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Ted Berger, PhD

TitleProfessor
InstitutionUniversity of Southern California
DepartmentEngineering
AddressDRB 164
University Park Campus
Los Angeles CA 90089-1111
Phone+1 213 740 8017
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    The research of Dr. T.W. Berger involves the complementary use of experimental and theoretical approaches to developing biologically constrained mathematical models of mammalian neural systems. The focus of the majority of current research is the hippocampus, a neural system essential for learning and memory functions. The goal of this research is to address three general issues: (1) the relation between cellular/molecular processes, systems-level functions, and learned behavior; (2) the extent of which the functional dynamics of neural systems are altered by activity-dependent synaptic plasticity; (3) the extent to which the essential functions of a neural system can be incorporated within a hardware representation (e.g., VLSI circuitry).

    Experimental studies involve the use of extracellular, intracellular, and whole-cell electrophysiological recording techniques, applied in vivo using anesthetized and chronically implanted animals, and in vitro using hippocampal slice preparations. A number of neurobiological issues are being investigated, including: (1) quantifying the signal processing capabilities of hippocampal neurons and the extent to which these capabilities reflect regulation due to feedforward and feedback circuitry vs. intrinsic neuronal mechanisms, such as voltage-dependent conductances or second messenger biochemical systems; (2) the spatio-temporal distribution of activity in neural networks and its dependence on input pattern and network connectivity; (3) the cellular mechanisms underlying changes in the strength of connections among neurons, i.e., synaptic plasticity, and the influence of synaptic plasticity on signal processing characteristics of neurons and the spatio-temporal distributions of activity in networks.

    These and other experimental studies are used in conjunction with several different theoretical approaches to develop models of: (1) the nonlinear, input/output properties of single hippocampal neurons and circuits composed of several populations of hippocampal neurons (in collaboration with Dr. V. Marmarelis, Biomedical Engineering, USC), (2) the hierarchical relationship between synaptic and neuronal events (in collaboration with Dr. G. Chauvet, Institute for Theoretical Biology, University of Angers, France), (3) the kinetic properties of glutamatergic receptor subtypes, and (4) adaptive properties expressed by the "hippocampal-like" neural networks implemented with analog VLSI technology (in collaboration with Dr. B. Sheu, Electrical Engineering, USC).


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    Collapse Research Activities and Funding
    Predictive modeling of bioelectric activity on mammalian multilayered neuronal st
    NIH/NIGMS U01GM104604Sep 15, 2012 - Aug 31, 2017
    Role: Co-Principal Investigator
    NONLINEAR SYSTEMS ANALYSIS OF HIPPOCAMPUS
    NIH/NIMH R01MH051722Sep 30, 1994 - Apr 30, 2000
    Role: Principal Investigator
    LIMBIC CORTICAL BASES OF ASSOCIATIVE LEARNING
    NIH/NIMH K05MH000343Jul 1, 1992 - Jun 30, 1999
    Role: Principal Investigator
    LIMOIC CORTICAL BASES OF ASSOCIATIVE LEARNING
    NIH/NIMH K02MH000343Apr 1, 1981 - Apr 30, 1993
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Hu E, Mergenthal A, Bingham CS, Song D, Bouteiller JM, Berger TW. A Glutamatergic Spine Model to Enable Multi-Scale Modeling of Nonlinear Calcium Dynamics. Front Comput Neurosci. 2018; 12:58. PMID: 30100870.
      View in: PubMed
    2. Qiao Z, Han Y, Han X, Xu H, Li WXY, Song D, Berger TW, Cheung RCC. ASIC Implementation of a Nonlinear Dynamical Model for Hippocampal Prosthesis. Neural Comput. 2018 Jun 27; 1-28. PMID: 29949460.
      View in: PubMed
    3. Hampson RE, Song D, Robinson BS, Fetterhoff D, Dakos AS, Roeder BM, She X, Wicks RT, Witcher MR, Couture DE, Laxton AW, Munger-Clary H, Popli G, Sollman MJ, Whitlow CT, Marmarelis VZ, Berger TW, Deadwyler SA. Developing a hippocampal neural prosthetic to facilitate human memory encoding and recall. J Neural Eng. 2018 Jun; 15(3):036014. PMID: 29589592.
      View in: PubMed
    4. Sandler RA, Geng K, Song D, Hampson RE, Witcher MR, Deadwyler SA, Berger TW, Marmarelis VZ. Designing Patient-Specific Optimal Neurostimulation Patterns for Seizure Suppression. Neural Comput. 2018 May; 30(5):1180-1208. PMID: 29566356.
      View in: PubMed
    5. Xu H, Hirschberg AW, Scholten K, Berger TW, Song D, Meng E. Acute in vivo testing of a conformal polymer microelectrode array for multi-region hippocampal recordings. J Neural Eng. 2018 Feb; 15(1):016017. PMID: 29044049.
      View in: PubMed
    6. Bingham CS, Loizos K, Yu GJ, Gilbert A, Bouteiller JC, Song D, Lazzi G, Berger TW. Model-Based Analysis of Electrode Placement and Pulse Amplitude for Hippocampal Stimulation. IEEE Trans Biomed Eng. 2018 Jan 25. PMID: 29993519.
      View in: PubMed
    7. Ramirez-Zamora A, Giordano JJ, Gunduz A, Brown P, Sanchez JC, Foote KD, Almeida L, Starr PA, Bronte-Stewart HM, Hu W, McIntyre C, Goodman W, Kumsa D, Grill WM, Walker HC, Johnson MD, Vitek JL, Greene D, Rizzuto DS, Song D, Berger TW, Hampson RE, Deadwyler SA, Hochberg LR, Schiff ND, Stypulkowski P, Worrell G, Tiruvadi V, Mayberg HS, Jimenez-Shahed J, Nanda P, Sheth SA, Gross RE, Lempka SF, Li L, Deeb W, Okun MS. Evolving Applications, Technological Challenges and Future Opportunities in Neuromodulation: Proceedings of the Fifth Annual Deep Brain Stimulation Think Tank. Front Neurosci. 2017; 11:734. PMID: 29416498.
      View in: PubMed
    8. Geng K, Shin DC, Song D, Hampson RE, Deadwyler SA, Berger TW, Marmarelis VZ. Mechanism-Based and Input-Output Modeling of the Key Neuronal Connections and Signal Transformations in the CA3-CA1 Regions of the Hippocampus. Neural Comput. 2018 Jan; 30(1):149-183. PMID: 29064783.
      View in: PubMed
    9. Hampson RE, Deadwyler SA, Berger TW. Multi-resolution multi-trial sparse classification model for decoding visual memories from hippocampal spikes in human. Conf Proc IEEE Eng Med Biol Soc. 2017 07; 2017:1046-1049. PMID: 29060053.
      View in: PubMed
    10. Weltman A, Scholten K, Meng E, Berger TW. Chronic multi-region recording from the rat hippocampus in vivo with a flexible Parylene-based multi-electrode array. Conf Proc IEEE Eng Med Biol Soc. 2017 07; 2017:1716-1719. PMID: 29060217.
      View in: PubMed
    11. Keller AF, Bouteiller JC, Berger TW. Development of a Computational Approach/Model to Explore NMDA Receptors Functions. Methods Mol Biol. 2017; 1677:291-306. PMID: 28986881.
      View in: PubMed
    12. Song D, Robinson BS, Hampson RE, Marmarelis VZ, Deadwyler SA, Berger TW. Sparse Large-Scale Nonlinear Dynamical Modeling of Human Hippocampus for Memory Prostheses. IEEE Trans Neural Syst Rehabil Eng. 2018 Feb; 26(2):272-280. PMID: 28113595.
      View in: PubMed
    13. Robinson BS, Berger TW, Song D. Identification of Stable Spike-Timing-Dependent Plasticity from Spiking Activity with Generalized Multilinear Modeling. Neural Comput. 2016 Aug 24; 1-32. PMID: 27557101.
      View in: PubMed
    14. A sparse Laguerre-Volterra autoregressive model for seizure prediction in temporal lobe epilepsy. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:1664-1667. PMID: 28324947.
      View in: PubMed
    15. Hu EY, Bouteiller JC. Development of a detailed model of calcium dynamics at the postsynaptic spine of an excitatory synapse. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:6102-6105. PMID: 28269645.
      View in: PubMed
    16. Yu GJ. Place field detection using grid-based clustering in a large-scale computational model of the rat dentate gyrus. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:1405-1408. PMID: 28268589.
      View in: PubMed
    17. Bingham CS, Loizos K. A large-scale detailed neuronal model of electrical stimulation of the dentate gyrus and perforant path as a platform for electrode design and optimization. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:2794-2797. PMID: 28268898.
      View in: PubMed
    18. A flexible parylene probe for in vivo recordings from multiple subregions of the rat hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:2806-2809. PMID: 28268901.
      View in: PubMed
    19. Robinson BS, Berger TW. Monte Carlo validation of spike-timing-dependent plasticity identification from spiking activity. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:1624-1627. PMID: 28268640.
      View in: PubMed
    20. Decoding memory features from hippocampal spiking activities using sparse classification models. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:1620-1623. PMID: 28268639.
      View in: PubMed
    21. Hendrickson PJ, Bingham C. A bi-directional communication paradigm between parallel NEURON and an external non-neuron process. Conf Proc IEEE Eng Med Biol Soc. 2016 08; 2016:1413-1416. PMID: 28268591.
      View in: PubMed
    22. Deadwyler SA, Hampson RE, Song D, Opris I, Gerhardt GA, Marmarelis VZ, Berger TW. A cognitive prosthesis for memory facilitation by closed-loop functional ensemble stimulation of hippocampal neurons in primate brain. Exp Neurol. 2017 01; 287(Pt 4):452-460. PMID: 27233622.
      View in: PubMed
    23. Hendrickson PJ, Yu GJ, Song D, Berger TW. Interactions between Inhibitory Interneurons and Excitatory Associational Circuitry in Determining Spatio-Temporal Dynamics of Hippocampal Dentate Granule Cells: A Large-Scale Computational Study. Front Syst Neurosci. 2015; 9:155. PMID: 26635545; PMCID: PMC4647071.
    24. Allam SL, Bouteiller JM, Hu EY, Ambert N, Greget R, Bischoff S, Baudry M, Berger TW. Synaptic Efficacy as a Function of Ionotropic Receptor Distribution: A Computational Study. PLoS One. 2015; 10(10):e0140333. PMID: 26480028; PMCID: PMC4610697.
    25. Opris I, Santos LM, Gerhardt GA, Song D, Berger TW, Hampson RE, Deadwyler SA. Distributed encoding of spatial and object categories in primate hippocampal microcircuits. Front Neurosci. 2015; 9:317. PMID: 26500473; PMCID: PMC4594006.
    26. Hu EY, Bouteiller JM, Song D, Baudry M, Berger TW. Volterra representation enables modeling of complex synaptic nonlinear dynamics in large-scale simulations. Front Comput Neurosci. 2015; 9:112. PMID: 26441622; PMCID: PMC4585022.
    27. Sandler RA, Song D, Hampson RE, Deadwyler SA, Berger TW, Marmarelis VZ. Hippocampal closed-loop modeling and implications for seizure stimulation design. J Neural Eng. 2015 Oct; 12(5):056017. PMID: 26355815.
      View in: PubMed
    28. Xin Y, Li WX, Zhang Z, Cheung RC, Song D, Berger TW. An Application Specific Instruction Set Processor (ASIP) for Adaptive Filters in Neural Prosthetics. IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct; 12(5):1034-47. PMID: 26451817.
      View in: PubMed
    29. Hendrickson PJ, Yu GJ, Song D, Berger TW. A Million-Plus Neuron Model of the Hippocampal Dentate Gyrus: Critical Role for Topography in Determining Spatiotemporal Network Dynamics. IEEE Trans Biomed Eng. 2016 Jan; 63(1):199-209. PMID: 26087482; PMCID: PMC4745257 [Available on 01/01/17].
    30. Hu EY, Bouteiller JM, Song D, Berger TW. The volterra functional series is a viable alternative to kinetic models for synaptic modeling--calibration and benchmarking. Conf Proc IEEE Eng Med Biol Soc. 2015; 2015:3291-4. PMID: 26736995; PMCID: PMC4856223.
    31. Hendrickson PJ, Yu GJ, Song D, Berger TW. A million-plus neuron model of the hippocampal dentate gyrus: Dependency of spatio-temporal network dynamics on topography. Conf Proc IEEE Eng Med Biol Soc. 2015; 2015:4713-6. PMID: 26737346; PMCID: PMC4878386.
    32. Robinson BS, Song D, Berger TW. Estimation of a large-scale generalized Volterra model for neural ensembles with group lasso and local coordinate descent. Conf Proc IEEE Eng Med Biol Soc. 2015; 2015:2526-9. PMID: 26736806.
      View in: PubMed
    33. Song D, Robinson BS, Hampson RE, Marmarelis VZ, Deadwyler SA, Berger TW. Sparse generalized volterra model of human hippocampal spike train transformation for memory prostheses. Conf Proc IEEE Eng Med Biol Soc. 2015; 2015:3961-4. PMID: 26737161.
      View in: PubMed
    34. Gilbert A, Loizos K, RamRakhyani AK, Hendrickson P, Lazzi G, Berger TW. A 3-D admittance-level computational model of a rat hippocampus for improving prosthetic design. Conf Proc IEEE Eng Med Biol Soc. 2015; 2015:2295-8. PMID: 26736751; PMCID: PMC4877026.
    35. Xu H, Weltman A, Hsiao MC, Scholten K, Meng E, Berger TW, Song D. Design of a flexible parylene-based multi-electrode array for multi-region recording from the rat hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2015; 2015:7139-42. PMID: 26737938.
      View in: PubMed
    36. Yu GJ, Hendrickson PJ, Song D, Berger TW. Topography-dependent spatio-temporal correlations in the entorhinal-dentate-CA3 circuit in a large-scale computational model of the Rat Hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2015; 2015:3965-8. PMID: 26737162; PMCID: PMC4858183.
    37. Deadwyler SA, Berger TW, Opris I, Song D, Hampson RE. Neurons and networks organizing and sequencing memories. Brain Res. 2015 Sep 24; 1621:335-44. PMID: 25553617; PMCID: PMC4485978.
    38. Sandler RA, Deadwyler SA, Hampson RE, Song D, Berger TW, Marmarelis VZ. System identification of point-process neural systems using probability based Volterra kernels. J Neurosci Methods. 2015 Jan 30; 240:179-92. PMID: 25479231; PMCID: PMC4286344.
    39. Song D, Chan RH, Robinson BS, Marmarelis VZ, Opris I, Hampson RE, Deadwyler SA, Berger TW. Identification of functional synaptic plasticity from spiking activities using nonlinear dynamical modeling. J Neurosci Methods. 2015 Apr 15; 244:123-35. PMID: 25280984; PMCID: PMC4383743.
    40. Sandler RA, Song D, Hampson RE, Deadwyler SA, Berger TW, Marmarelis VZ. Model-based asessment of an in-vivo predictive relationship from CA1 to CA3 in the rodent hippocampus. J Comput Neurosci. 2015 Feb; 38(1):89-103. PMID: 25260381; PMCID: PMC4297547.
    41. Hsiao MC, Yu PN, Song D, Liu CY, Heck CN, Millett D, Berger TW. An in vitro seizure model from human hippocampal slices using multi-electrode arrays. J Neurosci Methods. 2015 Apr 15; 244:154-63. PMID: 25244953.
      View in: PubMed
    42. Song D, Harway M, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Extraction and restoration of hippocampal spatial memories with non-linear dynamical modeling. Front Syst Neurosci. 2014; 8:97. PMID: 24904318; PMCID: PMC4036140.
    43. Yousefi A, Dibazar AA, Berger TW. Synaptic dynamics: linear model and adaptation algorithm. Neural Netw. 2014 Aug; 56:49-68. PMID: 24867390.
      View in: PubMed
    44. Hu EY, Bouteiller JM, Huang M, Song D, Berger T. A comparison between direct and indirect measurements of neurotransmitter vesicle release dynamics: a computational study. Conf Proc IEEE Eng Med Biol Soc. 2014; 2014:1155-8. PMID: 25570168; PMCID: PMC4485406.
    45. Song D, Robinson BS, Granacki JJ, Berger TW. Implementing spiking neuron model and spike-timing-dependent plasticity with generalized Laguerre-Volterra models. Conf Proc IEEE Eng Med Biol Soc. 2014; 2014:714-7. PMID: 25570058.
      View in: PubMed
    46. Xu H, Hsiao MC, Song D, Berger TW. Recording place cells from multiple sub-regions of the rat hippocampus with a customized micro-electrode array. Conf Proc IEEE Eng Med Biol Soc. 2014; 2014:4876-9. PMID: 25571084.
      View in: PubMed
    47. A testbed to explore the optimal electrical stimulation parameters for suppressing inter-ictal spikes in human hippocampal slices. Conf Proc IEEE Eng Med Biol Soc. 2014; 2014:5792-5. PMID: 25571312.
      View in: PubMed
    48. Robinson BS, Song D, Berger TW. Generalized Volterra kernel model identification of spike-timing-dependent plasticity from simulated spiking activity. Conf Proc IEEE Eng Med Biol Soc. 2014; 2014:6585-8. PMID: 25571505.
      View in: PubMed
    49. Li WX, Xin Y, Chan RH, Song D, Berger TW, Cheung RC. Laguerre-Volterra model and architecture for MIMO system identification and output prediction. Conf Proc IEEE Eng Med Biol Soc. 2014; 2014:4539-42. PMID: 25571001.
      View in: PubMed
    50. Yu G, Song D, Berger TW. Implementation of the excitatory entorhinal-dentate-CA3 topography in a large-scale computational model of the rat hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2014; 2014:6581-4. PMID: 25571504; PMCID: PMC4494103.
    51. Unstable periodic orbits in human epileptic hippocampal slices. Conf Proc IEEE Eng Med Biol Soc. 2014; 2014:5800-3. PMID: 25571314.
      View in: PubMed
    52. Deadwyler SA, Berger TW, Sweatt AJ, Song D, Chan RH, Opris I, Gerhardt GA, Marmarelis VZ, Hampson RE. Donor/recipient enhancement of memory in rat hippocampus. Front Syst Neurosci. 2013; 7:120. PMID: 24421759; PMCID: PMC3872745.
    53. Hampson RE, Song D, Opris I, Santos LM, Shin DC, Gerhardt GA, Marmarelis VZ, Berger TW, Deadwyler SA. Facilitation of memory encoding in primate hippocampus by a neuroprosthesis that promotes task-specific neural firing. J Neural Eng. 2013 Dec; 10(6):066013. PMID: 24216292; PMCID: PMC3919468.
    54. Li WX, Cheung RC, Chan RH, Song D, Berger TW. Real-time prediction of neuronal population spiking activity using FPGA. IEEE Trans Biomed Circuits Syst. 2013 Aug; 7(4):489-98. PMID: 23893208.
      View in: PubMed
    55. Song D, Wang H, Tu CY, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Identification of sparse neural functional connectivity using penalized likelihood estimation and basis functions. J Comput Neurosci. 2013 Dec; 35(3):335-57. PMID: 23674048; PMCID: PMC3805829.
    56. Hsiao MC, Song D, Berger TW. Nonlinear dynamical model based control of in vitro hippocampal output. Front Neural Circuits. 2013; 7:20. PMID: 23429994; PMCID: PMC3576714.
    57. Hampson RE, Fuqua JL, Huettl PF, Opris I, Song D, Shin D, Marmarelis VZ, Berger TW, Gerhardt GA, Deadwyler SA. Conformal ceramic electrodes that record glutamate release and corresponding neural activity in primate prefrontal cortex. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:5954-7. PMID: 24111095.
      View in: PubMed
    58. Bouteiller JM, Hu E, Allam SL, Ghaderi V, Song D, Berger TW. Insights on synaptic paired-pulse response using parametric and non-parametric models. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:1041-4. PMID: 24109869; PMCID: PMC4157129.
    59. Yu GJ, Hendrickson PJ, Robinson BS, Song D, Berger TW. The role of topography in the transformation of spatiotemporal patterns by a large-scale, biologically realistic model of the rat dentate gyrus. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:5950-3. PMID: 24111094; PMCID: PMC4156021.
    60. Hendrickson PJ, Yu GJ, Robinson BS, Song D, Berger TW. The contribution of relative activation levels between populations of cells to network activity in a large-scale biologically realistic model of the hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:5962-5. PMID: 24111097; PMCID: PMC4157909.
    61. Ghaderi VS, Song D, Bouteiller JM, Choma J, Berger TW. A programmable analog subthreshold biomimetic model for bi-directional communication with the brain. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:787-90. PMID: 24109805.
      View in: PubMed
    62. Opris I, Santos L, Gerhardt GA, Song D, Berger TW, Hampson RE, Deadwyler SA. Prefrontal cortical microcircuits bind perception to executive control. Sci Rep. 2013; 3:2285. PMID: 23893262; PMCID: PMC3725477.
    63. Robinson BS, Song D, Berger TW. Laguerre-Volterra identification of spike-timing-dependent plasticity from spiking activity: a simulation study. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:5578-81. PMID: 24111001.
      View in: PubMed
    64. Bouteiller JM, Allam SL, Ambert N, Greget R, Hu E, Bischoff S, Baudry M, Berger TW. Influence of ionotropic receptors localization on glutamatergic synaptic response to paired-pulse stimulation protocol. Conf Proc IEEE Eng Med Biol Soc. 2013; 2013:1037-40. PMID: 24109868; PMCID: PMC4157128.
    65. Opris I, Fuqua JL, Huettl PF, Gerhardt GA, Berger TW, Hampson RE, Deadwyler SA. Closing the loop in primate prefrontal cortex: inter-laminar processing. Front Neural Circuits. 2012; 6:88. PMID: 23189041; PMCID: PMC3504312.
    66. Allam SL, Ghaderi VS, Bouteiller JM, Legendre A, Ambert N, Greget R, Bischoff S, Baudry M, Berger TW. A computational model to investigate astrocytic glutamate uptake influence on synaptic transmission and neuronal spiking. Front Comput Neurosci. 2012; 6:70. PMID: 23060782; PMCID: PMC3461576.
    67. Opris I, Hampson RE, Gerhardt GA, Berger TW, Deadwyler SA. Columnar processing in primate pFC: evidence for executive control microcircuits. J Cogn Neurosci. 2012 Dec; 24(12):2334-47. PMID: 23016850; PMCID: PMC3754813.
    68. Hampson RE, Gerhardt GA, Marmarelis V, Song D, Opris I, Santos L, Berger TW, Deadwyler SA. Facilitation and restoration of cognitive function in primate prefrontal cortex by a neuroprosthesis that utilizes minicolumn-specific neural firing. J Neural Eng. 2012 Oct; 9(5):056012. PMID: 22976769; PMCID: PMC3505670.
    69. Berger T, Song D, Chan R, Shin D, Marmarelis V, Hampson R, Sweatt A, Heck C, Liu C, Wills J, Lacoss J, Granacki J, Gerhardt G, Deadwyler S. Role of the hippocampus in memory formation: restorative encoding memory integration neural device as a cognitive neural prosthesis. IEEE Pulse. 2012 Sep-Oct; 3(5):17-22. PMID: 23014702.
      View in: PubMed
    70. Marmarelis VZ, Shin DC, Song D, Hampson RE, Deadwyler SA, Berger TW. Nonlinear modeling of dynamic interactions within neuronal ensembles using Principal Dynamic Modes. J Comput Neurosci. 2013 Feb; 34(1):73-87. PMID: 23011343; PMCID: PMC3531564.
    71. Berger T, Meng E, George S, Khoo M, Marmarelis V, McCulloch A, Cauwenberghs G, Ohno-Machado L, Schultz J, Johnson JP. Southern California: a hotbed of biomedical engineering: nine bioengineers describe their research and why Southern California has the biotech market cornered. IEEE Pulse. 2012 Jul; 3(4):14-21. PMID: 23008840.
      View in: PubMed
    72. Hampson RE, Song D, Chan RH, Sweatt AJ, Riley MR, Goonawardena AV, Marmarelis VZ, Gerhardt GA, Berger TW, Deadwyler SA. Closing the loop for memory prosthesis: detecting the role of hippocampal neural ensembles using nonlinear models. IEEE Trans Neural Syst Rehabil Eng. 2012 Jul; 20(4):510-25. PMID: 22498704; PMCID: PMC3395725.
    73. Berger TW, Song D, Chan RH, Marmarelis VZ, LaCoss J, Wills J, Hampson RE, Deadwyler SA, Granacki JJ. A hippocampal cognitive prosthesis: multi-input, multi-output nonlinear modeling and VLSI implementation. IEEE Trans Neural Syst Rehabil Eng. 2012 Mar; 20(2):198-211. PMID: 22438335; PMCID: PMC3395724.
    74. Hampson RE, Song D, Chan RH, Sweatt AJ, Riley MR, Gerhardt GA, Shin DC, Marmarelis VZ, Berger TW, Deadwyler SA. A nonlinear model for hippocampal cognitive prosthesis: memory facilitation by hippocampal ensemble stimulation. IEEE Trans Neural Syst Rehabil Eng. 2012 Mar; 20(2):184-97. PMID: 22438334; PMCID: PMC3397311.
    75. Yousefi A, Dibazar AA, Berger TW. Synaptic dynamics: Linear model and adaptation algorithm. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:1362-5. PMID: 23366152.
      View in: PubMed
    76. Ghaderi VS, Roach S, Song D, Marmarelis VZ, Choma J, Berger TW. Analog low-power hardware implementation of a Laguerre-Volterra model of intracellular subthreshold neuronal activity. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:767-70. PMID: 23366005.
      View in: PubMed
    77. Yu GJ, Robinson BS, Hendrickson PJ, Song D, Berger TW. Implementation of topographically constrained connectivity for a large-scale biologically realistic model of the hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:1358-61. PMID: 23366151; PMCID: PMC4172365.
    78. Hendrickson PJ, Yu GJ, Robinson BS, Song D, Berger TW. Towards a large-scale biologically realistic model of the hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:4595-8. PMID: 23366951; PMCID: PMC4172354.
    79. Bouteiller JM, Legendre A, Allam SL, Ambert N, Hu EY, Greget R, Keller AF, Pernot F, Bischoff S, Baudry M, Berger TW. Modeling of the nervous system: from modulation of glutamatergic and gabaergic molecular dynamics to neuron spiking activity. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:6612-5. PMID: 23367445; PMCID: PMC4155903.
    80. Robinson BS, Yu GJ, Hendrickson PJ, Song D, Berger TW. Implementation of activity-dependent synaptic plasticity rules for a large-scale biologically realistic model of the hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:1366-9. PMID: 23366153; PMCID: PMC4172364.
    81. Allam SL, Bouteiller JM, Hu E, Greget R, Ambert N, Bischoff S, Baudry M, Berger TW. Influence of ionotropic receptor location on their dynamics at glutamatergic synapses. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:1374-7. PMID: 23366155.
      View in: PubMed
    82. Song D, Opris I, Chan RH, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Functional connectivity between Layer 2/3 and Layer 5 neurons in prefrontal cortex of nonhuman primates during a delayed match-to-sample task. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:2555-8. PMID: 23366446.
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    83. Li WX, Chan RH, Song D, Berger TW, Cheung RC. A dual mode FPGA design for the hippocampal prosthesis. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:4579-82. PMID: 23366947.
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    84. Hsiao MC, Yu PN, Song D, Liu CY, Heck CN, Millett D, Berger TW. Spatio-temporal inter-ictal activity recorded from human epileptic hippocampal slices. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:5166-9. PMID: 23367092.
      View in: PubMed
    85. Park HO, Dibazar AA, Berger TW. Nonlinear model for Dynamic Synapse Neural Network. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:5441-4. PMID: 23367160.
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    86. Roach SM, Lu U, Song D, Berger TW. An analysis of the expression locus of long-term potentiation in hippocampal CA1 neurons. Conf Proc IEEE Eng Med Biol Soc. 2012; 2012:5510-3. PMID: 23367177.
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    87. Greget R, Pernot F, Bouteiller JM, Ghaderi V, Allam S, Keller AF, Ambert N, Legendre A, Sarmis M, Haeberle O, Faupel M, Bischoff S, Berger TW, Baudry M. Simulation of postsynaptic glutamate receptors reveals critical features of glutamatergic transmission. PLoS One. 2011; 6(12):e28380. PMID: 22194830; PMCID: PMC3240618.
    88. Lu U, Roach SM, Song D, Berger TW. Nonlinear dynamic modeling of neuron action potential threshold during synaptically driven broadband intracellular activity. IEEE Trans Biomed Eng. 2012 Mar; 59(3):706-16. PMID: 22156947; PMCID: PMC3399271.
    89. Taghva A, Song D, Hampson RE, Deadwyler SA, Berger TW. Determination of relevant neuron-neuron connections for neural prosthetics using time-delayed mutual information: tutorial and preliminary results. World Neurosurg. 2012 Dec; 78(6):618-30. PMID: 22120279; PMCID: PMC3810969.
    90. Hampson RE, Sweatt AJ, Goonawardena AV, Song D, Chan RH, Marmarelis VZ, Berger TW, Deadwyler SA. Memory encoding in hippocampal ensembles is negatively influenced by cannabinoid CB1 receptors. Behav Pharmacol. 2011 Aug; 22(4):335-46. PMID: 21558844; PMCID: PMC3135765.
    91. Berger TW, Hampson RE, Song D, Goonawardena A, Marmarelis VZ, Deadwyler SA. A cortical neural prosthesis for restoring and enhancing memory. J Neural Eng. 2011 Aug; 8(4):046017. PMID: 21677369; PMCID: PMC3141091.
    92. Bouteiller JM, Allam SL, Hu EY, Greget R, Ambert N, Keller AF, Bischoff S, Baudry M, Berger TW. Integrated multiscale modeling of the nervous system: predicting changes in hippocampal network activity by a positive AMPA receptor modulator. IEEE Trans Biomed Eng. 2011 Oct; 58(10):3008-11. PMID: 21642035; PMCID: PMC3397143.
    93. Lu U, Song D, Berger TW. Nonlinear dynamic modeling of synaptically driven single hippocampal neuron intracellular activity. IEEE Trans Biomed Eng. 2011 May; 58(5):1303-13. PMID: 21233041; PMCID: PMC3125057.
    94. Bouteiller JM, Allam SL, Hu EY, Greget R, Ambert N, Keller AF, Pernot F, Bischoff S, Baudry M, Berger TW. Modeling of the nervous system: from molecular dynamics and synaptic modulation to neuron spiking activity. Conf Proc IEEE Eng Med Biol Soc. 2011; 2011:445-8. PMID: 22254344.
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    95. Song D, Chan RH, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Estimation and statistical validation of event-invariant nonlinear dynamic models of hippocampal CA3-CA1 population activities. Conf Proc IEEE Eng Med Biol Soc. 2011; 2011:3330-3. PMID: 22255052.
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    96. Lu U, Roach SM, Song D, Berger TW. A two-stage cascade nonlinear dynamical model of single neurons for the separation and quantification of pre- and post-synaptic mechanisms of synaptic transmission. Conf Proc IEEE Eng Med Biol Soc. 2011; 2011:1427-30. PMID: 22254586.
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    97. Li WX, Chan RH, Zhang W, Cheung RC, Song D, Berger TW. A hardware-based computational platform for Generalized Laguerre-Volterra MIMO model for neural activities. Conf Proc IEEE Eng Med Biol Soc. 2011; 2011:7282-5. PMID: 22256020.
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    98. Chan RH, Song D, Goonawardena AV, Bough S, Sesay J, Hampson RE, Deadwyler SA, Berger TW. Tracking the changes of hippocampal population nonlinear dynamics in rats learning a memory-dependent task. Conf Proc IEEE Eng Med Biol Soc. 2011; 2011:3326-9. PMID: 22255051.
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    99. Lu B, Dibazar A, Berger TW. Noise-robust acoustic signature recognition using nonlinear Hebbian learning. Neural Netw. 2010 Dec; 23(10):1252-63. PMID: 20655704.
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    100. Berger TW, Chen ZS, Cichocki A, Oweiss KG, Quian Quiroga R, Thakor NV. Signal processing for neural spike trains. Comput Intell Neurosci. 2010; 698751. PMID: 20454532; PMCID: PMC2864889.
    101. Berger TW, Song D, Chan RH, Marmarelis VZ. The Neurobiological Basis of Cognition: Identification by Multi-Input, Multioutput Nonlinear Dynamic Modeling: A method is proposed for measuring and modeling human long-term memory formation by mathematical analysis and computer simulation of nerve-cell dynamics. Proc IEEE Inst Electr Electron Eng. 2010 Mar 04; 98(3):356-374. PMID: 20700470.
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    102. Chan RH, Song D, Goonawardena AV, Bough S, Sesay J, Hampson RE, Deadwyler SA, Berger TW. Changes of hippocampal CA3-CA1 population nonlinear dynamics across different training sessions in rats performing a memory-dependent task. Conf Proc IEEE Eng Med Biol Soc. 2010; 2010:5464-7. PMID: 21096285.
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    103. Bouteiller JM, Allam SL, Greget R, Ambert N, Hu EY, Bischoff S, Baudry M, Berger TW. Paired-pulse stimulation at glutamatergic synapses - pre- and postsynaptic components. Conf Proc IEEE Eng Med Biol Soc. 2010; 2010:787-90. PMID: 21096110.
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    104. Lu U, Song D, Berger TW. Nonlinear dynamic analyses of single hippocampal neurons before and after long-term potentiation. Conf Proc IEEE Eng Med Biol Soc. 2010; 2010:2762-5. PMID: 21096216.
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    105. Dibazar AA, Park HO, Berger TW. Nonlinear dynamic modeling of impaired voice. Conf Proc IEEE Eng Med Biol Soc. 2010; 2010:2770-3. PMID: 21095964.
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    106. Song D, Wang H, Berger TW. Estimating sparse Volterra models using group L1-regularization. Conf Proc IEEE Eng Med Biol Soc. 2010; 2010:4128-31. PMID: 21096634.
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    107. Ambert N, Greget R, Haeberlé O, Bischoff S, Berger TW, Bouteiller JM, Baudry M. Computational studies of NMDA receptors: differential effects of neuronal activity on efficacy of competitive and non-competitive antagonists. Open Access Bioinformatics. 2010; 2:113-125. PMID: 21572937.
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    108. Marmarelis VZ, Zanos TP, Berger TW. Boolean modeling of neural systems with point-process inputs and outputs. Part I: theory and simulations. Ann Biomed Eng. 2009 Aug; 37(8):1654-67. PMID: 19517238; PMCID: PMC2917726.
    109. Zanos TP, Hampson RE, Deadwyler SE, Berger TW, Marmarelis VZ. Boolean modeling of neural systems with point-process inputs and outputs. Part II: Application to the rat hippocampus. Ann Biomed Eng. 2009 Aug; 37(8):1668-82. PMID: 19499341; PMCID: PMC2917724.
    110. Song D, Chan RH, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Nonlinear modeling of neural population dynamics for hippocampal prostheses. Neural Netw. 2009 Nov; 22(9):1340-51. PMID: 19501484; PMCID: PMC2821165.
    111. Hsiao MC, Song D, Berger TW. Using an open-loop inverse control strategy to regulate CA1 nonlinear dynamics for an in vitro hippocampal prosthesis model. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:1529-32. PMID: 19963755.
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    112. Chan RH, Song D, Berger TW. Nonstationary modeling of neural population dynamics. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:4559-62. PMID: 19963837.
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    113. Lu U, Song D, Berger TW. Nonlinear model of single hippocampal neurons with dynamical thresholds. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:3330-4. PMID: 19964070.
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    114. Song D, Chan RH, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Sparse generalized Laguerre-Volterra model of neural population dynamics. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:4555-8. PMID: 19963836.
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    115. Zanos TP, Courellis SH, Berger TW, Hampson RE, Deadwyler SA, Marmarelis VZ. Nonlinear modeling of causal interrelationships in neuronal ensembles. IEEE Trans Neural Syst Rehabil Eng. 2008 Aug; 16(4):336-52. PMID: 18701382; PMCID: PMC2729787.
    116. Bouteiller JM, Baudry M, Allam SL, Greget RJ, Bischoff S, Berger TW. Modeling glutamatergic synapses: insights into mechanisms regulating synaptic efficacy. J Integr Neurosci. 2008 Jun; 7(2):185-97. PMID: 18763719; PMCID: PMC2947192.
    117. Song D, Marmarelis VZ, Berger TW. Parametric and non-parametric modeling of short-term synaptic plasticity. Part I: Computational study. J Comput Neurosci. 2009 Feb; 26(1):1-19. PMID: 18506609; PMCID: PMC2770349.
    118. Song D, Wang Z, Marmarelis VZ, Berger TW. Parametric and non-parametric modeling of short-term synaptic plasticity. Part II: Experimental study. J Comput Neurosci. 2009 Feb; 26(1):21-37. PMID: 18504530; PMCID: PMC2749717.
    119. Dimoka A, Courellis SH, Marmarelis VZ, Berger TW. Modeling the nonlinear dynamic interactions of afferent pathways in the dentate gyrus of the hippocampus. Ann Biomed Eng. 2008 May; 36(5):852-64. PMID: 18299993; PMCID: PMC2749714.
    120. Dimoka A, Courellis SH, Gholmieh GI, Marmarelis VZ, Berger TW. Modeling the nonlinear properties of the in vitro hippocampal perforant path-dentate system using multielectrode array technology. IEEE Trans Biomed Eng. 2008 Feb; 55(2 Pt 1):693-702. PMID: 18270006; PMCID: PMC2749727.
    121. Song D, Hendrickson P, Marmarelis VZ, Aguayo J, He J, Loeb GE, Berger TW. Predicting EMG with generalized Volterra kernel model. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008:201-4. PMID: 19162628.
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    122. Zanos TP, Hampson RE, Deadwyler SA, Berger TW, Marmarelis VZ. Functional connectivity through nonlinear modeling: an application to the rat hippocampus. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008:5522-5. PMID: 19163968.
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    123. Dibazar AA, Yousefi A, Berger TW. A system for move-free and real time monitoring of readiness. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008:4879-82. PMID: 19163810.
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    124. Lu U, Song D, Berger TW. Nonparametric modeling of single neuron. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008:2469-72. PMID: 19163203.
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    125. Chan RH, Song D, Berger TW. Tracking temporal evolution of nonlinear dynamics in hippocampus using time-varying volterra kernels. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008:4996-9. PMID: 19163839.
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    126. Hsiao MC, Song D, Berger TW. Control theory-based regulation of hippocampal CA1 nonlinear dynamics. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008:5535-8. PMID: 19163971.
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    127. Berger TW, Gerhardt G, Liker MA, Soussou W. The impact of neurotechnology on rehabilitation. IEEE Rev Biomed Eng. 2008; 1:157-97. PMID: 22274903.
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    128. Soussou WV, Yoon GJ, Brinton RD, Berger TW. Neuronal network morphology and electrophysiologyof hippocampal neurons cultured on surface-treated multielectrode arrays. IEEE Trans Biomed Eng. 2007 Jul; 54(7):1309-20. PMID: 17605362.
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    129. Song D, Chan RH, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Nonlinear dynamic modeling of spike train transformations for hippocampal-cortical prostheses. IEEE Trans Biomed Eng. 2007 Jun; 54(6 Pt 1):1053-66. PMID: 17554824.
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    130. Gholmieh G, Courellis S, Marmarelis V, Berger T. Nonlinear dynamic model of CA1 short-term plasticity using random impulse train stimulation. Ann Biomed Eng. 2007 May; 35(5):847-57. PMID: 17380396.
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    131. Song D, Chan RH, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Statistical selection of multiple-input multiple-output nonlinear dynamic models of spike train transformation. Conf Proc IEEE Eng Med Biol Soc. 2007; 2007:4727-30. PMID: 18003061.
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    132. Lu S, Bansal A, Soussou W, Berger TW, Madhukar A. Receptor-ligand-based specific cell adhesion on solid surfaces: hippocampal neuronal cells on bilinker functionalized glass. Nano Lett. 2006 Sep; 6(9):1977-81. PMID: 16968011.
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    133. Marmarelis VZ, Zanos TP, Courellis SH, Berger TW. Boolean modeling of neural systems with point-process inputs and outputs. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:2114-7. PMID: 17946091.
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    134. Courellis SH, Zanos TP, Hsiao MC, Hampson RE, Deadwyler SA, Marmarelis VZ, Berger TW. Modeling hippocampal nonlinear dynamic transformations with principal dynamic modes. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:2300-3. PMID: 17946509.
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    135. Dibazar AA, Berger TW, Narayanan SS. Pathological voice assessment. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:1669-73. PMID: 17946059.
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    136. Bouteiller JM, Qiu Y, Ziane MB, Baudry M, Berger TW. EONS: an online synaptic modeling platform. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:4155-8. PMID: 17946227.
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    137. Song D, Chan RH, Marmarelis VZ, Hampson RE, Deadwyler SA, Berger TW. Physiologically plausible stochastic nonlinear kernel models of spike train to spike train transformation. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:6129-32. PMID: 17946359.
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    138. Zanos TP, Courellis SH, Hampson RE, Deadwyler SA, Marmarelis VZ, Berger TW. A multi-input modeling approach to quantify hippocampal nonlinear dynamic transformations. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:4967-70. PMID: 17946273.
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    139. Xie X, Song D, Wang Z, Marmarelis VZ, Berger TW. Interaction of short-term neuronal plasticity and synaptic plasticity revealed by nonlinear systems analysis in dentate granule cells. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:5543-6. PMID: 17946314.
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    140. Hsiao MC, Chan CH, Srinivasan V, Ahuja A, Erinjippurath G, Zanos TP, Gholmieh G, Song D, Wills JD, LaCoss J, Courellis S, Tanguay AR, Granacki JJ, Marmarelis VZ, Berger TW. VLSI implementation of a nonlinear neuronal model: a "neural prosthesis" to restore hippocampal trisynaptic dynamics. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:4396-9. PMID: 17946244.
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    141. Dimoka A, Courellis SH, Marmarelis VZ, Berger TW. Modeling the nonlinear dynamic interactions of the lateral and the medial perforant path of the hippocampal dentate gyrus. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:5539-42. PMID: 17946313.
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    142. Lu B, Yamada WM, Berger TW. Nonlinear dynamic neural network for text-independent speaker identification using information theoretic learning technology. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:2442-5. PMID: 17946959.
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    143. Gholmieh G, Soussou W, Han M, Ahuja A, Hsiao MC, Song D, Tanguay AR, Berger TW. Custom-designed high-density conformal planar multielectrode arrays for brain slice electrophysiology. J Neurosci Methods. 2006 Apr 15; 152(1-2):116-29. PMID: 16289315.
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    144. Berger TW, Ahuja A, Courellis SH, Deadwyler SA, Erinjippurath G, Gerhardt GA, Gholmieh G, Granacki JJ, Hampson R, Hsaio MC, LaCoss J, Marmarelis VZ, Nasiatka P, Srinivasan V, Song D, Tanguay AR, Wills J. Restoring lost cognitive function. IEEE Eng Med Biol Mag. 2005 Sep-Oct; 24(5):30-44. PMID: 16248115.
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    145. Gholmieh G, Courellis S, Dimoka A, Wills JD, LaCoss J, Granacki JJ, Marmarelis V, Berger T. An algorithm for real-time extraction of population EPSP and population spike amplitudes from hippocampal field potential recordings. J Neurosci Methods. 2004 Jul 30; 136(2):111-21. PMID: 15183263.
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    146. Gholmieh G, Courellis S, Fakheri S, Cheung E, Marmarelis V, Baudry M, Berger T. Detection and classification of neurotoxins using a novel short-term plasticity quantification method. Biosens Bioelectron. 2003 Oct 15; 18(12):1467-78. PMID: 12941562.
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    147. Namarvar HH, Berger TW. An efficient training algorithm for dynamic synapse neural networks using trust region methods. Neural Netw. 2003 Jun-Jul; 16(5-6):585-91. PMID: 12850011.
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    148. Gholmieh G, Courellis S, Marmarelis V, Berger T. An efficient method for studying short-term plasticity with random impulse train stimuli. J Neurosci Methods. 2002 Dec 15; 121(2):111-27. PMID: 12468002.
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    149. Wang Z, Song D, Berger TW. Contribution of NMDA receptor channels to the expression of LTP in the hippocampal dentate gyrus. Hippocampus. 2002; 12(5):680-8. PMID: 12440582.
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    150. Song D, Wang Z, Berger TW. Contribution of T-type VDCC to TEA-induced long-term synaptic modification in hippocampal CA1 and dentate gyrus. Hippocampus. 2002; 12(5):689-97. PMID: 12440583.
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