2007). Introduction to Cognitive Psychology. Lecture series given in course CAS PS336 in Fall 2007 at Boston University. Boston, MA.
electronic reprint:
reference to the web site of CAS PS336 Introduction to Cognitive Psychology Fall 2007 on Boston University CourseInfo

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

Oral Presentations

Koene, R.A. (2009). Obtaining in-vivo dynamic state and post-mortem neuronal circuit structure at large scale and high resolution. Presented at the Thirteenth International Conference on Cognitive and Neural Systems (ICCNS2009). Boston, MA.
electronic reprint: abstract PDF (46K), Powerpoint (53546K), PDF (1767K)
reference to the web site of the Thirteenth International Conference on Cognitive and Neural Systems (ICCNS2009).

Koene, R.A., Postma, F., van Pelt, J. and van Ooyen, A. (2008). Stochastic generation of large scale neuronal networks for the study of structural change in neuronal cell cultures and slice. Presented at the July 2008, Review Meeting of Neurovers-IT (Marie-Curie Program). Amsterdam, Netherlands.
electronic reprint: Powerpoint (27671K), PDF (5911K), presentation notes PDF (1847K)
reference to the web site of Neurovers-IT

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 (14801K), 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

Poster Presentations

Koene, R.A. (2009). Neuroprosthetic emulation: What data is needed to replicate accurate personal brain function? Presented at the 2009 Annual Meeting of the Society for Neuroscience. 2009 Neuroscience Meeting Planner. Program No. 389.13. Chicago, IL: Society for Neuroscience, 2009. Online.
electronic reprint: abstract PDF (152K) Society for Neuroscience Abstracts
reference to the web site of the 2009 Annual Meeting of the Society for Neuroscience

Estep, P. and Koene, R.A. (2009). The roles of real-world corroborative audiovisual data in brain reverse engineering. Presented at the 2009 Annual Meeting of the Society for Neuroscience. 2009 Neuroscience Meeting Planner. Program No. 389.11. Chicago, IL: Society for Neuroscience, 2009. Online.
electronic reprint: abstract PDF (154K) Society for Neuroscience Abstracts
reference to the web site of the 2009 Annual Meeting of the Society for Neuroscience

Nijboer, F., Halder, S., Furdea, S.A., Kleih, S.C., Koene, R.A. and Kubler, A. (2009). The effect of monetary reward and stimulus modality on motivation and performance in a Brain-Computer Interface paradigm based on event-related potentials. Presented at the 2009 Annual Meeting of the Society for Neuroscience. 2009 Neuroscience Meeting Planner. Program No. 289.14. Chicago, IL: Society for Neuroscience, 2009. Online.
electronic reprint: abstract PDF (158K) Society for Neuroscience Abstracts
reference to the web site of the 2009 Annual Meeting of the Society for Neuroscience

Koene, R.A. (2009). Using NETMORPH tools to teach neural and brain development. Presented at the 2009 Annual Meeting of the Society for Neuroscience. 2009 Neuroscience Meeting Planner. Program No. 23.13. Chicago, IL: Society for Neuroscience, 2009. Online.
electronic reprint: abstract PDF (152K) Society for Neuroscience Abstracts
reference to the web site of the 2009 Annual Meeting of the Society for Neuroscience

Koene, R.A. (2009). Toward a Virtual Brain Laboratory: Applications of NETMORPH. Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics. Doi: 10.3389/conf.neuro.11.2009.08.107. Demo. Pilsen, Czech Republic.
electronic reprint: abstract PDF (285K)
reference to the web site of the 2nd INCF Congress of Neuroinformatics

van Pelt, J., de Ridder, S., Hoedemaker, S., Postma, F., Koene, R. and van Ooyen, A. (2009). Emerging synaptic connectivity in simulated networks of outgrowing neurons with realistic morphologies using NETMORPH. Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics. Doi: 10.3389/conf.neuro.11.2009.08.040. Pilsen, Czech Republic.
electronic reprint: abstract PDF (285K)
reference to the web site of the 2nd INCF Congress of Neuroinformatics

de Ridder, A., van Ooyen, A., Postma, F., Hoedemaker, S., Koene, R.A. and van Pelt, J. (2009). Simulated Networks with Realistic Neuronal Morphologies show Small-World Connectivity. BMC Neuroscience, Proceedings of the Eighteenth Annual Computational Neuroscience Meeting CNS*2009. Vol. 10(supp.1), P5, Paper no.196. Berlin, Germany.
electronic reprint: abstract PDF (546K), preprint PDF (319K)
reference to the web site of the Eighteenth Annual Computational Neuroscience Meeting CNS*2009

Koene, R.A. (2009). Neuroengineering in alzheimer's disease research: using a virtual brain laboratory. Presented at the Alzheimer's Association 2009 International Conference on Alzheimer's Disease (ICAD2009). Vienna, Austria.
electronic reprint: abstract PDF (72K), poster PDF (1377K)
reference to the web site of the Alzheimer's Association 2009 International Conference on Alzheimer's Disease (ICAD2009)

Koene, R.A. (2009). Creating a Culture of Cognitive Health. Presented at the 31st Annual Conference of the Cognitive Science Society. Amsterdam, The Netherlands.
electronic reprint: abstract PDF (86K)
reference to the web site of the 31st Annual Conference of the Cognitive Science Society

Koene, R.A. and Hasselmo, M.E. (2008). One-shot method of buffering novel spatial content that enables sweeps at choice points during reward-directed navigation. Presented at the 2008 Annual Meeting of the Society for Neuroscience. Washington, DC.
electronic reprint: abstract PDF (34K) Society for Neuroscience Abstracts, poster PDF (696K)
reference to the web site of the 2008 Annual Meeting of the Society for Neuroscience

Postma, F., Koene, R.A., van Pelt, J. and van Ooyen, A. (2008). NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic morphology. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.089. INCF. Stockholm, Sweden.
electronic reprint: abstract PDF (78K), poster PDF (?K)
reference to the web site of the 2008 INCF Congress on Neuroinformatics

Koene, R.A., van Pelt, J. and van Ooyen, A. (2008). Stochastic generation and analysis of large scale neuronal networks with realistic morphology using NETMORPH. Presented at the 6th FENS Forum of European Neuroscience. Geneva, Switzerland.
electronic reprint: abstract PDF (36K), poster PDF (14093K)
reference to the web site of the 2008 FENS Forum of European Neuroscience

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. San Diego, CA.
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

Unpublished Manuscripts

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)

Subpages (1): publications