2021


Elyahoodayan, S., Jiang, W., Lee, C., Shao, A., Weiland, G., Whalen, J., Petrossians, A., and Song, D. Stimulation of recording of the hippocampus using the same Pt-Ir Coated Microelectrodes. Frontiers in Neuroscience, 2021, DOI: 10.3389/fnins.2021.616063.

Yu, P-N., Liu, C.Y., Heck, C.N., Berger, T.W. and Song, D. A Sparse multiscale nonlinear autoregressive model for seizure prediction. Journal of Neural Engineering, 2021, DOI: 10.1088/1741-2552/abdd43.

2020


Moore, B., Berger, T.W., and Song, D. Validation of a convolutional neural network model for spike transformation using a generalized linear model. Proceedings of the IEEE EMBC Conference, 2020, 3236-3239.

She, X., Berger, T.W., and Song, D. Accelerating estimation of a multi-input, multi-output model of the hippocampus with a parallel computing strategy. Proceedings of the IEEE EMBC Conference, 2020, 2479-2482.

Elyahoodayan, S., Larson, C., Cobo, A., Meng, E., and Song, D. Acute in vivo testing of a polymer cuff electrode with integrated microfluidic channels for stimulation, recording, and drug delivery on rat sciatic nerve. Journal of Neuroscience Methods, 2020, 336, 108634, DOI: 10.1016/j.jneumeth.2020.108634.

Bingham, C.S., Paknahad, J., Girard, C.B.C., Loizos, K., Bouteiller, J-M.C., Song, D., Gianluca, L., and Berger, T.W. Admittance method for estimating local field potentials generated in a multi-scale neuron model of the hippocampus. Frontiers in Computational Neuroscience, DOI: 10.3389/fncom.2020.00072.

Scholten, K., Larson, C., Xu, H., Song, D., and Meng, E. A 512-channel multi-layer polymer-based neural probe array. IEEE Journal of Microelectromechanical Systems, 2020, 29(5), 1054-1058, DOI: 10.1109/JMEMS.2020.2999550.

Wang, X., Hirschberg, A.W., Xu, H., Slingsby-Smith, Z., Lecomte, A., Scholten, K., Song, D., and Meng, E. A Parylene neural probe array for multi-region deep brain recordings. IEEE Journal of Microelectromechanical Systems, 2020, 29(4), 499-513, DOI: 10.1109/JMEMS.2020.3000235.

Scholten, K., Meng, E., Knaack, G., and Song, D. Editorial: interfacing with the peripheral nervous system. Journal of Neuroscience Methods, 2020, 340, 108745, DOI: 10.1016/j.jneumeth.2020.108745.

Bingham, C.S., Mergenthal, A., Bouteiller, J-M.C., Song, D., Gianluca, L., and Berger, T.W. ROOTS: An algorithm to generate biologically realistic cortical axons and an application to electroceutical modeling. Frontiers in Computational Neuroscience, 2020, DOI: 10.3389/fncom.2020.00013.

2019


Elyahoodayan, S., Jiang, W., Xu, H., and Song, D. A multi-channel asynchronous neurostimulator with artifact suppression for neural code-based stimulations. Frontiers in Neuroscience, 2019, DOI: 10.3389/fnins.2019.01011.

Geng, K., Shin, D., Song, D., Hampson, R.E., Deadwyler, S.A., Berger, T.W., and Marmarelis, V.Z. Multi-input, multi-output neuronal mode network approach to modeling the encoding dynamics and functional connectivity of neural systems. Neural Computation, 2019, 31, 1-29, DOI: 10.1162/NECO_a_01204.

Yu, G., Bouteiller J-M.C., Song, D., and Berger, T.W. Axonal anatomy optimizes spatial encoding in the rat entorhinal-dentate system: a computational study. IEEE Transactions on Biomedical Engineering, 2019, 66(10), 2728-2739, DOI: 10.1109/TBME.2019.2894410.

Cobo, A.M., Larson, C., Scholten, K., Miranda, J.A., Elyahoodayan, S., Song, D., Pikov, V., and Meng, E. Parylene-based cuff electrode with integrated microfluidics for peripheral nerve recording, stimulation and drug delivery. Journal of Microelectromechanical Systems, 2019, 38, 36-49, DOI: 10.1109/JMEMS.2018.2881908.

2018


Hu E., Bouteiller J-M.C., Song D., and Berger T.W. Simulated postsynaptic calcium dynamics using an integrated model of spine properties, membrane channels, and pumps: validation, and an extension towards multi-scale calcium modeling. Frontiers in Computational Neuroscience, 2018, DOI: 10.3389/fncom.2018.00058.

Qiao, Z., Han, Y., Han, X., Xu, H., Li, W.X.Y., Song, D., Berger, T.W., and Cheung, R.C.C. ASIC implementation of a nonlinear dynamical model for hippocampal prosthesis. Neural Computation, 2018, 30, 2472-2499, DOI:10.1162/neco_a_01107.

Hampson, R.E., Song, D., Robinson, B.S., Fetterhoff, D., Dakos, A.S., Roeder, B.M., Wicks, R.T., Witcher, M.R., Couture, D.E., Laxton, A.W., Munger-Clary, H., Popli, G., Sollman, M.J., Marmarelis, V.Z., Berger, T.W., and Deadwyler, S.A. A hippocampal neural prosthetic for restoration of human memory function. Journal of Neural Engineering, 2018, 15, 036014, DOI: 10.1088/1741-2552/aaaed7.

Song, D., Robinson, B.S., Hampson, R.E., Marmarelis, V.Z., Deadwyler, S.A., and Berger, T.W. Sparse large-scale nonlinear dynamical modeling of human hippocampus for memory prostheses. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 2018, 26(2), 272-280, DOI: 10.1109/TNSRE.2016.2604423.

Bingham, C.S., Loizos, K., Yu, G., Gilbert, A., Bouteiller, J-M.C., Song, D., Gianluca, L., and Berger, T.W. Model-based analysis of electrode placement and pulse amplitude for hippocampal stimulation. IEEE Transactions on Biomedical Engineering, 2018, DOI: 10.1109/TBME.2018.2791860.

Ramirez-Zamora, A., Giordano, J., Gunduz, A., Brown, P., Sanchez, J., Foote, K.D., Almeida, L., Starr, P., Bronte-Stewart, H.M., Hu, W., McIntyre, C., Goodman, W., Kumsa, D., Grill, W.M., Walker, H., Johnson, M., Vitek, J.L., Greene, D., Rizzuto, D.S., Song, D., Berger, T.W., Hampson, R.E., Deadwyler, S.A., Hochberg, L., Schiff, N., Stypulkowski, P., Worrell, G., Tiruvadi, V., Mayberg, H., Jimenez-Shahed, J., Pranav, N., Sheth, S., Gross, R., Lempka, S.F., Deeb, W., and Okun, M.S. Evolving applications, technological challenges and future opportunities in neuromodulation: Proceedings of the Fifth Annual Deep Brain Stimulation Think Tank. Frontiers in Neuroscience, 2018, DOI: 10.3389/fnins.2017.00734.

Xu, H., Hirschberg, A.W., Scholten, K., Berger, T.W., Song, D., and Meng, E. Acute in vivo testing of a conformal polymer microelectrode array for multi-region hippocampal recording. Journal of Neural Engineering, 2018, 15, 016017, DOI: 10.1088/1741-2552/aa9451.

2017


Geng, K., Shin, D., Song, D., Hampson, R.E., Deadwyler, S.A., Berger, T.W., and Marmarelis, V.Z. Mechanism-based and input-output modeling of the key neuronal connections and signal transformations in the CA3-CA1 regions of the hippocampus. Neural Computation, 2017, 30, 149-183, DOI: 10.1162/NECO_a_01031.

Sienkiewicz, E., Song, D., Breidt, F.J., Wang, H. Sparse functional dynamical model—a big data approach. Journal of Computational and Graphical Statistics, 2017, 26(2), 319-329, DOI: 10.1080/10618600.2016.1222292.

2016


Robinson, B.S., Berger, T.W., and Song, D. Identification of stable spike-timing-dependent plasticity from spiking activity with generalized multilinear modeling. Neural Computation, 2016, 28:11, 2320-2351, DOI: 10.1162/NECO_a_00883.

Deadwyler, S.A., Hampson, R.E., Song, D., Opris, I., Gerhardt, G.A., Marmarelis, V.Z., and Berger, T.W. A cognitive prosthesis for memory facilitation by closed-loop functional ensemble stimulation of hippocampal neurons in primate brain. Experimental Neurology, 2016, DOI: 10.1016/j.expneurol.2016.05.031.

Li, W.X.Y., Cheung, R.C.C., Xin, Y., Song, D., and Berger, T.W. An FPGA-based high-performance neural ensemble spiking activity simulator utilizing generalized Volterra kernel and complexity analysis. Journal of Circuits, Systems, and Computers, 2016, 25(1), 164004.

2015


Hendrickson, P., Yu, G., Song, D., and Berger, T.W. Interactions between inhibitory interneurons and excitatory associational circuitry in determining spatio-temporal dynamics of hippocampal dentate granule cells: a large-scale computational study. Frontiers in Systems Neuroscience, 2015, DOI: 10.3389/fnsys.2015.00155.

Opris, I., Santos, L., Gerhardt, G.A., Song, D., Berger, T.W., Hampson, R.E., and V.Z., Deadwyler, S.A. Distributed encoding of spatial and object categories in primate hippocampal microcircuits. Frontiers in Neuroscience, 2015, DOI: 10.3389/fnins.2015.00317.

Hu, E, Bouteiller, J-M.C., Song, D., Baudry, M., and Berger, T.W. Volterra representation enables modeling of complex synaptic nonlinear dynamics in large-scale simulations. Frontiers in Computational Neuroscience, 2015, DOI: 10.3389/fncom.2015.00112.

Sandler, R., Song, D., Hampson, R.E., Deadwyler, S.A., Berger, T.W., and Marmarelis, V.Z. Hippocampal closed-loop modeling and implications for seizure stimulation design. Journal of Neural Engineering, 2015, 12, 056017.

Hendrickson, P., Yu, G., Song, D., and Berger, T.W. A million-plus neuron model of the hippocampal dentate gyrus: critical role for topography in determining spatio-temporal network dynamics. IEEE Transactions on Biomedical Engineering, 2015, 63, 199-209. DOI: 10.1109/TBME.2015.2445771.

Song, D., Chan, R.H.M., Robinson, B.S., Marmarelis, V.Z., Opris, I., Hampson, R.E., Deadwyler, S.A., and Berger, T.W. Identification of functional synaptic plasticity from spiking activities using nonlinear dynamical modeling. Journal of Neuroscience Methods, 2015, 244, 123-135, DOI: 10.1016/j.jneumeth.2014.09.023.

Hsiao, M-C., Yu, P-N., Song, D., Liu, C.Y., Heck, C.N., Millett, D., and Berger, T.W. An in vitro seizure model from human hippocampal slices using multi-electrode arrays. Journal of Neuroscience Methods, 2015, 244, 154-163, DOI: 10.1016/j.jneumeth.2014.09.010.

Xin, Y., Li, W.X.Y., Zhang, Z., Cheung, R.C.C., Song, D., and Berger, T.W. An application specific instruction set processor (ASIP) for adaptive filters in neural prosthetics. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015, DOI: 10.1109/TCBB.2015.2440248.

Ghaderi, V., Song, D., Choma, J., and Berger, T.W. Nonlinear cognitive signal processing in ultra-low-power programmable analog hardware. IEEE Transaction on Circuits and Systems II, 2015, 62(2), 124-128.

Deadwyler, S.A., Berger, T.W., Opris, I., Song, D., and Hampson, R.E. Neurons and networks organizing and sequencing memories. Brain Research, 2015, DOI: 10.1016/j.brainres.2014.12.037.

2014


Song, D., Harway, M., Marmarelis, V.Z., Hampson, R.E., Deadwyler, S.A., and Berger, T.W. Extraction and restoration of hippocampal spatial memories with nonlinear dynamical modeling. Frontiers in Systems Neuroscience, 2014, DOI: 10.3389/fnsys.2014.00097.

Sandler, R., Deadwyler, S.A., Hampson, R.E., Song, D., Berger, T.W., and Marmarelis, V.Z. System identification of point-process neural systems using probability based Volterra kernels. Journal of Neuroscience Methods, 2015, 179-192, DOI: 10.1016/j.jneumeth.2014.11.013.

Sandler, R., Song, D., Hampson, R.E., Deadwyler, S.A., Berger, T.W., and Marmarelis, V.Z. Model-based assessment of an in-vivo predictive relationship from CA1 to CA3 in the rodent hippocampus. Journal of Computational Neuroscience, 2015, 38, 89-103, DOI: 10.1007/s10827-014-0530-8.

Xin, Y., Li, W.X.Y., Cheung, R.C.C., Chan, R.H.M., Yan, H., Song, D., and Berger, T.W. An FPGA based scalable architecture of a stochastic state point process filter (SSPPF) to track the nonlinear dynamics underlying neural spiking. Microelectronics Journal, 2014, 45(6), 690-701.

2013


Song, D., Wang, H., Tu, C.Y., Marmarelis, V.Z., Hampson, R.E., Deadwyler, S.A., and Berger, T.W. Identification of sparse neural functional connectivity using penalized likelihood estimation and basis functions. Journal of Computational Neuroscience, 2013, 35, 335-357.

Marmarelis, V.Z., Shin, D., Song, D., Hampson, R.E., Deadwyler, S.A., and Berger, T.W. On parsing the neural code in the prefrontal cortex of primates using principle dynamic modes. Journal of Computational Neuroscience, 2013, DOI: 10.1007/s10827-013-0475-3.

Deadwyler, S.A., Berger, T.W., Sweat, A., Song, D., Chan, R.H.M., Opris, I., Gerhardt, G.A., Marmarelis, V.Z., and Hampson, R.E. Donor/recipient enhancement of memory in rat hippocampus. Frontiers in Systems Neuroscience, 2013, DOI: 10.3389/fnsys.2013.00120.

Hampson, R.E., Song, D., Opris, I., Santos, L., Shin, D., Gerhardt, G.A., Marmarelis, V.Z., Berger, T.W., and Deadwyler, S.A. Facilitation of memory encoding in primate hippocampus by a neuroprosthesis that promotes task specific neural firing. Journal of Neural Engineering, 2013, 10, 066013.

Opris, I., Santos, L., Gerhardt, G.A., Song, D., Berger, T.W., Hampson, R.E., and V.Z., Deadwyler, S.A. Prefrontal cortical microcircuits bind perception to executive control. Scientific Reports, 2013, DOI: 10.1038/srep02285.

Li, W.X.Y., Chan, R.H.M., Song, D., Berger, T.W., and Cheung, R.C.C. Real-time prediction of neuronal population spiking activity using FPGA. IEEE Transactions on Biomedical Circuits and Systems, 2013, 7, 489-498.

Hsiao, M-C., Song, D., and Berger, T.W. Nonlinear dynamical model based control of in vitro hippocampal output. Frontiers in Neural Circuits, 2013, 7: Article 20, 1-14.

Marmarelis, V.Z., Shin, D., Song, D., Hampson, R.E., Deadwyler, S.A., and Berger, T.W. Nonlinear modeling of dynamic interactions within neuronal ensembles using principal dynamic modes. Journal of Computational Neuroscience, 2013, 34(1): 73-87.

2012


Marmarelis, V.Z., Shin, D., Hampson, R.E., Deadwyler, S.A., Song, D., and Berger, T.W. Design of optimal stimulation patterns for neuronal ensembles based on Volterra-type hierarchical modeling. Journal of Neural Engineering, 2012, 9, 066003.

Berger, T.W., Song, D., Chan, R.H.M., Shin, D., Marmarelis, V.Z., Hampson, R.E., Sweatt, A.J., Heck, C.N., Liu, C.Y., Wills, J., LaCoss, J., Granacki, J.J., Gerhardt, G.A., and Deadwyler, S.A. Role of the hippocampus in memory formation: restorative encoding memory integration neural device as a cognitive neural prosthesis. IEEE Pulse, 2012, 3(5): 17-22.

Hampson, R.E., Gerhardt, G.A., Marmarelis, V.Z., Song, D., Opris, I., Santos, L., Berger, T.W., Deadwyler, S.A. Facilitation and restoration of cognitive function in primate prefrontal cortex by a neuroprosthesis that utilizes minicolumn-specific neural firing. Journal of Neural Engineering, 2012, 9(5): 056012.

Hampson, R.E., Song, D., Chan, R.H.M., Sweatt, A.J., Riley, M., Goonawardena, A., Marmarelis, V.Z., Gerhardt, G.A., Berger, T.W., and Deadwyler, S.A. Closing the loop for memory prostheses: detecting the role of hippocampal neural ensembles using nonlinear models. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 2012, 20(4): 510-525.

Berger, T.W., Song, D., Chan, R.H.M., Marmarelis,V.Z., LaCoss, J., Wills, J., Hampson, R.E., Deadwyler, S.A., and Granacki, J.J. A hippocampal cognitive prosthesis: Multi-input, multi-output nonlinear modeling and VLSI implementation. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 2012, 20(2): 198-211.

Hampson, R.E., Song, D., Chan, R.H.M., Sweatt, A.J., Fuqua, J., Gerhardt, G.A., Marmarelis, V.Z., Berger, T.W., and Deadwyler, S.A. A nonlinear model for cortical prosthetics: memory facilitation by hippocampal ensemble stimulation. IEEE Transactions on Neural Systems and Rehabilitation Engineering, 2012, 20(2): 184-197.

Taghva, A., Song, D., Hampson, R.E., Deadwyler, S.A., and Berger, T.W. Determination of relevant neuron-neuron connections for neural prosthetics using time-delayed mutual information: Tutorial and preliminary results. World Neurosurgery, 2012, doi: 10.1016/j.wneu.2011.09.002.

Lu, U., Roach, S.M., Song, D., and Berger, T.W. Nonlinear dynamic modeling of neuron action potential threshold during synaptically-driven broadband intracellular activity. IEEE Transactions on Biomedical Engineering, 2012, 59, 706-716.

2011


Li, W.X.Y., Chan, R.H.M., Zhang, W., Cheung, R.C.C., Song, D., and Berger, T.W. High-performance and scalable system architecture of generalized Laguerre-Volterra MIMO models for neural population spiking activities. IEEE Journal on Emerging and Selected Topics in Circuits and Systems, 2011, 1(4): 489-501.

Berger, T.W., Hampson, R.E., Song, D., Goonawardena, A., Marmarelis, V.Z., and Deadwyler, S.A. A cortical neural prosthesis for restoring and enhancing memory. Journal of Neural Engineering, 2011, 8, 046017.

Hampson, R.E., Sweatt, A.J., Goonawardena, A.V., Song, D., Chan, R.H.M., Berger, T.W., and Deadwyler, S.A. Memory encoding in hippocampus is negatively influenced by cannabinoid CB1 receptors. Behavioural Pharmacology, 2011, 22(4): 335-346.

2010


Lu, U., Song, D., and Berger, T.W. Nonlinear dynamic modeling of synaptically driven single hippocampal neuron intracellular activity. IEEE Transactions on Biomedical Engineering, 2010, 58, 1303-1313.

Berger, T.W., Song, D., Chan, R.H.W., and Marmarelis, V.Z. The neurobiological basis of cognition: Identification by multi-input, multi-output nonlinear dynamic modeling. Proceedings of the IEEE, 2010, 98, 356-374.

2009


Song, D., Chan, R.H.M., Marmarelis, V.Z., Hampson, R.E., Deadwyler, S.A., and Berger, T.W. Nonlinear modeling of neural population dynamics for hippocampal prostheses. Neural Networks, 2009, 22, 1340-1351.

Song, D., Marmarelis, V.Z., and Berger, T.W. Parametric and non-parametric modeling of short-term synaptic plasticity. Part I: Computational study. Journal of Computational Neuroscience, 2009, 26, 1-19.

Song, D., Wang, Z., Marmarelis, V.Z., and Berger, T.W. Parametric and non-parametric modeling of short-term synaptic plasticity. Part II: Experimental study. Journal of Computational Neuroscience, 2009, 26, 21-37.

2007


Song, D., Chan, R.H.M., Marmarelis, V.Z., Hampson, R.E., Deadwyler, S.A., and Berger, T.W. Nonlinear dynamic modeling of spike train transformations for hippocampal-cortical prostheses. IEEE Transactions on Biomedical Engineering, 2007, 54, 1053-1066.

2006


Gholmieh, G., Soussou, W., Han, M., Ahuja, A., Hsiao, M.-C., Song, D., Tanguay, Jr., A.R., and Berger, T.W. Custom-designed, high-density conformal planar multielectrode arrays for brain slice electrophysiology. Journal of Neuroscience Methods, 2006, 152, 116-129.

2005


Berger, T.W., Ahuja, A., Courellis, S.H., Deadwyler, S.A., Erinjippurath, G., Gerhardt, G.A., Gholmieh, G, Granacki, J.J., Hampson, R., Hsiao, M-C., LaCoss, J., Marmarelis, V.Z., Nasiatka, P., Srinivasan, V., Song, S., Tanguay, Jr., A.R., and Wills, J. Restoring lost cognitive function: Hippocampal-cortical neural prostheses. IEEE Engineering in Medicine and Biology Magazine, 2005, 24, 30-44.

2002


Song, D., Wang, Z., and Berger, T.W. Contribution of T-type VDCCs to TEA-induced long-term synaptic modification in hippocampal CA1 and dentate gyrus. Hippocampus, 2002, 12, 689-697.

Wang, Z., Song, D., and Berger, T.W. Contribution of NMDA receptor-channels to the expression of LTP in the hippocampal dentate gyrus. Hippocampus, 2002, 12, 680-688.

2001


Song, D., Xie, X., Wang, Z., and Berger, T.W. Differential effect of TEA on long-term synaptic modification in hippocampal CA1 and dentate gyrus in vitro. Neurobiology of Learning and Memory, 2001, 76, 375-387.