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Dong Song, PhD

Title(s)Research Associate Professor
Phone+1 213 740 8063
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    Dong Song is a research associate professor in the Department of Biomedical Engineering, University of Southern California. He received the B.S. degree in Biophysics from the University of Science and Technology of China in 1994, and the Ph.D. degree in biomedical engineering from the University of Southern California in 2003. His research interests include nonlinear systems analysis of the nervous system, cortical neural prosthesis, electrophysiological mechanisms of learning and memory formation, and development of novel modeling techniques incorporating both statistical and mechanistic modeling methods. Together with Drs. Marmarelis and Berger, he developed the multiple-input, multiple-output (MIMO) nonlinear dynamical model that serves as the computational basis of the hippocampal memory prosthesis. He has published over 50 peer-reviewed journal articles and book chapters. He is a member of the American Statistical Association, the Biomedical Engineering Society, the IEEE, and the Society for Neuroscience.

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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. Geng K, Shin DC, Song D, Hampson RE, Deadwyler SA, Berger TW, Marmarelis VZ. Multi-Input, Multi-Output Neuronal Mode Network Approach to Modeling the Encoding Dynamics and Functional Connectivity of Neural Systems. Neural Comput. 2019 Jul; 31(7):1327-1355. PMID: 31113305.
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    2. 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.
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    3. 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 05; 30(5):1180-1208. PMID: 29566356.
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    4. 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.
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    5. 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 01; 30(1):149-183. PMID: 29064783.
      View in: PubMed
    6. Robinson BS, Berger TW, Song D. Identification of Stable Spike-Timing-Dependent Plasticity from Spiking Activity with Generalized Multilinear Modeling. Neural Comput. 2016 Nov; 28(11):2320-2351. PMID: 27557101.
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    7. 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.
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    8. 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.
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    9. 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
    10. 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.
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    11. 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.
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    12. 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.
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    13. 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.
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    14. 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.
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    15. 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.
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    16. Hsiao MC, Song D, Berger TW. Nonlinear dynamical model based control of in vitro hippocampal output. Front Neural Circuits. 2013; 7:20. PMID: 23429994.
      View in: PubMed
    17. 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.
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    18. 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.
      View in: PubMed
    19. 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.
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    20. 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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    21. 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.
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    22. 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.
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    23. 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.
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    24. 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.
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    25. 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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    26. 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.
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    27. 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.
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    28. 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.
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    29. 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.
      View in: PubMed
    30. 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.
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    31. 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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    32. 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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    33. 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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    34. 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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    35. 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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    36. 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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    37. 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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    38. 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.
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    39. 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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    40. 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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    41. 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.
      View in: PubMed
    42. 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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    43. 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.
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    44. 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.
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    45. 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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    46. 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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    47. 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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    48. 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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    49. 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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    50. 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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    51. 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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    52. 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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    53. 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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    54. 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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    55. 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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    56. 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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    57. 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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    58. Song D, Xie X, Wang Z, Berger TW. Differential effect of TEA on long-term synaptic modification in hippocampal CA1 and dentate gyrus in vitro. Neurobiol Learn Mem. 2001 Nov; 76(3):375-87. PMID: 11726243.
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