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   Bakkum, Douglas J., Dr.

Member of D-BSSE

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  • Dr. Douglas Bakkum

  • ETH Zurich, D-BSSE
    Bio Engineering Laboratory (BEL)
    Office: 3.62
    Mattenstrasse 26
    CH-4058 Basel, SWITZERLAND


The mind has always been a great fascination, and I have been pursuing its study currently in the Bio Engineering Lab (BEL) at ETH Zurich, and formerly in the Kanzaki-Takahashi laboratory, in the Graduate School of Information Science and Technology at the University of Tokyo, and as a doctoral student in the Potter Lab, a part of the Neurolab in the joint department of Bioengineering between Emory University and Georgia Institute of Technology. I have had sojourns to earn Bachelor and Master degrees in Mechanical Engineering, a certificate in Cognitive Science, and graduate research in Robotics and Artificial Intelligence. I now culture cortical neurons over 11,011-electrode CMOS arrays and seek how rules of neural network communication can scale to produce cognition: learning, memory, and creativity.

 
 
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Research highlights

Background on cultured neurons

Code

Curriculum Vitae

  Education
Experience
Publications
Conferences
Art exhibitions
Honors
 
   
   
   
   
   
   
   
   
   

 

Research highlights

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  11,011-electrode high-density CMOS array

[pdf article]

The brain's unique cognitive abilities are thought to emerge from the processing of information by networks of neurons. To better study such networks, multi-electrode arrays were developed. However, due to the limited number and location of electrodes, only a small subset of neurons could be accessed.

To address these limitations, the BEL lab developed a CMOS circuit containing 11,011 electrodes within a 3.4mm2 area. Its high resolution means that any neuron growing above the array can be stimulated or have its activity recorded. This unprecedented level of access is expected to provide a wealth of novel data to advance our basic understanding of how neurons and networks function and contribute to the brain's capabilities.

colorMEA_combined
 

Plasticity of action potential propagation

[online article]

The neural orchestra is comprised of not only synapses but many instruments, in part tuned by propagation plasticity. From the viewpoint of a neuron, the specific timings of afferent input from the action potentials of its synaptic partners determines whether or not and when that neuron will fire its own action potential. Tuning such input provides a powerful mechanism to adjust neuron function and in turn, that of the brain. However, axons in the mammalian cortex have traditionally been regarded as stable transmission cables. This view is more likely due to a lack of, rather than support from, experimental evidence because their small diameter (<1um) makes direct recordings at multiple sites difficult.

By using an MEA to robustly detect and track changes in the propagation of electrically evoked action potentials, we found that variation of a simple stimulation pattern modulated action potential propagation. Even though the induction of plasticity depended on synaptically evoked action potentials, its expression was non-synaptic: action potential propagation. Propagation varied for different stimulation patterns and became more stable for unvarying patterns, attributes necessary for playing a role in encoding memories. Latencies and amplitudes increased and decreased in an un-correlated manner, potentially allowing a neuron to have variable synaptic transmission among multiple post-synaptic neurons. The results suggest that propagation plasticity could serve as a cellular mechanism to tune temporal coding schemes and information processing in neural networks and potentially learning and memory in the brain.

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  Adaptive goal-directed behavior

[pdf article]

An adaptive training algorithm was developed, whereby a neocortical network learned to modulate its dynamics and achieve pre-determined activity states within tens of minutes through the application of patterned training stimuli using a multi-electrode array. A priori knowledge of functional connectivity was not necessary. Instead, effective training sequences were continuously discovered and refined based on real-time feedback of performance. The short-term neural dynamics in response to training became engraved in the network, requiring progressively fewer training stimuli to achieve successful behavior in a movement task. Interestingly, a given sequence of effective training stimuli did not induce significant plasticity, let alone desired behavior, when replayed to the network and no longer contingent on feedback.

For neurological disorders, targeted distributed artificial stimulation of the brain contingent on the activity of the body or even of the brain itself could direct neuronal plasticity to bypass or accommodate aberrant neuronal activity, for example that occurring after a stroke. Our results encourage further in vitro and in vivo investigations of applications for neuro-rehabilitation.

MEA-aRT2
  Meart  -  An art science collaboration

[online article]
[homepage]

Art and Science !?!

Electrical activity from rat neurons cultured in a glass dish commanded the movement of a robotic drawing arm, and images of the drawing commanded electrical stimulation fed back to the neurons. The feedback changed the neural activity, in turn changing the drawing and subsequent feedback, creating a closed-loop behaving bio-robotic system called Meart.

Meart examines the consequences of melding technology and biology. What forms of intelligence can emerge from rat neurons connected to a mechanical body? Can Meart learn and remember? Is Meart's drawing a product of creativity, a work of art? Is art exclusively a human endeavor? What are the implications for the internet and technology to expand our cognition? This question is dramatically framed by Meart's physical separation of brain and body, often located in different continents. Meart has performed at galleries throughout the world, providing a forum to educate the public in biological sciences and raise ethical discussions on the body and the individual.

 
 
 

Background on cultured neurons


When I first started my PhD I was fascinated that even left to themselves save for food and shelter, the thousands of neurons in a culture spontaneously grow and branch out and reach for their neighbors. They have an inherent drive to form networks and begin communicating with each other, self-organizing both functionally and morphologically. Early in my PhD, I made this time-lapse movie of neurons and glia growing from day 1 to day 6 over an MEA. Axons and dendrites branch out; neurons and especially glia, which have a 'flatter' appearance, can be seen moving around, including one in the middle-right that dies early in the movie.


The next movie contains voltage traces from a subset of electrode showing neuronal action potentials or 'spikes' occurring, often firing in a correlated manner within network 'bursts', which occur in isolated networks both in vitro and in vivo.


Despite lacking the 3-D structure and the complimentary sub-cortical areas present in the brain, the basis of cellular and network computation persists, and many important results are continuing to be published. The cultures retain many morphological, pharmacological, and electrical properties of cortical networks in vivo and have been studied for several decades. In particular, major neuroscientific advances about neural plasticity have been first described using cultures, including quantifying rules governing connection strengths (spike-timing dependent plasticity rule; STDP) [Bi & Poo 1998] and discovering homeostatic mechanisms to maintain stability in firing rates [Turrigiano 1999].


Cortical neurons in particular are attractive because the cortex can be considered as a type of general processing engine that is responsible for learning and memory. For example, sensory input from a ferret’s visual cortex was surgically routed to its auditory cortex [Sur et al 1988]. The auditory cortex then developed the structure and function of a visual cortex. This indicates that cortical tissue adapts to best handle the type of input it receives. In turn, cortical networks in vitro may have the ability to adapt their morphology and function in response to patterns of stimuli input via a multi-electrode array.


Indeed, conventional 60-electrode arrays have already provided fundamental insights into neural information processing. Electrical stimulation of rat cortical cultures has demonstrated the existence of "pathway-specific" [Jimbo et al 1999] and "region-specific" [Chao et al 2007] plasticity, suggesting plasticity rules exist at the network level. Recently, multi-electrode arrays demonstrated that local chemical stimuli, in addition to electrical stimuli, could alter network activity states [Baruchi & Ben-Jacob 2007], and that a novel form of plasticity of action potential propagation exists [Bakkum et al 2008a]. By utilizing recordings to determine the feedback of subsequent stimulation patterns, closed-loop systems were created to investigate “learning in vitro” [Potter et al 2001; Bakkum et al 2004]. The first report of learning used electrical stimuli to train a neural response to occur within a predetermined time interval [Shahaf & Marom 2001]. Later, adaptive goal-directed behavior was observed in simulated [Chao et al 2008] and real [Bakkum et al 2008b] networks, and applied to cultured neurons controlling a robotic drawing machine [Bakkum et al 2007]. 


Much remains yet to be learned!

 
 
 

Code

  • Meabench + National Instruments DAQs

I modified Meabench in 2008 in order to use National Instruments data acquisition cards (PCI or PCIe 6259 x2) via Comedi drivers. Meabench is an open-source tool to conduct experiments with commercial 60-electrode arrays and MultiChannel Systems hardware. NI DAQ cards offer significant cost savings and superior features, including 16-bit data acquisition. The software is available as a tar file containing the source code. Look at the included README file for instructions and refer to the user guide. Also contact me for information on using the NI DAQ analog output to apply stimulation pulses.

Additionally, refer to "A low-cost multielectrode system for data acquisition enabling real-time closed-loop processing with rapid recovery from stimulation artifacts." [Rolston et al] for a system using multi-electrode arrays, NI DAQs, and the NeuroRighter software.

 
 
 

Curriculum Vitae

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Education


Georgia Institute of Technology
Joint program with Emory University
Ph.D., Department of Bioengineering  (5/2008)
Certificate in Cognitive Science (5/2004)
M.S. Mech Eng, Dept of Automation & Mechatronics (5/2002)
Presidential Fellow.


Ecole Nationale Superieure d’Arts et Metiers – Paris / Metz
Attended one year of graduate study and research in France
through a joint program with Georgia Tech. (8/2000 - 6/2001)


University of Wisconsin - Madison
B.S. Mechanical Engineering (5/2000)
Dean’s list each semester. Graduated with honors.

 
 

Experience


Group Leader and Swiss National Science Foundation Ambizione Research Scientist
ETH Zurich, Bio Engineering Laboratory headed by Dr. Andreas Hierlemann. Study the cellular and network mechanisms of cultured neurons using multi-electrode array electrophysiology, microfluidics, genetics, pharmacology, and optics. (6/2010 - present)

Japanese Society for the Promotion of Science (JSPS) Post-doctoral Fellow
The University of Tokyo, Kanzaki-Takahashi laboratory. Studied the cellular and network mechanisms of cultured neurons using multi-electrode array electrophysiology, genetics, pharmacology, and optics. (5/2008 - 5/2010)

Graduate Research Assistant
Georgia Institute of Technology under Dr. Steve Potter. Studied the cellular and network mechanisms of cultured neurons using multi-electrode array electrophysiology, pharmacology, and optics. (8/2002 - 12/2007)

Art and Science Collaborator: Meart
Georgia Institute of Technology and the University of Western Australia. Dr. Steve Potter’s lab in collaboration with the SymbioticA Research Group. Maintained and interfaced cultured neurons to a robotic drawing machine. Contributed to the scientific and artistic dialog. (1/2003 – 5/2008)

Graduate Teaching Assistant - Hybrid Neural Microsystems
Georgia Institute of Technology under Dr. Steve Potter. Prepared biological wet labs and taught experimental techniques, including neural culturing and electrophysiology. (Fall 2004; Spring 2006)

Graduate Research Assistant
Georgia Institute of Technology under Dr. Ronald Arkin. Implemented autonomous proprioceptive control in a legged 6-wheel mobile robot to operate over rough terrain using the MissionLab software package. Paper accepted to the 2003 IEEE International Conference on Robotics and Automation (ICRA). (10/2001 – 5/2002)

Graduate Teaching Assistant - Experimental Engineering (Robotics)
Georgia Institute of Technology under Dr. Imme Ebert-Uphoff. Supervised course projects on parallel manipulators, vision systems, and autonomous vehicles. (Fall 2001)

International Summer Research Intern
University of Zilina, Slovakia under Professor Vladimir Kompis through IAESTE. Modeled hydroplaning for hydrodynamic power generation and automobile applications using ADINA software. Results presented at the Numerical Methods in Continuum Mechanics 2000 conference, Slovakia. Edited additional papers for publication. (Summer 2000)

Undergraduate Research Project
University of Wisconsin - Madison under Dr. Nicola Ferrier. Automated re-orientation of a non-holonomic mobile robot. Applications include control of powered wheelchairs and automated parallel parking with minimal user input. (12/1999 - 5/2000)

CAD designer
Agricultural Engineering Department, Madison, WI. Drafted agricultural harvesting equipment on Pro/Engineer 2000i. Published in pamphlets, magazines, and online. (9/1999 - 5/2000)

Engineering Intern
Brookhaven National Laboratory, Upton, NY. Designed, acquired materials, and constructed an apparatus for vacuum chamber experiments using plasma as a window transmitting a laser. Integral use of AutoCAD 13. (Fall 1998)

Engineering Intern
Los Alamos National Laboratory, Los Alamos, NM. Helped build a muon detector for use in high-energy particle accelerator. Provided quality control during construction. (Summer 1998)

 
 

Publications

Citation report
Journal articles


Mueller J, Bakkum DJ, Hierlemann A. (2012) “Sub-millisecond closed-loop feedback stimulation between arbitrary sets of individual neurons” Front. Neural Circuits 6:121.

Franke F, Jäckel D, Dragas J, Müller J, Radivojevic M, Bakkum D, Hierlemann A (2012) “High-density microelectrode array recordings and real-time spike sorting for closed-loop experiments: an emerging technology to study neural plasticity.” Front. Neural Circuits 6:105.

Fiscella M, Farrow K, Jones IL, Jackel D, Mueller J, Frey U, Bakkum DJ, Hantz P, Roska B, Hierlemann A. (2012) "Recording from defined populations of retinal ganglion cells using a high-density CMOS-integrated microelectrode array with real-time switchable electrode selection". J Neuroscience Methods. 211(1): 103-13

Tanada N, Sakurai T, Mitsuno H, Bakkum DJ, Kanzaki R, Takahashi H. (2012) "Dissociated neuronal culture expressing ionotropic odorant receptors as a hybrid odorant biosensor". Analyst 137 (15): pp. 3452-8

Takahashi H, Sakurai T, Sakai H, Bakkum DJ, Suzurikawa J, Kanzaki R. (2012) "Light-addressed single-neuron stimulation in dissociated neuronal cultures with sparse expression of ChR2". Biosystems 107 (2): pp. 106-112.

Frey U, Sedivy J, Heer F, Pedron R, Ballini M, Mueller J, Bakkum D, Hafizovic S, Faraci FD, Greve F, Kirstein KU, Hierlemann A. (2010) "Switch-Matrix-Based High-Density Microelectrode Array in CMOS Technology". IEEE Journal of Solid-State Circuits, 45(2)

Livi P, Heer F, Frey U, Bakkum DJ, Hierlemann A. (2010) "Compact voltage and current stimulation buffer for high-density microelectrode arrays". IEEE Transaction on Biomedical Circuits and Systems, 4 (6): pp. 372-8

Bakkum DJ
, Chao ZC, Potter SM. (2008) "Spatio-temporal electrical stimuli shape behavior of an embodied cortical network in a goal-directed learning task". J Neural Engineering: 5(3) 310-323.
  † Featured Article in volume 5(3).
  † Selected as one of the Journal of Neural Engineering's Highlights of 2008.

Bakkum DJ, Chao ZC, Potter SM. (2008) "Long-term plasticity of action potential propagation in a cortical network". PLoS ONE 3(5).

Chao ZC, Bakkum DJ, Potter SM. (2008) "Shaping embodied neural networks for adaptive goal-directed behavior". PLoS Computational Biology 4(3).

Bakkum DJ
, Gamblen P, Ben-Ary G, Chao ZC, Potter SM. (2007) "MEART: The semi-living artist". Frontiers in Neurorobotics: 1(5)

Chao ZC, Bakkum DJ, Potter SM. (2007) "Region-specific network plasticity in simulated and living cortical networks: comparison of the Center of Activity Trajectory (CAT) with other metrics." J. Neural Engineering: 4:294-308.

Chao ZC, Bakkum DJ, Wagenaar DA, Potter SM. (2005) “Effects of random external background stimulation on network synaptic stability after tetanization: a modeling study.” in Neuroinformatics: 3(3):263-80.

Bakkum DJ
, Shkolnik AC, Ben-Ary G, Gamblen P, DeMarse TD, Potter SM. (2004) “Removing some of the 'A' from AI: Embodied Cultured Networks” in Proceedings of the Dagstuhl Conference on Embodied Artificial Intelligence, Luc Steels and Rolf Pfeiffer, editors, Springer.

Conferences
2012

Bakkum DJ, Frey U, Mueller J, Fiscella M, Roscic B, Takahashi H, Hierlemann A. (2012) "Capability of an 11,011-electrode CMOS array to study action potential propagation plasticity". Soc. for Neurosci. (SfN) Conf.: 322.07. (talk)

Bakkum DJ, Frey U, Mueller J, Fiscella M, Roscic B, Takahashi H, Hierlemann A. (2012) "Uncovering neuronal cellular and network function using a high-desntiy 11,011-microelectrode CMOS array". Swiss Society for Neuroscience Annual Meeting, Zurich, Switzerland: Symposium 1-1. (invited talk)

Bakkum DJ, Frey U, Mueller J, Fiscella M, Takahashi H, Hierlemann A. (2012) "Towards an ideal interface to neural cultures: recording and stimulation via high-density CMOS electrode arrays".  Medical Physics and Biomedical Engineering (MPBE) World Congress, Beijing, China, May 26th: TH.16/01.1-1. (invited talk)

Bakkum DJ, Frey U, Mueller J, Fiscella M, Roscic B, Takahashi H, Hierlemann A. (2012) "Capabilities of a High-Density CMOS Microelectrode Array to Identify, Record, and Stimulate Individual Neurons in Cultured Networks". 8th International Meeting on Substrate-Integrated Micro Electrode Arrays (SIMEA), Reutlingen, July 10, 2012. (poster)

Radivojevic M, Jaeckel D, Mueller J, Fiscella M, Frey U, Roscic B, Hierlemann A, Bakkum DJ. (2012) "Methods for Long-term High-resolution Characterization of In Vitro Developing Neuronal Networks Grown over High-density CMOS-based Microelectrode Arrays". 8th International Meeting on Substrate-Integrated Micro Electrode Arrays (SIMEA), Reutlingen, July 10, 2012.

Mueller J, Bakkum DJ, Roscic B, Hierlemann A. (2012) "A flexible system to provide sub-millisecond feedback stimulation loops between multiple sets of individually identifiable neurons". 8th International Meeting on Substrate-Integrated Micro Electrode Arrays (SIMEA), Reutlingen, July 10, 2012.

Fiscella M, Farrow K, Jones IL, Jaeckel D, Mueller J, Frey U, Bakkum DJ, Roska B, Hierlemann A. (2012) "Targeting Defined Populations of Retinal Ganglion Cells with CMOS Microelectrode Arrays". 8th International Meeting on Substrate-Integrated Micro Electrode Arrays (SIMEA), Reutlingen, July 10, 2012.

Lewandowska MK, Frey O, Bakkum DJ, Hierlemann A. (2012) "Integrated microfluidic neuronal culture chamber on high density CMOS MEA". 22nd Anniversary World Congress on Biosensors, Cancun, Mexico, 15 May: 3B-1.

Ishihara Y, Mita T, Bakkum DJ, Frey U, Hierlemann A, Kanzaki R,  Takahashi H. (2012). "高密度CMOSアレイ上での細胞内刺激のための刺 激電極誘導法" or "Navigation of stimulation microelectrode for intracellular stimulation on high density CMOS array". Conference of Japanese Society for Medical and Biological Engineering (JSMBE), Fukuoka, Japan, May.

2011

Bakkum DJ, Frey U, Mueller J, Fiscella M, Takahashi H, Hierlemann A (2011) "Advancing Neuronal Cellular and Network Analysis Using a High-Density 11,011-Microelectrode CMOS Array". 8th International Brain Research Organization (IBRO) World Congress of Neuroscience, Florence, July 14th. (poster)

Mita T, Bakkum DJ, Frey U, Hierlemann A, Kanzaki R,  Takahashi H. (2011) "分散培養神経細胞の高空間解像度な機能的ネットワーク解析" or "Functional Network Analysis of Dissociated Cultured Neurons at High Spatial Resolution". Annual Conference of Electronics, Information and Systems Society, Toyama, Japan: GS6-3, pp.1305-1310, September 7-9.

Mita T, Bakkum DJ, Frey U, Hierlemann A, Kanzaki R,  Takahashi H. (2011) "Comparison of Functional Network by Conditional Firing Probability and Mutual Information", The Papers of Technical Meeting on Medical and Biological Engineering, IEE Japan: MBE-11-026-038, pp.1-6.

Mita T, Bakkum DJ, Frey U, Hierlemann A, Kanzaki R,  Takahashi H. (2011) ”Measurement of Action Potentials of Dissociated Cultured Neurons by High Density CMOS Array and Network Analysis”, The 34th annual meeting of the Japan Neuroscience Society (JNS), Yokohama, Japan: pp. P4–v08.

Tanada N, Sakurai T, Mitsuno H, Bakkum D,  Kanzaki R, Takahashi H (2011) “神経細胞の分散培養系にイオンチャネル一体型嗅覚受容体を発現させた匂いバイオセンサの提案と実現性の検証” or “Feasibility study of odor biosensor using dissociate neuronal culture with gene expression of ionotropic odorant receptors”.
  † 50th Annual Conference of the Japanese Society for Medical and Biological Engineering, Tokyo, April 29th
  † Institute of Electrical Engineers of Japan (IEEJ) Trans EIS, 131 (1), pp. 35-41

Jackel D, Mueller J, Khalid MU, Frey U, Bakkum DJ, Hierlemann A (2011) "High-Density Microelectrode Array System and Optimal Filtering for Closed-Loop Experiments". 16th International Conference on Solid-State Sensors, Actuators, and Microsystems: Transducers '11, Beijing, June 5th.

2010

Bakkum DJ, Frey U, Mueller J, Fiscella M, Hierlemann A, Takahashi H (2010) "Novel Neuronal Cellular and Network Measurements Enabled by a High-Density 11,011-Microelectrode CMOS Array”. 7th International Meeting on Substrate-Integrated Micro Electrode Arrays (SIMEA), Reutlingen, June 29th, p324-6. (talk)

Bakkum DJ, Frey U, Takahashi H, Hierlemann A (2010) “Subcellular-Resolution Recording of Electrical Activity Using a CMOS-Microelectrode System”. 2nd Global COE International Symposium EDIS2009 - session: Advances in Neuroengineering III, Osaka, Feb. 1st (talk)

Bakkum DJ, Frey U, Mita T, Mueller J, Fiscella M, Takahashi H, Hierlemann A (2010) “Neuronal cellular and network analysis using a high-density 11,011-electrode CMOS array”. The 33nd Annual Meeting of the Japan Neuroscience Society (JNS), Kobe, Sept. 14th: O2-10-2-4 (talk)

Mita T, Bakkum DJ, Frey U, Hierlemann A, Kanzaki R, Takahashi H (2010) “高密度 CMOS アレイ上の培養神経回路の細胞間機能結合の解析” or “Functional Connectivity of Cultured Neural Circuitry on High Density CMOS Array”. Proceedings of the 25th Symposium on Biological and Physiological Engineering (BPES)

Tanada N, Sakurai T, Mitsuno H, Bakkum D,  Kanzaki R, Takahashi H (2010) “The feasibility study of novel odor biosensor using dissociate neuronal culture expressing ion channel built-in odor receptors”. The 33nd Annual Meeting of the Japan Neuroscience Society (JNS), Kobe, Sept. 14th, 2010: O2-8-1-4

Tanada N, Sakurai T, Mitsuno H, Bakkum D,  Kanzaki R, Takahashi H (2010) “Odor biosensor using dissociate neuronal culture expressing ion channel built-in odor receptors” or “神経細胞の分散培養系にイオンチャネル型嗅覚受容体を発現させた匂いバイオセンサー”. Asia-Pacific Radio Science Conference (AP-RASC), Toyama, Sept. 22nd.

Livi P, Heer F, Frey U, Bakkum DJ, Hierlemann A (2010) " Voltage and Current Stimulation Buffer for High- Density Microelectrode Arrays”. 7th International Meeting on Substrate-Integrated Micro Electrode Arrays (SIMEA), Reutlingen, June 29th, p340-1.

2009

Bakkum DJ, Frey U, Mueller J, Fiscella M, Hierlemann A, Takahashi H (2009) "11,011 個の計測電極を有するCMOS アレイによる神経回路の活動の評価" or "Accessing neuronal network activity with an 11,011 electrode CMOS array". Proceedings of the 24th Symposium on Biological and Physiological Engineering (BPES), Sendai: 1A2-4. (talk)
  † Won the Society of Instrument and Control Engineers (SICE) Young Investigators award for best paper.

Bakkum DJ, Frey U, Mueller J, Fiscella M, Hierlemann A, Takahashi H (2009) "Subcellular-resolution electronic recording and stimulation of cultured cortical networks using an 11,011 electrode CMOS array".
  † Society for Neuroscience (SfN) Conference 2009, Chicago, Oct 19: 390.23/HH31 (poster)
  † The 32nd Annual Meeting of the Japan Neuroscience Society (JNS), Nagoya, Sept. 17th, 2009: O2-I5-2 (talk)

Bakkum DJ, Chao ZC, Potter SM. (2009) "Homeostasis of neuronal network firing rate during the induction of plasticity" IEEE EMBS Conference on Neural Engineering (NER), Antalya.

Sakai H, Bakkum D, Sakurai T, Suzurikawa J, Kanzaki R, Takahashi H (2009) "チャネルロドプシンを発現させた培養神経回路の光アドレス刺激" or "Light-addressable stimulation of channelrhodopsin-2-expressing cultured neuronal network". Institute of Electrical Engineers of Japan Seminar.

2008

Bakkum DJ, Chao ZC, Potter SM (2008) "Adaptive goal-directed behavior in embodied networks of cultured cortical neurons". Proceedings of the 23rd Symposium on Biological and Physiological Engineering (BPES), Nagoya. (talk)

Bakkum DJ, Chao ZC, Potter SM (2008) "Long-term activity-dependent plasticity of action potential propagation delay and amplitude in cortical networks". 6th International Meeting on Substrate-Integrated Micro Electrode Arrays (SIMEA), Reutlingen, p37-38.

Chao ZC, Bakkum DJ, Potter SM (2008). "Shaping goal-directed behavior of embodied cultured networks with electrical stimulation." Proc. 6th Int. Mtg. on Substrate-Integrated Micro-Electrode Arrays (SIMEA), p47-48.

2007

Bakkum DJ, Chao ZC, Potter SM. (2007) "Adaptive goal-directed behavior in embodied cultured networks: living neuronal networks and a simulated model". IEEE EMBS Conf on Neural Engineering (NER), Hawaii: Paper ThC1.1

Bakkum DJ, Chao ZC, Potter SM. (2007) "Embodying cultured neurons with a robotic drawing machine". IEEE EMBS Conference, Lyon: Paper FrC08.1

Ben-Ary G, Gamblen P, Bakkum DJ, Potter SM (2007) "A brief biography of a semi living artist". Subtle Technologies Festival


Ross JD, Reddy NE, Bakkum DJ, Potter SM, DeWeerth, SP. (2007) "Experimental platform for the study of region specific excitation and inhibition in neural tissue". IEEE EMBS Conference, Lyon: Paper SaP1D2.5

2006

Bakkum DJ, Chao ZC, Potter SM (2006) "Plasticity of action potential propagation". Society for Neuroscience (SfN) Conference: 636.17

Chao ZC, Bakkum DJ, Potter SM (2006) "Long-term network plasticity in simulated and living cortical networks: comparison of the Center of Activity Trajectory (CAT) with other metrics". Society for Neuroscience (SfN) Conference: 341.

Chao ZC, Bakkum DJ, Potter SM (2006) "A more animal-like in vitro model for the study of learning and embodiment". Biomedical Engineering Society (BMES) Conference

Chao ZC, Bakkum DJ, Wagenaar DA, Potter SM (2006) "Network plasticity in simulated and living cortical networks: comparison of the Center of Activity Trajectory (CAT) with other metrics". Proc. 5th Int. Mtg. on Substrate-Integrated Micro-Electrode Arrays (SIMEA), p14-15.


Madhavan R, Chao ZC, Wagenaar DA, Bakkum DJ, Potter SM. (2006). "Multi-site stimulation quiets network-wide spontaneous bursts and enhances functional plasticity in cultured cortical networks." IEEE EMBS Conference, p1593-1596.

2005 and earlier

Bakkum DJ, Chao ZC, Wagenaar DA, Potter SM (2005) "Self-regulation and electrically evoked precisely timed cortical culture activity as a means to control a hybrot". Society for Neuroscience (SfN) Conference: 276.19

Potter SM, DeMarse TB, Bakkum DJ, Booth MC, Brumfield JR, Chao ZC, Madhavan R, Passaro PA, Rambani K, Shkolnik AC, Towal RB, Wagenaar DA (2004) "Hybrots: hybrids of living neurons and robots for studying neural computation". Brain Inspired Cognitive Systems (BICS)

Waldron KJ, Arkin RC, Bakkum D, Merrill E, Abdallah M. (2003) “Proprioceptive Control for a Robotic Vehicle over Geometric Obstacles”. IEEE International Conference on Robotics and Automation (ICRA): 109-114.

Grajciar I, Bakkum D. (2000) "The aspects of a numerical simulation of the lubricated deformable rolling problem". Numerical Methods in Continuum Mechanics, Liptovský Ján, Slovak Republic

 
 

Art Exhibitions

MEART – the semi-living artist

Strange Attractors – Australian Art & Science Exhibition
Zendai gallery, Shanghai, 2006

Eyedrum gallery, Atlanta, 2006

Artrage, Black Box, Perth, 2005

1st Moscow Biennial for Contemporary Art
art_digital_2004
M’ARS gallery, Moscow, 2005

2004: Australia Culture Now
Australian Center for the Moving Image and the
National Gallery of Victoria, Melbourne, 2004

Cyber@rts - Mercado del Ensanche, Bilbao, 2004

Artbots: The Robot Talent Show
Eyebeam gallery, New York, 2003

Selected Press

Experiments in Art,
BBC Horizons Online, October 2006, Human v2.0.

Artistic Neurons, by Fenella Saunders.
Discover. Vol. 24, No. 11, November 2003, Mind & Brain.

Portraits from a Petri Dish.
Random Samples, Science, Vol. 301, No. 5632, July 25 2003.

Artbots show talent: Brain cells draft portraits via robot more than
a thousand kilometers away, by Helen Pearson. Nature Science Update, July 15 2003.

 
 

Honors

Swiss National Science Foundation Ambizione Research Scientist (2011 - 2014)
Japanese Society for the Promotion of Science Postdoctoral Fellowship (2008 - 2010)
University of Tokyo, Research Center for Advanced Science and Technology internal grant (2008 - 2009)
Center for Behavioral Neuroscience Graduate Scholar (2007)
Georgia Tech University Presidential Fellowship (2000 - 2007)
Georgia Tech ME Department Presidential Fellowship (2000 - 2005)
Graduated with honors – BSME (5/2000)
Undergraduate Scholarships (before 2000)
  - Carol J. Foster Scholarship
  - Donald I. Bohn Scholarship
  - National Honor Society Scholarship
Captain of high school soccer team

 
 
 
 
 
 
 
 
 
 
 

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