Journal Articles

J. M. Nagarah and D. A. Wagenaar, 2012. Ultradeep fused silica glass etching with an HF-resistant photosensitive resist for optical imaging applications. J. Micromech. Microeng. 22(3), 035011. AbstractPreprint (pdf)GScholar

D. A. Wagenaar, 2012. An optically stabilized fast-switching light emitting diode as a light source for functional neuroimaging. PLoS ONE 7(1), e29822. AbstractFull text (pdf)PubMedGScholar

C. M. Harley, J. Cienfuegos, and D. A. Wagenaar, 2011. Developmentally regulated multisensory integration for prey localization in the medicinal leech. J. Exp. Biol. 214, 3801–3807. AbstractFull text (pdf)Supplemental material (pdf)PubMedGScholar
(JEB featured this work in this News-and-Views article by Kathryn Knight in the same issue of the journal.)

D. A. Wagenaar, R. Gonzalez, D. C. Ries, W. B. Kristan, and K. A. French, 2010. Alpha-conotoxin ImI disrupts central control of swimming in the medicinal leech. Neurosci. Lett. 485, 151–156. AbstractPreprint (pdf)Supplemental material (pdf)PubMedGScholar

D. A. Wagenaar, M. S. Hamilton, T. Huang, W. B. Kristan, and K. A. French, 2010. A hormone-activated central pattern generator for courtship. Curr. Biol. 20(6), 487–495. AbstractPreprint (pdf)Movie S2Movie S1PubMedGScholar
(Kevin Crisp reviewed this work in this News-and-Views article in the same issue of the journal.)

D. A. Wagenaar and W. B. Kristan, 2010. Automated video analysis of animal movements using Gabor orientation filters. Neuroinform. 8(1), 33–42. AbstractFull text (pdf)PubMedGScholar

S. M. Baca*, A. Marin-Burgin*, D. A. Wagenaar*, and W. B. Kristan, 2008. Widespread inhibition proportional to excitation controls the gain of a leech behavioral circuit. Neuron 57(2), 276–289. AbstractPreprint (pdf)PubMedGScholar

D. L. Fortin, M. R. Banghart, T. W. Dunn, K. Borges, D. A. Wagenaar, Q. Gaudry, M. H. Karakossian, T. S. Otis, W. B. Kristan, D. Trauner, and R. H. Kramer, 2008. Photochemical control of endogenous ion channels and cellular excitability. Nat. Methods 5(4), 331–338. AbstractPreprint (pdf)PubMedGScholar

J. D. Rolston, D. A. Wagenaar, and S. M. Potter, 2007. Precisely timed spatiotemporal patterns of neural activity in dissociated cortical cultures. Neurosci. 148(1), 294–303. AbstractPubMedGScholar

D. A. Wagenaar, Z. Nadasdy, and S. M. Potter, 2006. Persistent dynamic attractors in activity patterns of cultured neuronal networks. Phys. Rev. E 73, art. no. 051907. AbstractPreprint (pdf)PubMedGScholar

D. A. Wagenaar, J. Pine, and S. M. Potter, 2006. An extremely rich repertoire of bursting patterns during the development of cortical cultures. BMC Neurosci. 7, art. no. 11. AbstractPreprint (pdf)PubMedGScholar

D. A. Wagenaar, J. Pine, and S. M. Potter, 2006. Searching for plasticity in dissociated cortical cultures on multi-electrode arrays. J. Negat. Results BioMed. 5, art. no. 16. AbstractCorrected version (pdf)PubMedGScholar

Z. C. Chow, D. J. Bakkum, D. A. Wagenaar, and S. M. Potter, 2005. Effects of random external background stimulation on network synaptic stability after tetanization: a modeling study. Neuroinform. 3(3), 263–280. AbstractPubMedGScholar

C. Fonck, B. N. Cohen, R. Nashmi, P. Whiteaker, D. A. Wagenaar, N. Rodrigues-Pinguet, P. Deshpande, S. McKinney, S. Kwoh, J. Munoz, C. Labarca, A. C. Collins, M. J. Marks, and H. A. Lester, 2005. Novel seizure phenotype and sleep disruptions in knock-in mice with hypersensitive α4* nicotinic receptors. J. Neurosci. 25(49), 11396–11411. AbstractPubMedGScholar

D. A. Wagenaar, R. Madhavan, J. Pine, and S. M. Potter, 2005. Controlling bursting in cortical cultures with closed-loop multi-electrode stimulation. J. Neurosci. 25(3), 680–688. AbstractPreprint (pdf)PubMedGScholar
(The Economist featured this work in this article on February 5, 2005.)

D. A. Wagenaar and C. Adami, 2004. Influence of chance, history, and adaptation on digital evolution. Artif. Life 10(2), 181–190. AbstractPubMedGScholar

D. A. Wagenaar and S. M. Potter, 2004. A versatile all-channel stimulator for electrode arrays, with real-time control. J. Neural Eng. 1, 39–44. AbstractFull text (pdf)PubMedGScholarPCB layout and code available on request.

D. A. Wagenaar, J. Pine, and S. M. Potter, 2004. Effective parameters for stimulation of dissociated cultures using multi-electrode arrays. J. Neurosci. Methods 138(1–2), 27–37. AbstractPreprint (pdf)PubMedGScholar

D. A. Wagenaar and S. M. Potter, 2002. Real-time multi-channel stimulus artifact suppression by local curve fitting. J. Neurosci. Methods 120, 113–120. AbstractPreprint (pdf)PubMedGScholarCode available on request.

T. B. DeMarse, D. A. Wagenaar, A. W. Blau, and S. M. Potter, 2001. The neurally controlled animat: Biological brains acting with simulated bodies. Auton. Robots 11(3), 305–310. AbstractPubMedGScholar

* These three authors contributed equally to this work. [back]

Book Chapters

S. M. Potter, D. A. Wagenaar, and T. B. DeMarse, 2006. Closing the loop: Stimulation feedback systems for embodied MEA cultures. In: Advances in network electrophysiology using multi-electrode arrays, M. Taketani and M. Baudry, eds., Kluwer, New York. Preprint (pdf)GScholar

Conference Proceedings

R. Madhavan, Z. C. Chao, D. A. Wagenaar, and S. M. Potter, 2006. Multi-site stimulation quiets network-wide spontaneous bursts and enhances functional plasticity in cultured cortical networks. Conf. Proc. IEEE Eng. Med. Biol. Soc., 1593-1596. AbstractGScholar

D. A. Wagenaar, T. B. DeMarse, and S. M. Potter, 2005. MEABench: A toolset for multi-electrode data acquisition and on-line analysis. Proc. 2nd Int. IEEE EMBS Conf. Neural Eng., M. Akay, L. J. Wolf, and J. Stock, eds., 518–521. AbstractPreprint (pdf)GScholar

S. M. Potter, T. B. DeMarse, D. J. Bakkum, M. C. Booth, J. R. Brumfield, Z. C. Chao, R. Madhavan, P. A. Passaro, K. Rambani, A. C. Shkolnik, R. B. Towal, and D. A. Wagenaar, 2004. Hybrots: hybrids of living neurons and robots for studying neural computation. Proc. Brain Inspired Cognitive Systems, 1094-1099. AbstractGScholar

S. M. Potter, T. B. DeMarse, A. W. Blau, and D. A. Wagenaar, 2003. Multi-photon time-lapse microscopy and optical recording to study neural processing and plasticity. Microsc. Microanal. 9(S2), 184–185. Preprint (pdf)GScholar

D. A. Wagenaar and C. Adami, 2000. Influence of chance, history and adaptation on evolution in Digitalia. Proc. Alife 7, 216–220. AbstractPreprint (pdf)GScholar

Poster Abstracts

C. M. Harley, J. M. Nagarah, J. Cienfuegos, M. Rossi, and D. A. Wagenaar. Multisensory integration underlying host detection in the medicinal leech. 41st Annual Meeting of the Society for Neuroscience, Washington, DC, November 2011. AbstractGScholar

P. H. Siegel, V. Pikov, S. Romenenko, and D. A. Wagenaar. Neuronal responses to low-power millimeter waves. Air Force Office of Scientific Research Workshop on Photo-Electric-Magnetic Bio-stimulation, San Antonio, TX, November 2011. AbstractGScholar

C. M. Harley and D. A. Wagenaar. Finding the right food: Developmental regulation of prey sensing. Flow Sensing in Air and Water, Bonn, Germany, July 2011. AbstractGScholar

J. M. Nagarah, P. L. Baljon, and D. A. Wagenaar. Multisuction electrode arrays to investigate multi-sensory integration in neural tissue. 55th Annual Meeting of the Biophysical Society, Baltimore, MD, March 2011. AbstractGScholar

P. L. Baljon, D. A. Wagenaar, and S. Martinoia. Interactions of electrically evoked responses in dissociated cortical cultures. 40th Annual Meeting of the Society for Neuroscience, San Diego, CA, November 2010. AbstractGScholar

C. M. Harley, J. Cienfuegos, and D. A. Wagenaar. Frequency dependence of behavioral responses to prey in the medicinal leech. 40th Annual Meeting of the Society for Neuroscience, San Diego, CA, November 2010. AbstractGScholar

J. M. Nagarah, P. L. Baljon, and D. A. Wagenaar. Transparent multi-suction electrode arrays for simultaneous electrophysiology and voltage sensitive dye measurements. 40th Annual Meeting of the Society for Neuroscience, San Diego, CA, November 2010. AbstractGScholar

C. M. Harley and D. A. Wagenaar. Frequency dependence of prey localization responses in the leech Hirudo medicinalis during different life stages. 9th International Congress on Neuroethology, Salamanca, Spain, August 2010. AbstractGScholar

P. L. Baljon, J. Nagarah, and D. A. Wagenaar. Combining MEA and VSD to study cells in a pattern generator. Substrate-Integrated Microelectrode Arrays, Reutlingen, Germany, July 2010. AbstractGScholar

J. Nagarah, P. L. Baljon, and D. A. Wagenaar. Transparent multisuction electrode arrays for tissue immobilization and simultaneous MEA and VSD measurements. Substrate-Integrated Microelectrode Arrays, Reutlingen, Germany, July 2010. AbstractGScholar

D. A. Wagenaar, J. Nagarah, P. L. Baljon, and C. M. Harley. Toward panneuronal recording of multisensory information processing in the medicinal leech. Substrate-Integrated Microelectrode Arrays, Reutlingen, Germany, July 2010. AbstractGScholar

J. M. Nagarah, D. A. Wagenaar, and J. R. Heath. Planar patch-clamp electrodes for single cell and neural network studies. 54th Annual Meeting of the Biophysical Society, San Francisco, CA, February 2010. AbstractGScholar

D. A. Wagenaar, M. S. Hamilton, T. Huang, W. B. Kristan, and K. A. French. Neuronal control of motor behavior associated with reproduction in the medicinal leech. 38th Annual Meeting of the Society for Neuroscience, Washington, DC, 2008. Prog. no. 491.11. AbstractGScholar

D. A. Wagenaar, S. M. Baca, A. Marin-Burgin, and W. B. Kristan. Role of inhibition in the local bend response of the medicinal leech. Eighth International Congress of Neuroethology, Vancouver, Canada, 2007. Prog. no. PO226. AbstractGScholar

D. A. Wagenaar, S. M. Baca, A. Marin-Burgin, and W. B. Kristan. Inhibition helps shape the spatial and temporal profiles of the local bend response of the medicinal leech. 37th Annual Meeting of the Society for Neuroscience, San Diego, CA, 2007. Prog. no. 312.10. AbstractGScholar

Z. C. Chao, D. J. Bakkum, D. A. Wagenaar, and S. M. Potter. Network plasticity in simulated and living cortical networks: comparison of the Center of Activity Trajectory (CAT) with other metrics. Substrate-Integrated Micro-Electrode Arrays, Reutlingen, Germany, July 2006. AbstractGScholar

D. A. Wagenaar, J. Pine, and S. M. Potter. Large database of spontaneous and evoked activity patterns in developing networks. Substrate-Integrated Micro-Electrode Arrays, Reutlingen, Germany, July 2006. AbstractGScholar

J. D. Rolston, D. A. Wagenaar, and S. M. Potter. Precisely timed spatiotemporal patterns of neural activity in dissociated cortical cultures. 36th Annual Meeting of the Society for Neuroscience, Atlanta, GA, 2006. Prog. no. 432.11. AbstractGScholar

D. A. Wagenaar, R. Gonzalez, K. A. French, and W. B. Kristan. Alpha-conotoxin Im1 makes leeches swim erratically. 36th Annual Meeting of the Society for Neuroscience, Atlanta, GA, 2006. Prog. no. 253.2. AbstractGScholar

D. A. Wagenaar, T. Huang, W. B. Kristan, and K. A. French. A snail’s approach to leech reproduction. 36th Annual Meeting of the Society for Neuroscience, Atlanta, GA, 2006. Prog. no. 259.8. AbstractGScholar

D. J. Bakkum, Z. C. Chao, D. A. Wagenaar, and S. M. Potter. Self-regulation and electrically evoked precisely timed cortical culture activity as a means to control a hybrot. 35th Annual Meeting of the Society for Neuroscience, Washington, DC, 2005. Prog. no. 276.19. AbstractGScholar

D. A. Wagenaar, J. Pine, and S. M. Potter. Cortical cultures exhibit an extremely rich repertoire of bursting patterns. 35th Annual Meeting of the Society for Neuroscience, Washington, DC, 2005. Prog. no. 249.14. AbstractGScholar

D. A. Wagenaar, R. Madhavan, J. Pine, and S. M. Potter. Multi-site stimulation for controlling bursting in cortical ensembles. NIH Workshop on Neural Interfaces, Bethesda, MD, Nov 15–17, 2004. AbstractGScholar

D. A. Wagenaar, J. Pine, and S. M. Potter. Control of bursting in neuronal ensembles by closed-loop control of tonic firing rates. Dynamical Neuroscience XII (“Closing the loop”), satellite at 34th Annual Meeting of the Society for Neuroscience, San Diego, CA, Oct 21–22, 2004. AbstractGScholar

D. A. Wagenaar, H. Glidden, S. M. Potter, and J. Pine. Waking up dissociated cultures of cortical neurons by substituting cholinergic afferents. FENS Forum, Lisbon, July 2004. AbstractGScholar

D. A. Wagenaar, S. M. Potter, and J. Pine. Real-time bidirectional communication with neuronal cultures. Substrate-Integrated Micro-Electrode Arrays, Reutlingen, Germany, July 2004. AbstractGScholar

R. Madhavan, D. A. Wagenaar, Z. C. Chow, and S. M. Potter. Control of bursting in dissociated cortical cultures on multi-electrode arrays. Substrate-Integrated Micro-Electrode Arrays, Denton, TX, 2003. Abstract (pdf)GScholar

R. Madhavan, D. A. Wagenaar, and S. M. Potter. Multi-site stimulation quiets bursts and enhances plasticity in cultured networks. 33rd Annual Meeting of the Society for Neuroscience, New Orleans, LA, 2003. AbstractGScholar

Z. Nadasdy, D. A. Wagenaar, and S. M. Potter. Attractor dynamics of superbursts in living neural networks. 33rd Annual Meeting of the Society for Neuroscience, New Orleans, LA, 2003. AbstractGScholar

S. M. Potter, D. A. Wagenaar, R. Madhavan, and T. B. DeMarse. Long-term bidirectional neuron interfaces for robotic control and in vitro learning studies. 25th Annual International Conference of IEEE EMBS, Cancun, Mexico, 2003. AbstractGScholar

D. A. Wagenaar, R. Madhavan, and S. M. Potter. Stimulating news for MEA enthusiasts. Substrate-Integrated Micro-Electrode Arrays, Denton, TX, 2003. Abstract (pdf)GScholar

D. A. Wagenaar, J. Pine, and S. M. Potter. Parameters for voltage- and current-controlled stimulation of cortical cultures through multi-electrode arrays. 33rd Annual Meeting of the Society for Neuroscience, New Orleans, LA, 2003. AbstractGScholar

T. B. DeMarse, D. A. Wagenaar, and S. M. Potter. The neurally-controlled artificial animal: a neural-computer interface between cultured neural networks and a robotic body. 32nd Annual Meeting of the Society for Neuroscience, Orlando, FL, 2002. AbstractGScholar

Z. Nadasdy, R. Quian Quiroga, Y. Ben-Shaul, B. Pesaran, D. A. Wagenaar, and R. Andersen. Comparison of unsupervised algorithms for on-line and off-line spike sorting. 32nd Annual Meeting of the Society for Neuroscience, Orlando, FL, 2002. AbstractGScholar

D. A. Wagenaar, T. B. DeMarse, J. Pine, and S. M. Potter. Precise timing in early response to electric stimulation in dense cultures of cortical neurons. Proc. Mathematics in Molecular Biology, Santa Fe, NM, 2002. AbstractGScholar

D. A. Wagenaar, T. B. DeMarse, and S. M. Potter. Response properties of cultured cortical networks as a substrate for the study of learning in vitro. Int. Conf. Cognitive and Neural Systems, Boston University, Boston, MA, 2002. AbstractGScholar

D. A. Wagenaar, T. B. DeMarse, J. Pine, and S. M. Potter. Development of complex activity patterns in cortical networks cultured on multi-electrode arrays. 31st Annual Meeting of the Society for Neuroscience, San Diego, CA, 2001. AbstractGScholar

D. A. Wagenaar, T. B. DeMarse, and S. M. Potter. A toolset for realtime analysis of network dynamics in dense cultures of cortical neurons. 7th Joint Symposium on Neural Computation, University of California at San Diego, La Jolla, CA, 2001. AbstractGScholar

T. B. DeMarse, D. A. Wagenaar, A. W. Blau, and S. M. Potter. Neurally controlled computer-simulated animals: a new tool for studying learning and memory in vitro. 30th Annual Meeting of the Society for Neuroscience, New Orleans, LA, 2000. Prog. No. 467.20. AbstractGScholar

T. B. DeMarse, D. A. Wagenaar, A. W. Blau, and S. M. Potter. Interfacing neuronal cultures to a computer generated virtual world. 6th Joint Symposium on Neural Computation, University of Southern California, Los Angeles, CA, 2000. AbstractGScholar

PhD Thesis

Development and control of epileptiform bursting in dissociated cortical cultures. California Institute of Technology, defended June 21st, 2005. AbstractFull text (pdf)Supplemental movieGScholar

Master’s Theses

Training Kanter’s bit generator by natural gradient descent. Dept. of Mathematics, King’s College London, 1998. AbstractFull text (pdf)GScholar

Particles in string theory. Dept. of Physics, University of Amsterdam, 1997. AbstractFull text (pdf)GScholar

Other Writing

Cortical stimulation for the evocation of visual perception. Term paper for CNS247: Cerebral cortex, class by R. Andersen, Caltech, 2004. Full text (pdf)GScholar

Review of prototype of new MEAs from MultiChannel Systems. Email to “MEA users” group, February 2003. Full textGScholar

Navigating a 2D world using a 1D compound eye. Term project for CNS186: Vision, class by C. Koch, P. Perona, and S. Shimojo, Caltech, 2002. Full text (pdf)GScholar

Can patterned external input carve out patterned functional neuronal networks in vitro? Research proposal, Caltech, 2002. Full text (pdf)GScholar

Sensitivity of cortical cells to precisely timed paired pulse stimulation in culture. Research proposal, Caltech, 2002. Full text (pdf)GScholar

Information routing by visual attention in striate and extrastriate cortex. Term project for CNS 120: Neural basis of consciousness, class by C. Koch, Caltech, 2001. Full text (pdf)GScholar

Use of information theory in studies of efficiency of cortical coding of natural stimuli. Term project for Ph/Bi 103b: Introduction to neuroscience for physicists and engineers, class by J. Pine, Caltech, 2000. Full text (pdf)GScholar

FSMEM for MoG. Term project for CS/CNS/EE 156b: Learning systems, class by P. Perona and M. Welling, Caltech, 2000. Full text (pdf)GScholar

Information geometry for neural networks. Term paper for reading course with A. C. C. Coolen, King’s College London, 1998. AbstractFull text (pdf)GScholar

D. Bourilkov and D. A. Wagenaar. The resolution of the L3 TEC after the calibration using the SMD. L3 technical note 1871, CERN, Geneva, 1995. AbstractFull text (pdf)GScholar

 


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