How to cite the Neuroscience Gateway

If you used resources available from the NSG for your research, please cite us as follows:
S Sivagnanam, A Majumdar, K Yoshimoto, V Astakhov, A Bandrowski, M. E. Martone, and N. T. Carnevale. Introducing the Neuroscience Gateway, IWSG, volume 993 of CEUR Workshop Proceedings, CEUR-WS.org, 2013.

Neuroscience publications, presentations, posters enabled by NSG:

  1. Amit Naskar, Anirudh Vattikonda, Gustavo Deco, Dipanjan Roy, Arpan Banerjee, "Multi-scale dynamic mean field model (MDMF) relates resting-state brain dynamics with local cortical excitatory–inhibitory neurotransmitter homeostasis", May 2021 Network Neuroscience , DOI: 10.1162/netn_a_00197
  2. Arnaud Delorme, Dung Truong, Ramon Martinez- Cancino, Cyril Pernet, Subha Sivagnanam, Kenneth Yoshimoto, Russ Poldrack, Amit Majumdar, Scott Makeig, "Tools for Importing and Evaluating BIDS-EEG Formatted Data", 10th International IEEE EMBS Conference On Neural Engineering (NER'21), May 4-6, 2021
  3. Mia Salans, BA MAS, Michelle D Tibbs, MD MAS, Roshan Karunamuni, PhD, Anthony Yip, BS MAS, Minh-Phuong Huynh-Le, MD MAS, Anna Christina Macari, MA, Anny Reyes, MS, Kathryn Tringale, MD MAS, Carrie R McDonald, PhD, Jona A Hattangadi-Gluth, MD, Longitudinal change in fine motor skills after brain radiotherapy and in vivo imaging biomarkers associated with decline, Neuro-Oncology, 2021;, noab017, https://doi.org/10.1093/neuonc/noab017
  4. Viktor János Oláh , Nigel P Pedersen & Matthew JM Rowan, "Ultrafastlarge-scalesimulationsof biophysicallyrealistic neurons usingdeep learning", bioRxiv, doi: https://doi.org/10.1101/2021.02.22.432356; Feb 2021
  5. Viktor János Oláh, Gergely Tarcsay, János Brunner, "Small size of recorded neuronal structures confines the accuracy in direct axonal voltage measurements", bioRxiv 2021.01.29.428709; doi: https://doi.org/10.1101/2021.01.29.428709 ; Feb 2021
  6. Pavel Sanda, Paola Malerba, Xi Jiang, Giri P Krishnan, Jorge Gonzalez-Martinez, Eric Halgren, Maxim Bazhenov, Bidirectional Interaction of Hippocampal Ripples and Cortical Slow Waves Leads to Coordinated Spiking Activity During NREM Sleep, Cerebral Cortex, Volume 31, Issue 1, January 2021, Pages 324-340, https://doi.org/10.1093/cercor/bhaa228
  7. C. Ramon, M. D. Holmes, "Increased Phase Cone Turnover in 80-250 Hz Bands Occurs in the Epileptogenic Zone During Interictal Periods", Front. Hum. Neurosci., 23 December 2020 | https://doi.org/10.3389/fnhum.2020.615744
  8. S. Hsu, Y Lin, J Onton, TP Jung, S. Makeig, "Unsupervised Learning of Brain State Dynamics during Emotion Imagery using High-Density EEG", October 2020, BioRxiv, https://doi.org/10.1101/2020.10.29.361394
  9. Shweta Prasad Archith Rajan Shaik Afsar Pasha Sandhya Mangalore Jitender Saini Madhura Ingalhalikar Pramod Kumar Pal, "Abnormal structural connectivity in progressive supranuclear palsy - Richardson syndrome", Neurologica, Published 11 November 2020, https://doi.org/10.1111/ane.13372.
  10. A D Bird, L H Deters, H Cuntz, Excess Neuronal Branching Allows for Local Innervation of Specific Dendritic Compartments in Mature Cortex, Cerebral Cortex, , bhaa271, https://doi.org/10.1093/cercor/bhaa271
  11. Prager, Eric M., Dorman, Daniel B. , Hobel, Zachary B., Malgady, Jeffrey M., Blackwell, Kim T., & Plotkin, Joshua L. (2020). Dopamine Oppositely Modulates State Transitions in Striosome and Matrix Direct Pathway Striatal Spiny Neurons. Neuron. 108. 1-12. 10.1016/j.neuron.2020.09.028
  12. Michelle D. Tibbs, Minh-Phuong Huynh-Le, Roshan Karunamuni, Anny Reyes, Anna Christina Macari, Kathryn R. Tringale, Mia Salans, Anthony Yip, Eulanca Liu, Aaron Simon, Carrie R. McDonald, Jona A. Hattangadi-Gluth, "Microstructural Injury to Left-Sided Perisylvian White Matter Predicts Language Decline After Brain Radiation Therapy", International Journal of Radiation Oncology, Biology, Physics, Published:July 23, 2020DOI:https://doi.org/10.1016/j.ijrobp.2020.07.032
  13. Lupascu Carmen A., Morabito Annunziato, Ruggeri Federica, Parisi Chiara, Pimpinella Domenico, Pizzarelli Rocco, Meli Giovanni, Marinelli Silvia, Cherubini Enrico, Cattaneo Antonino, Migliore Michele, "Computational Modeling of Inhibitory Transsynaptic Signaling in Hippocampal and Cortical Neurons Expressing Intrabodies Against Gephyrin", Frontiers in Cellular Neuroscience, Vol 14, 2020; DOI=10.3389/fncel.2020.00173, URL=https://www.frontiersin.org/article/10.3389/fncel.2020.00173
  14. Felix Neumaier, Serdar Alpdogan, Jürgen Hescheler, Toni Schneider; Zn2+-induced changes in Cav2.3 channel function: An electrophysiological and modeling study. J Gen Physiol 7 September 2020; 152 (9): e202012585. doi: https://doi.org/10.1085/jgp.202012585
  15. Guet-McCreight A and Skinner FK, "Computationally going where experiments cannot: a dynamical assessment of dendritic ion channel currents during in vivo-like states," F1000Research 2020, 9:180 (https://doi.org/10.12688/f1000research.22584.1)
  16. Xiao Luo, Alexandre Guet-McCreight, Vincent Villette, Ruggiero Francavilla, Beatrice Marino, Simon Chamberland, Frances K Skinner, Lisa Topolnik, Synaptic Mechanisms Underlying the Network State-Dependent Recruitment of VIP-Expressing Interneurons in the CA1 Hippocampus, Cerebral Cortex, Volume 30, Issue 6, June 2020, Pages 3667-3685, https://doi.org/10.1093/cercor/bhz334
  17. Viktor János Oláh, David Lukacsovich, Jochen Winterer, Antónia ArszovszkAndrea Lorincz, Zoltan Nusser, Csaba Földy, János Szabadics, "Functional specification of CCK+ interneurons by alternative isoforms of Kv4.3 auxiliary subunits', eLife 2020;9:e58515 doi: 10.7554/eLife.58515
  18. Jeremy Magland, James J Jun, Elizabeth Lovero, Alexander J Morley, Cole Lincoln Hurwitz, Alessio Paolo Buccino, Samuel Garcia, Alex H Barnett, "SpikeForest, reproducible web-facing ground-truth validation of automated neural spike sorters" , eLife 2020;9:e55167, May 2020; doi: 10.7554/eLife.55167
  19. S. Appukuttan, D. Mandge and R. Manchanda, "Implementation of Syncytial Models in NEURON Simulator for Improved Efficiency," 2020 28th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), Västerås, Sweden, 2020, pp. 266-273, doi: 10.1109/PDP50117.2020.00048.
  20. Tovbis D, Agur A, Mogk JPM, Zariffa J (2020) Automatic three-dimensional reconstruction of fascicles in peripheral nerves from histological images. PLOS ONE 15(5): e0233028. https://doi.org/10.1371/journal.pone.0233028, May, 2020.
  21. Navas-Olive, A., Valero, M., Jurado-Parras, T. et al. Multimodal determinants of phase-locked dynamics across deep-superficial hippocampal sublayers during theta oscillations. Nat Commun 11, 2217 (2020). https://doi.org/10.1038/s41467-020-15840-6
  22. Othman, M.H., Bhattacharya, M., Møller, K,Sren, K., Johannes, G., Jesper, K., Dutta, A.,and Kondziella, D. Resting-State NIRS-EEG in Unresponsive Patients with Acute Brain Injury: A Proof-of-Concept Study. Neurocrit Care (2020). https://doi.org/10.1007/s12028-020-00971-x; Published April 24, 2020
  23. Ramon Martinez-Cancino, Arnaud Delorme, Dung Truong, Fiorenzo Artoni, Kenneth Kreutz-Delgado, Subhashini Sivagnanam, Kenneth Yoshimoto, Amitava Majumdar, Scott Makeig, "The Open EEGLAB Portal Interface: High-Performance Computing with EEGLAB," NeuroImage, 2020, 116778, ISSN 1053-8119, https://doi.org/10.1016/j.neuroimage.2020.116778. (http://www.sciencedirect.com/science/article/pii/S1053811920302652)
  24. Yina Wei, Giri P. Krishnan, Lisa Marshall, Thomas Martinetz and Maxim Bazhenov, "Stimulation Augments Spike Sequence Replay and Memory Consolidation during Slow-Wave Sleep," Journal of Neuroscience 22 January 2020, 40 (4) 811-824; DOI: https://doi.org/10.1523/JNEUROSCI.1427-19.2019
  25. Moritz Groden, Marvin Weigand, Jochen Triesch, Peter Jedlicka, Hermann Cuntz, A Model of Brain Folding Based on Strong Local and Weak Long-Range Connectivity Requirements, Cerebral Cortex, , bhz249, https://doi.org/10.1093/cercor/bhz249, December 2019
  26. Sai Swathi Sivarathri, Prasad Calyam, Yuanxun Zhang, Ashish Pandey, Cong Chen, Dong Xu, Trupti Joshi and Satish Nair, "Chatbot Guided Domain-science Knowledge Discovery in a Science Gateway Application", Gateways 2019, San Diego, CA, USA, September 23-25, 2019. https://osf.io/meetings/gateways2019/
  27. Majoral D, Zemmar A, Vicente R (2020) A model for time interval learning in the Purkinje cell. PLoS Comput Biol 16(2): e1007601. https://doi.org/10.1371/journal.pcbi.1007601
  28. C. C.H. Cohen, M. A. Popovic, J. Klooster, M-T Weil, W. Mobius, K-A Nave, and M. H.P. Kole, "Saltatory Conduction along MyelinatedAxons Involves a Periaxonal Nanocircuit", 2020, Cell180, 311-322, January 23, 2020, Published by Elsevier Inc.https://doi.org/10.1016/j.cell.2019.11.039.
  29. K. TIAN, A. A. PRINZ, Neuronal and synaptic parameter degeneracy in central pattern generator activity, Society for Neuroscience Annual Meeting, Chicago, November, 2019.
  30. K. TIAN1, Y. LI2, M. L. MCKINNON2, *S. HOCHMAN3, A. A. PRINZ, Hyperexcitation in mouse sympathetic neurons after spinal cord injury, Society for Neuroscience Annual Meeting, Chicago, November, 2019
  31. B Latimer, T Banks, M Gahl, V Guntu, D.J Schulz, S.S Nair (2019) Computational modeling of the neural circuit of rodent lower urinary tract. 071.09/R19 Society for Neuroscience. Chicago.
  32. Johnson, J.T., & Wheaton, L.A. (October 19, 2019). Does Haptic Feedback Support Motor Learning with a Prosthesis? A Neurobehavioral Evaluation. Chicago, IL: American Society of Neurorehabilitation, 2019
  33. T Banks, V Guntu, A.M Hummos, S.S Nair (2019) Characterizing resonant and synchronizing mechanisms in a hippocampal theta model. 161.06/W17 Society for Neuroscience. Chicago.
  34. D Dopp, T Banks, P Samarth, D Kick, D Schulz, S.S Nair (2019) Detailed biologically realistic model of a crustacean cardiac ganglion network. 230.09/O8 Society for Neuroscience. Chicago.
  35. S.S Nair, T Banks, B Latimer, Z Chen, Z LYU, Z Chen, D Dopp, A Fotoohighiam, P Calyam, T Joshi, D. Xu (2019) Software automation or research and training in neural engineering. 431.17/DD22 Society for Neuroscience. Chicago.
  36. F Feng, D Headley, D Pare, S Nair (2019) Intrinsic gamma mechanisms differ in model lateral and basal amygdala networks. 465.19/C4 Society for Neuroscience. Chicago.
  37. Q Wei, T Banks, B Latimer, Z Chen, S.S Nair (2019) Automating development of biophysical single cell models. 615.03/DD40 Society for Neuroscience. Chicago.
  38. Z Chen, F Feng, D Headley, D.K.C Ho, D Pare, S.S Nair (2019) Detection and characterization of gamma bursts in LFP signals. 707.10/DD44 Society for Neuroscience. Chicago.
  39. DH Hadjiabadi, M Lovett-Barron, I Raikov, SC Baraban, J Leskovec, K Deisseroth, I Soltesz. Whole brain seizure networks at single cell resolution. Park City Epilepsy Meeting, 2019.
  40. Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV (2019) Think: Theory for Africa. PLoS Comput Biol 15(7): e1007049. https://doi.org/10.1371/journal.pcbi.1007049
  41. Oláh, Viktor & Lukacsovich, David & Winterer, Jochen & Lorincz, Andrea & Nusser, Zoltan & Foldy, Csaba & Szabadics, Janos. (2019). Functional specification of CCK+ interneurons by alternative isoforms of Kv4.3 auxiliary subunits, https://www.biorxiv.org/content/10.1101/683755v1 .
  42. Padraig Gleeson, Matteo Cantarelli, Boris Marin, Adrian Quintana, Matt Earnshaw, Sadra Sadeh, Eugenio Piasini, Justas Birgiolas, Robert C. Cannon, N. Alex Cayco-Gajic, Sharon Crook, Andrew P. Davison, Salvador Dura-Bernal, Andra´s Ecker, Michael L. Hines, Giovanni Idili, Frederic Lanore, Stephen D. Larson, William W. Lytton, Amitava Majumdar, Robert A. McDougal, Subhashini Sivagnanam, Sergio Solinas, Rokas Stanislovas, Sacha J. van Albada, Werner van Geit, and R. Angus Silver1,"Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits",2019 (June), Neuron 103, 1-17; https://doi.org/10.1016/j.neuron.2019.05.019 .
  43. Dura-Bernal, Salvador & Suter, Benjamin & Gleeson, Padraig & Cantarelli, Matteo & Quintana, Adrian & Rodriguez, Facundo & J Kedziora, David & L Chadderdon, George & Kerr, Cliff & Neymotin, Sam & Mcdougal, Robert & Hines, Michael & M G Shepherd, Gordon & Lytton, William. (2019). NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 8. 10.7554/eLife.44494.
  44. D. Tovbis, A. Agur, J. Mogk, and J. Zariffa, 'Identifying Fascicles in Peripheral Nerves using a Region-Based Convolutional Neural Network', 8th National Spinal Cord Injury Conference, Niagara Falls, ON, 2019.
  45. Latimer, Benjamin and Bergin, David and Guntu, Vinay and Schulz, David and Nair, Satish, "Integrating model-based approaches into a neuroscience curriculum - an interdisciplinary neuroscience course in engineering", vol 62, nubmer 1, pages 48-56, issn 0018-9359, IEEE Transactions on Education, 2019, DOI: 10.1109/TE.2018.28594111
  46. Guet-McCreight A, Skinner FK (2019) Using computational models to predict in vivo synaptic inputs to interneuron specific 3 (IS3) cells of CA1 hippocampus that also allow their recruitment during rhythmic states. PLoS ONE 14 (1): e0209429. https://doi.org/10.1371/journal.pone.0209429 (2019).
  47. Hanuschkin A., Yim M.Y., Wolfart J. (2018) A Network Model Reveals That the Experimentally Observed Switch of the Granule Cell Phenotype During Epilepsy Can Maintain the Pattern Separation Function of the Dentate Gyrus. In: Cutsuridis V., Graham B., Cobb S., Vida I. (eds) Hippocampal Microcircuits. Springer Series in Computational Neuroscience. Springer, Cham; DOI https://doi.org/10.1007/978-3-319-99103-0_23
  48. A. Delorme, A. Majumdar, S. Sivagnanam, R. Martinez-Cancino, K. Yoshimoto, S. Makeig, "The Open EEGLAB Portal," 9th International IEEE EMBS Conference on Neural Engineering, San Francisco, CA, March 20-23, 2019.
  49. Latimer, Benjamin and Bergin, David and Guntu, Vinay and Schulz, David and Nair, Satish, "Open source software tools for teaching neuroscience", Journal of Undergraduate Neuroscience Education, volume 16, issue 3, pages A197-A202, issn 1544-2896, 2018
  50. Feng F, Headley DB, Amir A, Kanta V, Chen Z, Paré D, Nair S (2019) Gamma oscillations in the basolateral amygdala: biophysical mechanisms and computational consequences.ENEURO.0388-0318.2018. http://www.eneuro.org/content/early/2019/01/11/ENEURO.0388-18.2018
  51. Fischer BJ, Wydick JL, KöpplC , PeñaJL, ,"Multidimensional stimulus encoding in the auditory nerve of the barn owl,"J Acoust Soc Am. 2018 Oct;144(4):2116. doi: 10.1121/1.5056171.
  52. Ceon Ramon, Mark D. Holmes, Mackenzie V. Wise, Don Tucker, Kevin Jenson, and Samuel R. Kinn, Oscillatory Patterns of Phase Cone Formations near to Epileptic Spikes Derived from 256-Channel Scalp EEG Data, Computational and Mathematical Methods in Medicine, vol. 2018, Article ID 9034543, 15 pages, 2018. https://doi.org/10.1155/2018/9034543.
  53. A. J. Asp, J. K. Trevathan, E. N. Nicolai, K. A. Ludwig, J. L. Lujan, "Movement-based classification of striatal ensembles during DBS". Program No. 756.02. 2018 Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience, 2018. Online.
  54. Trevathan, J.K., Asp, A.J., Nicolai, E.N., Trevathan, J.M., Kremer, N.A., Kozai, T.D.Y., Cheng, D., Schachter, M.J., Nassi, J.J., Otte, S.L., Parker, J.G., Lujan, L., Ludwig, K.A., 2018. Calcium imaging in freely-moving mice during electrical stimulation of deep brain structures. bioRxiv 460220. https://doi.org/10.1101/460220
  55. Senk Johanna, Carde Corto, Hagen Espen, Kuhlen Torsten W., Diesmann Markus, Weyers Benjamin, "VIOLA-A Multi-Purpose and Web-Based Visualization Tool for Neuronal-Network Simulation Output," Front. Neuroinform., 08 November 2018 | https://doi.org/10.3389/fninf.2018.00075
  56. Gratiy SL, Billeh YN, Dai K, Mitelut C, Feng D, Gouwens NW, et al. (2018) BioNet: A Python interface to NEURON for modeling large-scale networks. PLoS ONE 13(8): e0201630. https://doi.org/10.1371/journal.pone.0201630
  57. Latimer B, Banks T, Feng F, Ankathatti A, Calyam P and Nair S (2018) Software Automation for Biologically Realistic Neuro Big Data Simulations. In: Big Data Neuroscience Workshop. Case Western Reserve University, Cleveland, OH
  58. P. Calyam, S S Nair, "Experiences from a Multi-disciplinary Course Sequence Development on Cyber and Software Automation in Neuroscience", Gateways 2018, University of Texas, Austin, TX, September 25-27, 2018. https://gateways2018.figshare.com/
  59. Chou, Ting-Shuo & J Kashyap, Hirak & Xing, Jinwei & Listopad, Stanislav & Rounds, Emily & Beyeler, Michael & Dutt, Nikil & Krichmar, Jeff. (2018). CARLsim 4: An Open Source Library for Large Scale, Biologically Detailed Spiking Neural Network Simulation using Heterogeneous Clusters. 10.1109/IJCNN.2018.8489326.
  60. Ngwe Sin Phyo, Erin Munro Krull,"Action potential propagation in axons: Effect on sodium conductance of collateral and sub-branch distance from soma," Poster, CNS 2018, Seattle, WA https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205781/
  61. Yizhe Tang, Erin Munro Krull, "Action potential propagation in axons: how sodium conductance can estimate propagation as collateral and sub-branch length vary", Poster, CNS 2018, Seattle, WA https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205781/
  62. R.C. Gerkin, R.J. Jarvis, S.M. Crook, "Toward systematic, data-driven validation of a collaborative, multi-scale model of C. elegans", Philosophical Transactions of the Royal Society B, 373 20170381, 10.1098/rstb.2017.0381, 2018.
  63. J. Birgiolas, R.C. Gerkin, S.M. Crook, "Rapid Selection of NeuroML Models via NeuroML-DB.org", Organization for Computational Neuroscence Meeting, Seattle, 2018.
  64. R.C. Gerkin, R.J. Jarvis, S.M. Crook, "Multiscale Model Validation with SciUnit", Organization for Computational Neuroscience Meeting, Seattle, 2018.
  65. Dura-Bernal S, Neymotin SA, Suter BA, Shepherd GMG, Lytton WW. (2018) Long-range inputs and H-current regulate different modes of operation in a multiscale model of mouse M1 microcircuits. bioRxiv. 201707 [Preprint]; DOI: 10.1101/201707
  66. Gleeson P, Cantarelli M, Quintana A, Earnsah M, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic A, Crook S, Davison AP, Dura-Bernal S, et al. (2018) Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits. bioRxiv, 229484 [Preprint] (Under review in Neuron)
  67. Cantarelli M, Marin B, Quintana A, Earnshaw M, Court R, Gleeson P, Dura-Bernal S, Silver RA, Idili G (2018). Geppetto: a reusable modular open platform for exploring neuroscience data and models. Phil. Trans. R. Soc. B 20170380. DOI:10.1098/rstb.2017.0380
  68. Dura-Bernal S, Neymotin SA, Suter BA, Shepherd GMG, Lytton WW. (2018) Data-driven multiscale model of primary motor cortex microcircuits. NIH IMAG Multiscale Modeling meeting 2018 (Abstract/Poster)
  69. Dura-Bernal S, Suter BA, Quintana A, Cantarelli M, Gleeson P, Neymotin SA, Hines M, Shepherd GMG, Lytton WW. (2018) NetPyNE: a high-level interface to NEURON to facilitate the development, parallel simulation and analysis of data-driven multiscale network models. Computational Neuroscience (CNS 2018) (Abstract/Poster)
  70. Dura-Bernal S, Suter BA, Quintana A, Cantarelli M, Gleeson P, Rodriguez F, Neymotin SA, Hines M, Shepherd GMG, Lytton WW. (2018) NetPyNE: a GUI-based tool to build, simulate and analyze large-scale, data-driven network models in parallel NEURON. Society for Neuroscience (SFN 2018) (Abstract/Poster)
  71. Astrid A. Prinz, Kun Tian, "An ensemble modeling approach to identifying ion channel correlations," Society for Neuroscience (SfN) Annual Meeting, San Diego, CA, Nov. 3-7, 2018.
  72. Kun Tian, Michael McKinnon, Shawn Hochman, Astrid A. Prinz , "Identifying cellular dynamics in mouse sympathetic neurons: A computational modeling approach", Society for Neuroscience (SfN) Annual Meeting, San Diego, CA, Nov. 3-7, 2018.
  73. Marvin Weigand, "Optimal wiring imposes fixed cortical hypercolumn sizes," Poster, Computational Neuroscience (OCNS) Annual Meeting, Seattle, WA, July 13-18, 2018.
  74. Doherty, DW, Sivagnanam, S., Dura-Bernal, S, and Lytton, WW., "Simulation of avalanches in mouse primary motor cortex (M1)", Poster, Computational Neuroscience (OCNS) Annual Meeting, Seattle, WA, July 13-18, 2018.
  75. Krishnan GP, Rosen BQ, Chen J-Y, Muller L, Sejnowski TJ, Cash SS, et al. (2018) Thalamocortical and intracortical laminar connectivity determines sleep spindle properties. PLoS Comput Biol 14(6): e1006171. https://doi.org/10.1371/journal.pcbi.1006171
  76. Y. Wei, G. P. Krishnan, M. Komarov, M. Bazhenov, "Differential roles of sleep spindles and sleep slow oscillations in memory consolidation", PLos Computational Biology 14(7):e1006322 DOI: 10.1371/journal.pcbi.1006322. July, 2018
  77. Johnson, J.T., Hammond, F.L., & Wheaton, L.A. (November 5, 2018). Neurobehavioral effects of dissonant sensory feedback. San Diego, CA: Society for Neuroscience, 2018
  78. Johnson, J.T., & Wheaton, L.A. (November 2, 2018). Does Haptic Feedback Support Motor Learning with a Prosthesis? A Neurobehavioral Evaluation. San Diego, CA: American Society of Neurorehabilitation, 2018
  79. Kun Tian, Michael McKinnon, Shaw Hochman, Astrid A. Printz, "An Ensemble Modeling Approach to Identifying Cellular Mechanisms in Thoracic Sympathetic Neurons", Computational Neuroscience (OCNS) Annual Meeting, Seattle, WA, July 13-18, 2018.
  80. N.A. Pelot, B.J. Thio, C.E. Behrend, C.S. Henriquez, W.M. Grill, "Computational Modeling of Neural Stimulation: Electrical Parameter Values and Numerical Methods", Postar, Neural Interfaces Conference, Minneapolis, MN, June, 2018.
  81. E.D. Musselman, N.A. Pelot, G. Goldhagen, W.M. Grill, "Nerve Fiber Recruitment in a Model of Human Cervical Vagus Nerve Stimulation," Poster, Neural Interfaces Conference, Minneapolis, MN, June, 2018.
  82. R.C. Gerkin, R.J. Jarvis, S.M. Crook, "Multiscale Model Validation with SciUnit", Organization for Computational Neuroscience Meeting, Seattle, 2018.
  83. Lealem Mulugeta, Andrew Drach, Ahmet Erdemir, C. A. Hunt, Marc Horner, Joy P. Ku, Jerry G. Myers Jr., Rajanikanth Vadigepalli and William W. Lytton, "Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience", Front. Neuroinform. 12:18. doi: 10.3389/fninf.2018.00018, April, 2018.
  84. Jason S. Sherfey, Austin E. Soplata, Salva Ardid, Erik A. Roberts, David A. Stanley, Bengamin R. Pittman-Polletta, Nancy J. Kopell, "DynaSim: A MATLAB Toolbox for neural Modeling and Simulation, " Frontiers in Neuroinformatics, Vol. 12, March 2018 ,URL=https://www.frontiersin.org/article/10.3389/fninf.2018.00010 DOI=10.3389/fninf.2018.00010
  85. Oliva, Valeria & Cartoni, Emilio & Latagliata, Emanuele & Puglisi-Allegra, Stefano & Baldassarre, Gianluca. (2017). Interplay of prefrontal cortex and amygdala during extinction of drug seeking. Brain Structure and Function. 223. 10.1007/s00429-017-1533-9.
  86. Feng F, Headley D, Chen Z, Latimer B, Amir A, Paré D, Nair SS (2017, "Gamma oscillations in BLA - a computational perspective. Gordon Research Conferences: Amygdala Function in Emotion, Cognition, and Disease," Stonehill College, MA, 2017.
  87. Feng F, Headley D, Chen Z, Latimer B, Amir A, Paré D (2017)." Gamma oscillations in BL - a computational perspective," Society for Neuroscience Poster, Washington, DC. 2017.
  88. Feng F, Chen Z, Latimer B, Nair SS (2017). "Gamma oscillations in BLA - a computational perspective," Workshop on Brain Dynamics and Neurocontrol Engineering. Washington University in St. Louis. 2017.
  89. Latimer B, Feng F, Samarth P, Nair SS (2017). "Central amygdala model integrates intra-amygdalar inputs during fear conditioning," Workshop on Brain Dynamics and Neurocontrol Engineering. Washington University in St. Louis.
  90. Latimer B, Feng F, Samarth P, Pare D, Nair SS (2017). "Central amygdala model integrates intra-amygdalar inputs during fear conditioning," Gordon Research Conferences: Amygdala Function in Emotion, Cognition, and Disease. Stonehill College. 2017.
  91. Stockton, D.B. & Santamaria, F. "Automating NEURON Simulation Deployment in Cloud Resources", Neuroinform (2017) 15: 51. https://doi.org/10.1007/s12021-016-9315-8
  92. Latimer B, Feng F, Samarth P, Pare D, Nair SS (2017). "Central amygdala model integrates intra-amygdalar inputs during fear conditioning." Society for Neuroscience. Washington, D.C. 2017.
  93. J. M. Allen, S. M. Elbasiouny, "The effects of model composition design choices on high-fidelity simulations of motoneuron recruitment and firing behaviors", Accepted Manuscript online 28 November 2017, Journal of Neural Engineering , 2017 IOP Publishing Ltd., http://iopscience.iop.org/article/10.1088/1741-2552/aa9db5/meta
  94. D. Caligiore, F. Mannella, M. A. Arbib, G. Baldassarre, "Dysfunctions of the basal ganglia-cerebellar-thalamo-cortical system produce motor tics in Tourette syndrom," PLOS Computational Biology, March 30, 2017, https://doi.org/10.1371/journal.pcbi.1005395
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  116. Pelot NA, Behrend C, Grill W. Modeling the response of small myelinated axons in a compound nerve to kilohertz frequency signals, J. Neural Engineering, 2017 Mar 31, doi: 10.1088/1741-2552/aa6a5f
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  118. Karunamuni, Roshan A., Tyler M. Seibert, Nathan S. White, Linda McEvoy, Nikdokht Farid, James Brewer, Anders M. Dale, Carrie R. McDonald, and Jona A. Hattangadi-Gluth. "Abnormalities in hippocampal volume of glioma patients prior to radiotherapy." Acta Oncologica (2017): 1-4.
  119. Krishnan, Giri P., Sylvain Chauvette, Isaac Shamie, Sara Soltani, Igor Timofeev, Sydney S. Cash, Eric Halgren, and Maxim Bazhenov. "Cellular and neurochemical basis of sleep stages in the thalamocortical network." eLife 5 (2016): e18607.
  120. Short SM, Morse TM, McTavish TS, Shepherd GM, and Verhagen, "Respiration Gates Sensory Input Resonses in the Mitral Cell Layer of the Olfactory Bulb," PLoS One, 2016 Dec 22; 11(12);e0168356. doi:10.1371/journal.pone.0168356. eCollection 2016.
  121. Marianne J Bezaire, Ivan Raikov, Caren Armstrong, Ivan Soltesz, "SimTracker tool and code template to design, manage and analyze neural network model simulations in parallel NEURON", bioRxiv 081927; doi: https://doi.org/10.1101/081927, 2016
  122. Marianne J Bezaire, Ivan Raikov, Kelly Burk, Dhrumil Vyas, Ivan Soltesz, "Interneuronal mechanisms of hippocampal theta oscillation in a full-scale model of the rodent CA1 circuit," eLife December 2016; 10.7554/eLife.18566; DOI: http://dx.doi.org/10.7554/eLife.18566.
  123. Samuel A Neymotin, Benjamin A Suter, Salvador Dura-Bernal, Gordon M. G. Shepherd, Michele Migliore, William W. Lytton, "Optimizing computer models of corticospinal neurons to replicatae in vitro dynamics," Journal of Neurophysiology Oct 2016, Vol. 117, pages 148--162, Jn. 00570.2016; DOI: 10.1152/jn.00570.2016
  124. Evans, Benjamin D., and Konstantin Nikolic. "From bytes to insights with modelling as a service a new paradigm for computational modelling illustrated with PyRhO." In Biomedical Circuits and Systems Conference (BioCAS), 2016 IEEE, pp. 316-319. IEEE, 2016.
  125. William W. Lytton, Alexandra H. Seidenstein, Salvador Dura-Bernal, Robert A. McDougal, Felix Schurmann and Michael L. Hines , "Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON," Neural Computation 2016 28:10, 2063-2090 .
  126. G. P. Krishnan, M. Komarov, S. Skorheim, M. Bazhenov, "Slow-wave sleep improves learning through spike sequence replay", Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  127. P. Sanda, P. Malerba, G. P. Krishnan, M. Bazhenov, "Precise Ripple Timing affects Spatio-Temporal pattern of sleep slow oscillations in a Model of Memory Consolidation", Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  128. P. Malerba, A. L. Fodder, M. W. Jones, M. Bazhenov, "Modeling of coordinated sequence replay in ca3 and ca1 during sharp wave-ripples", Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  129. Y. Wei, G. P. Krishnan, M. Bazhenov, "Effect of learning cues on sleep-related memory consolidation depends on the phase of sleep slow oscillation," Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  130. Y. Wei, G. P. Krishnan, M. Bazhenov, "Synaptic mechanisms of memory consolidation during NREM sleep", Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  131. Short SM, Morse TM, McTavish TS, Shepherd GM, Verhagen JV, "Respiration Gates Sensory Input Responses in the Mitral Cell Layer of the Olfactory Bulb," poster 524. 38th Annual AChemS Meeting, 2016.
  132. McDougal, Robert A. and Morse, Thomas M. and Carnevale, Ted and Marenco, Luis and Wang, Rixin and Migliore, Michele and Miller, Perry L. and Shepherd, Gordon M. and Hines, Michael L., "Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience", journal="Journal of Computational Neuroscience", year="2016", pages="1--10",issn="1573-6873", doi="10.1007/s10827-016-0623-7", url="http://dx.doi.org/10.1007/s10827-016-0623-7"
  133. Rumbell, Timothy H., Danel Dragulji., Aniruddha Yadav, Patrick R. Hof, Jennifer I. Luebke, and Christina M. Weaver. "Automated evolutionary optimization of ion channel conductances and kinetics in models of young and aged rhesus monkey pyramidal neurons." Journal of computational neuroscience (2016): 1-26. http://www.ncbi.nlm.nih.gov/pubmed/27106692
  134. Van Geit W, Gevaert M, Chindemi G, Rossert C, Courcol J, Muller EB, Schurmann F, Segev I and Markram H (2016). BluePyOpt: Leveraging open source software and cloud infrastructure to optimise model parameters in neuroscience. Front. Neuroinform. 10:17. doi: 10.3389/fninf.2016.00017
  135. R. McDougal; A. Bulanova; W. Lytton, "Reproducibility in Computational Neuroscience Models and Simulations," in IEEE Transactions on Biomedical Engineering , vol. 63, pages. 2021--2035, doi: 10.1109/TBME.2016.2539602
  136. Hodge, Victoria; Jessop, Mark; Fletcher, Martyn; Weeks, Michael; Turner, Aaron; Jackson, Tom; Ingram, Colin; Smith, Leslie and Austin, Jim", "A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience", journal="Neuroinformatics", vol. 14, no. 1, pp 23-40, year 2016.
  137. Dura-Bernal S, Suter BA, Neymotin SA, Kerr CC, Quintana A, Gleeson P, Shepherd GMG, Lytton WW. NetPyNE: a Python package for NEURON to facilitate development and parallel simulation of biological neuronal networks. Computational Neuroscience (CNS), 2016.
  138. Guet-McCreight A, Camire. O, Topolnik L, Skinner FK. Using A Semi-Automated Strategy To Develop Multi-Compartment Models That Predict Biophysical Properties Of Interneuron Specific 3 (IS3) Cells In Hippocampus. eNeuro. 3(4). 2016, pii: ENEURO.00877-16.2016 .
  139. Short SM, McTavish TS, Morse TM, Shepherd GM, Verhagen JV," Circuit models identify mechanisms of respiration driven lateral inhibition underlying mitral activity", SfN Nanosymposium 561.08, 2015.
  140. Shahand, S. (2015). Science gateways for biomedical big data analysis.
  141. Dura-Bernal S, Majumdar A, Neymotin SA, Sivagnanam S, Francis JT, Lytton WW. A dynamic data-driven approach to closed-loop neuroprosthetics based on multiscale biomimetic brain models. IEEE Conference on High Performance Computing 2015 Workshop: Dynamic Data Driven Applications Systems (DDDAS), 2015.
  142. Stockton DB, Santamaria F. NeuroManager: a workflow analysis based simulation management engine for computational neuroscience. Frontiers in Neuroinformatics. 2015;9:24. doi:10.3389/fninf.2015.00024.
  143. S.A Neymotin, B.A. Suter, M. Migliore, S. Dura-Bernal, G.M.G. Shepard, W.W. Lytton, .Optimizing computer models of layer 5 motor cortex pyramidal neurons using somatic whole cell recordings,. Society for Neuroscience Annual Meeting (poster), Chicago, IL, October, 2015.
  144. Dura-Bernal S, Suter BA, Neymotin SA, Quintana AJ, Gleeson P, Shepherd GMG, Lytton WW. .Normalized cortical depth (NCD) as a primary coordinate system for cell connectivity in cortex: experiment and model.. Society for Neuroscience (SFN), Chicago, IL, October 2015.
  145. A. Seidenstein, S.A. Neymotin, A. Fesharaki, M.L. Hines, R.A., McDougal, A.S. Bulanova, W.W. Lytton, .Neuronal network bump attractors augmented by calcium up-regulation of lh in multiscale computer model of prefrontal cortex,. Society for Neuroscience Annual Meeting (poster), Chicago, IL, October, 2015.
  146. C. Mitelut, S. L. Gratiy, D. Denman, J. H. Siegle, S. Durand, K. Godfrey, C. Lee, R.C. Reid, M. Hawrylycz, C. Koch, N.V. Swindle, C. Anastassiou, .Standardizing spike sorting: an In vitro, in silico and In vivo study to develop quantitative metrics for sorting extracellularly recorded spiking activity,. Society for Neuroscience Annual Meeting (poster), Chicago, IL, October, 2015.
  147. A.H. Seidenstein, R.A. McDougal, M.L. Hines, A.Fesharaki, W.W. Lytton, .Parallelizing large networks using NEURON-python,. Computational Neuroscience (CNS) Annual Meeting (poster), Prague, July, 2015.
  148. Pelot, Nicole A., Christina E. Behrend, and Warren M. Grill. "Modeling the response of small myelinated and unmyelinated axons to kilohertz frequency signals." In 2015 7th International IEEE/EMBS Conference on Neural Engineering (NER), pp. 406-409. IEEE, 2015.
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Cyberinfrastructure related NSG publications, presentationa, posters:

  1. S. SIVAGNANAM, K. YOSHIMOTO, A. DELORME, R. MARTINEZ, D. TRUONG, M. KANDES, S. YEU, S. MAKEIG, T. CARNEVALE, A. MAJUMDAR, "Neuroscience Gateway - Large Scale Data Processing and Modeling Using High Performance and High Throughput Computing Resources", SfN Global Connectome, Jan 11-13, 2021.
  2. S. Goyal, S. Purkayastha, T. Phillips, R. Quick, A. Britt, "Enabling Secure and Effective Biomedical Data Sharing throught Cyberinfrastructure Gateways," Gateways 2020, October 12-23, 2020.
  3. Sivagnanam S, Yoshimoto K, Kandes M, Yeu SH, Carnevale T, Majumdar A, "Neuroscience Gateway - providing computational and experimental neuroscientists access to neuroscience software for modeling and data processing on HPC and HTC resources," Poster, Gateways2020, October 2020.https://sciencegateways.org/web/gateways2020/welcome; https://osf.io/easjd/
  4. Majumdar A, Sivagnanam S, Yoshimoto K, Kandes M, Yeu SH, Carnevale T (2020) Neuroscience Gateway Enabling Large Scale Modeling and Data Processing on Supercomputers. Bernstein Conference 2020. doi: doi.org/10.12751/nncn.bc2020.0160
  5. S. Sivagnanam, K. Yoshimoto, T. Carnevale, D. Nadeau, M. Kandes, T. Petersen, D. Troung, R. Martinez, A. Delorme, S. Makeig, and A. Majumdar. "Neuroscience Gateway Enabling Large Scale Modeling and Data Processing in Neuroscience Research," Poster Paper, July 26-30, 2020 PEARC Virtual Conference.
  6. Subhashini Sivagnanam, "Neuroscience Gateway", Workshop on Tools and resources for developing and sharing models in computational neuroscience, Virtual CNS 2020 Annual Meeting, 18-22 July 2020.
  7. Amitava Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Dave Nadeau, Martin Kandes, Trever Petersen, Ramon Martinez, Dung Troung, Arnaud Delorme, Scott Makeig, Ted Carnevale, "Neuroscience gateway enabling modeling and data processing using high performance and high throughput computing resources," 29th Annual Computational Neuroscience Meeting: CNS*2020. BMC Neurosci 21, 54 (2020). https://doi.org/10.1186/s12868-020-00593-1
  8. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, "Neuroscience Gateway Enabling Large Scale Modeling and Data Processing," Poster 6th Annual BRAIN Initiative Investigators Meeting, June 1-2, 2020, Virtual Conference.
  9. Amitava Majumdar, Scott Makeig, Arnaud Delorme, Dave Nadeau, Dung Truong, Kenneth Yoshimoto, Ramon Martinez-Cancino, Subhashini Sivagnanam, Russell A. Poldrack, "NEMAR: A Human Neuroelectrophysiological Data, Tools, and Compute Resource," Poster 6th Annual BRAIN Initiative Investigators Meeting, June 1-2, 2020, Virtual Conference.
  10. NSGPORTAL: High-Performance Computing with EEGLAB. Martínez-Cancino, M., Delorme, A., Truong, D., Artoni, F., Kreutz-Delgado, K., Sivagnanam, S., Yoshimoto, K., Majumdar, A., Makeig, S. Brain, Mind, and Body: Cognitive Neuroengineering for Health and Wellness An IEEE EMBS Symposium and Workshop, Dec. 19-20, 2019, UC San Diego, La Jolla CA.
  11. A. Majumdar , S. Sivagnanam, K. Yoshimoto (all SDSC), N. T. Carnevale (Yale U), The Neuroscience Gateway Enabling Large Scale Modeling and Data Processing in Neuroscience on Supercomputers, Society for Neuroscience Annual Meeting Poster, October 18-23, 2019, Chicago.
  12. A. Chourasia, S. Sakai, M. Shapiro and S. Gallo, "Improving Science Gateways usage reporting for XSEDE", Poster, PEARC '19: Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning)July 2019 Article No.: 109 Pages 1-4 https://doi.org/10.1145/3332186.3338096
  13. N. T. Carnevale, S. Sivagnanam, K. Yoshimoto, A. Majumdar, The Neuroscience Gateway: Enabling large scale modeling and data processing in neuroscience, Poster, Society for Neuroscience Annual Meeting, November 6, 2018, San Diego CA.
  14. Patrice Calegari, Marc Levrier, and Pawel Balczynski. 2019. Web Portals for High-performance Computing: A Survey. ACM Trans. Web 13, 1, Article 5 (February 2019), 36 pages. DOI: https://doi.org/10.1145/3197385
  15. P. S. Kumbhar, S. Sivagnanam, K. Yoshimoto, M. Hines, T. Carnevale and A. Majumdar, "Performance Analysis of Computational Neuroscience Software NEURON on Knights Corner Many Core Processors," Software Challenges to Exascale Computing, Dec 13-14, 2018, Delhi, India, Springer Communications in Computer and Information Science (CCIS) .
  16. N.T. Carnevale, S. Sivagnanam, K. Yoshimoto, A. Majumdar, "The Neuroscience Gateway: enabling large scale modeling and data processing in neuroscience", Poster Society for Neuroscience (SfN) Annual Meeting, San Diego, CA, Nov 3-7, 2018.
  17. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, A. Peyser, "High Performance Computing Resources for Parallel Simulations and Data Analysis: NSG and HPAC," NSG Satellite Workshop at Society for Neuroscience (SfN) Annual Meeting, San Diego, CA, Nov 3-7, 2018.
  18. K. Yoshimoto, "Neuroscience Gateway - Scalable infrastructure for computationally-intensive cognitive neuroscience", Tutorial at CogSci18, Wisconsin, MD, July 25-28, 2018.
  19. S. Sivagnanam, K. Yoshimoto, T. Carnevale, A. Majumdar, "The Neuroscience Gateway - Enabling Large Scale Modeling and Data Processing in Neuroscience," Practice & Experience in Advanced Research Computing PEARC18, Pittsburgh, PA, July 22-26, 2018.
  20. M. Pierce, M. Miller, A. Majumdar, S. Pamidighantam, S. Marru, "Introduction to Science Gateways for New Users," Tutorial, Practice & Experience in Advanced Research Computing PEARC18, Pittsburgh, July 22-26, 2018.
  21. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, "Neuroscience Gateway and Large Scale Neural Systems Simulations and Tools," Workshop, Organization of Computational Neuroscience (CNS) Annual Conference, Seattle, WA, July 13-18, 2018.
  22. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, "Neuroscience Gateway - Enabling Large Scale Simulations and Data Processing and Dissemination of Neuroscience Tools/Software", Poster, Organization of Computational Neuroscience (CNS) Annual Conference, Seattle, WA, July 13-18, 2018.
  23. S. Sivagnanam, "Enabling computational modeling and big data analysis through Neuroscience Gateway," Neural Interfaces Conference, Minneapolis June 2018.
  24. S. Sivagnanam, A. Majumdar, K. Yoshimoto, T. Carnevale, "Neuroscience Gateway: Enabling Easy Path to Supercomputing for Neuroscience Research and Education," Poster, Neural Interfaces Conference 2018, Minneapolis, MN, June 25-27, 2018.
  25. A. Wagner, K Pezzoli, A. Majumdar, J. Bottum, N. Wilkins-Diehr, "Science Gateways and their impact on research and scholarship nationally and internationally," Internet 2, Global Summit, May 6-9, 2018, San Diego, CA.
  26. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, "Neuroscience gateway - enabling easy path to supercomputing for neuroscience research and education," BRAIN Initiative PI Meeting, Bethesda, MD, April 9-14, 2018.
  27. A. Majumdar, S. Sivagnanam, K. Yoshimoto (UCSD), N.T. Carnevale (Yale U.), A. Peyser (Jülich Supercomputer Center), "High Performance Computing (HPC) Resources for Parallel Simulations and Data Analysis: NSG and HPAC," Satellite Workshop, Society for Neuroscience Annual Meeting 2017, Washington D.C., November 2017.
  28. T. Carnevale, A. Majumdar, S. Sivagnanam, K. Yoshomoto, "The Neuroscience Gateway Portal: high performance computing for neuroscientists", Poster, Society for Neuroscience Annual Meeting, Nov 10-15, 2017, Washington D.C.
  29. A. Majumdar, "Neuroscience Gateway," August, 2017, NEUROCOMP17, Madison, WI.
  30. A. Majumdar, S. Sivagnanam, T. Carnevale, "Neuroscience Gateway: Enabling Developers and Users to Utilize Open High Performance Computing Resources for Large Scale Simulations," Workshop Computational Neuroscience Annual Meeting (CNS 2017), July 2017, Antwerp, Belgium.
  31. T. Carnevale, A. Majumdar, S. Sivagnanam, K. Yoshimoto, "The Neuroscience Gateway Portal - High Performance Computing for Neuroscientists," Computational Neuroscience Annual Meeting (CNS 2017) Poster Presentation, Antwerp, Belgium, July 2017.
  32. A. Majumdar, "Science Gateways - Access to HPC", University of California Los Angeles, April, 2017.
  33. A. Majumdar, "HPC Resources and Science Gateways,", University of California Davis, March, 2017.
  34. Supun Nakandala, Suresh Marru, Marlon Pierce, Sudhakar Pamidighantam, Kenneth Yoshimoto, Terri Schwartz, Subhashini Sivagnanam, Amit Majumdar and Mark Miller, "Apache Airavata Sharing Service: A Tool for Enabling User Collaboration in Science Gateways," PEARC17, July 09-13, 2017, new Orleans, LA, USA. ACM ISBN 978-1-4503-5272-7/17/07.
  35. S. Strande, H. Cai, T. Cooper, K. Flammer, C. Irving, G. Laszewski, A. Majumdar, D. Mishin, P. Papadopoulos, W. Pfeiffer, R. Sinkovits, M. Tatineni, R. Wagner, F. Wang, N. Wilkins-Diehr, N. Wolter, and M. Norman, "Comet - Tales from the Long Tail - Two Years In and 10,000 Users Later," PEARC17, July 09-13, 2017, new Orleans, LA, USA. ACM ISBN 978-1-4503-5272-7/17/07. http://dx.doi.org/10.1145/3093338.3093383
  36. A. Majumdar, S. Sivagnanam, T. Carnevale, K. Yoshimoto, "The Neuroscience Gateway - Enabling Large-Scale Neuroscience Simulations and Data Processing Using Supercomputers, " Poster, Third Annual BREAIN Initiative PI Meeting, Bethesda, MD, Dec 12-14, 2016.
  37. S. Sivagnanam, A. Majumdar, P. Kumbhar, M. Hines, K. Yoshomoto, T. Carnevale, "Neuroscience Gateway - Understanding the scaling behavior of NEURON application, " Poster, SC16, Salt Lake City, Utah, November, 2016.
  38. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnecvale, "Understanding Collaborative Cyberinfrastructure Need of Neuroscientists - Survey Results", White Paper, September, 2016.
  39. S. Sivagnanam, A. Majumdar, K. Yoshimoto, T. Carnevale, "NSG-R: Programmatic Access to Neuroscience Applications on HPC," Poster XSEDE16, Miami, July 17-21, 2016.
  40. N. T. Carnevale, P. Gleeson, R. A. Silver, A. Majumdar, S. Sivagnanam, K. Yoshimoto, "Seamless Integration of Neuroscience Models and Tools with High Performance Computing, " Poster, Society for Neuroscience Annual Meeting, San Diego, Nov 12-16, 2016.
  41. Majumdar, A., Sivagnanam, S., Yoshimoto, K., Carnevale, N. T., Quintana, A., Gleeson, P. and Silver, R. A., "NSG-R Programmatic access to neuroscience applications", poster, Workshop Collaborative Development of Data-Driven Models of Neural Systems, HHMI Janelia Research Campus, Virginia, USA, Sept 18-21, 2016.
  42. Majumdar A, Sivagnanam S, Carnevale NT, Yoshimoto K, Gleeson P, Quintana A and Silver RA (2016), "Neuroscience Gateway - Cyberinfrastructure Providing Supercomputing Resources for Large Scale Computational Neuroscience Research," Front. Neuroinform. Conference Abstract: Neuroinformatics 2016. Neuroinformatics 2016, Reading, United Kingdom, 3 Sep - 4 Sep, 2016. doi: 10.3389/conf.fninf.2016.20.00008
  43. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, "Understanding the Evolving Cyberinfrastructure Needs of the Neuroscience Community," Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale (XSEDE16). ACM, New York, NY, USA, , Article 45 , 7 pages. DOI: http://dx.doi.org/10.1145/2949550.2949657
  44. S. Sivagnanam, A. Majumdar, K. Yoshimoto, T. Carnevale, "NSG-R: Programmatic Access to Neuroscience Applications," (poster) Proceedings XSEDE16, Miami, July 17-21, 2016.
  45. S. Dura-Bernal, S. A. Neymotin, W. L. Lytton, A. Majumdar, and S. Sivagnanam, " A Dynamic Data-Driven Approach to Closed-loop Neuroprosthetics Based on Multiscale Biomimetic Brain Models," Dynamic data Driven Application Systems Workshop, IEEE International Conference on High Performance Computing, Dec. 16-19, 2015, Bengaluru, India.
  46. S. Sivagnanam, A. Majumdar, P. Kumbhar, M. Hines, K. Yoshimoto, T. Carnevale, .Neuroscience Gateway . Enabling HPC for Computational Neuroscience,. Supercomputing 2015 (poster), Austin, TX, November, 2015.
  47. T. Carnevale, A. Majumdar, S. Sivagnanam, K. Yoshimoto, P. Gleeson, R.A. Silver. Seamless integration of neuroscience models and tools with high performance computing. Poster, Society for Neuroscience Annual Meeting, Chicago, IL, Oct. 17 - 21, 2015.
  48. B. Lytton, M. Hines, .NEURON and the Neuroscience Gateway Portal,. HPC Workshop, 2015 Computational Neuroscience Annual Meeting, Prague, July, 2015.
  49. M. Miller, T. Schwartz, P. Hoover, K. Yoshimoto, S. Sivagnanam, A. Majumdar, "The CIPRES Workbench: A Flexible Framework for Creating Science Gateways", Proceedings XSEDE15, St. Louis, MO, July 26-30, 2015.
  50. A. Majumdar, S. Sivagnanam, K. Yoshimoto, T. Carnevale, .Neuroscience Gateway . Seamless Access to XSEDE High Performance Computing Resources for the Computational Neuroscience Community,. XSEDE 15 Conference (poster), St. Louis, MO, July 26-30, 2015.
  51. Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Vadim Astakhov, Anita Bandrowski, Maryann Martone, The Neuroscience Gateway Portal - High Performance Computing Made Easy, Poster, Computational Neuroscience (CNS) 2014 Annual Meeting, Quebec City, Canada, July 26-31, 2014.
  52. S. Sivagnanam, A. Majumdar, K. Yoshimoto, V. Astakhov, A. Bandrowski, M. Martone, and N. T. Carnevale, "Early experiences in developing and managing the neuroscience gateway," Journal of Concurrency and Computation: Practice and Experience,Vol 27, Issue 2, pages 473-488, 2015 UR: http://dx.doi.org/10.1002/cpe.3283.
  53. Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Vadim Astakhov, Anita Bandrowski, Maryann Martone, " High performance computing in neuroscience via the Neuroscience Gateway Portal", Poster, Society for Neuroscience Annual Meeting, Washington D.C, Nov. 15 - 19, 2014.
  54. Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Vadim Astakhov, Anita Bandrowski, Maryann Martone, .The Neuroscience Gateway Portal - High Performance Computing Made Easy,. BMC Neuroscience, Vol 15, No 1, 2014, doi="10.1186/1471-2202-15-S1-P101", url="http://dx.doi.org/10.1186/1471-2202-15-S1-P101.
  55. N.T. Carnevale, A. Majumdar, S. Sivagnanam, K. Yoshimoto, V. Astakhov, A. Bandrowski, M. Martone, "The Neuroscience Gateway Portal: facilitating access to high performance computing resources," Poster, Society for Neuroscience Annual Meeting, San Diego, Nov. 9-13, 2013.
  56. S. Sivagnanam, K. Yoshimoto, A. Majumdar, N. T. Carnevale, V. Astakhov, M. Martone, A. Bandrowski, "A Neuroscience Gateway: Software and Implementation," Proceedings XSEDE13 Gateway to Discovery, San Diego, CA, July 22-25, 2013.
  57. S. Sivagnanam, A. Majumdar, K. Yoshimoto, N. T. Carnevale, V. Astakhov, A. Bandrowski, M. Martone, "Introducing The Neuroscience Gateway," Proceedings International Workshop on Science Gateways , Zurich, Switzerland, June 3-5, 2013.
  58. N.T. Carnevale, S. Sivagnanam, K. K. Yoshimoto, V. Astakhov, A. E. Bandrowski, M. E. Martone, A. Majumdar, "A Neuroscience Gateway for High Performance Computing," Poster,Society for Neuroscience Annual Meeting, New Orleans, October 13-17, 2012.

Educational projects/publications and Training/workshops:

  1. A. Majumdar, S. Sivagnanam, K. Yoshimoto, Martin Kandes, Steven Yeu, Neuroscience Gateway Training Webinar on Developers Platform and Neuroscience Software Dissemination, March 18, 2021.
  2. A. Majumdar, S. Sivagnanam, K. Yoshimoto, Ted Carnevale, Arnaud Delorme, Neuroscience Gateway Using NEURON and EEGLAB - Training Webinar, Friday, November 20, 2020.
  3. Methods and tools for characterizing transient phase-amplitude coupling in neural oscillations. Ph.D. dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Electrical Engineering (Intelligent Systems, Robotics, and Control) by Ramon Martinez Cancino, November, 2020.
  4. A. Majumdar, S. Sivagnanam, K. Yoshimoto (all SDSC), T. Carnevale, Yale U., Alex Peyser, Jülich Supercomputing Center, Society for Neuroscience Annual Conference Workshop," NSG and HPAC Large Scale Modeling and Data Analysis - NSG and HPAC," October 10, 2019, Chicago, IL.
  5. Daniel Tovbis, "Automatic Segmentation and Three-Dimensional Reconstruction of Fascicles in Peripheral Nerves ," MS Thesis, University of Toronto, 2019.
  6. A. Majumdar, S. Sivagnanam (all SDSC), T. Carnevale, Yale U., Alex Peyser, Jülich Supercomputingg Center, Society for Neuroscience Annual Conference Workshop, NSG and HPA Large Scale Simulations and Data Processing, October 19, 2019, Chicago, IL.
  7. A. Majumdar, S. Sivagnanam, K. Yoshimoto (all SDSC), T. Carnevale, Yale U., Alex Peyser, Jülich Supercomputing Center, Society for Neuroscience Annual Conference Workshop - High Performance Computing Resources for Parallel Simulations and Data Analysis - NSG and HPAC, November 3rd, 2018, San Diego CA.
  8. Paolo Muratore, University of Rome, Italy, MS Thesis, "Maximum Likelihood Methods for Biologically Plausible Learning in Recurrent Spiking Networks", October, 2019.
  9. NSG was used as a part of EEGLAB workshop in December, 2018.
  10. ohnson, J.T. (December 17, 2018). The Neurobehavioral Effects of Sensorimotor Dissonance on Grasp-Related Motor Tasks. Georgia Institute of Technology, Atlanta, GA: Applied Physiology Thesis Proposal
  11. NIH BRAIN Initiative Summer Course (1 weeks; 7/14-7/20 2019): Models and Neurobiology, Interdisciplinary Research Training in Computational Neuroscience for PhD students, post-docs, medical students, residents, and faculty
  12. Dura-Bernal S, McDougal R, Lytton WW. (2018) Multiscale modeling from molecular level to large network level (using NEURON, RxD and NetPyNE). Computational Neuroscience (CNS 2018) (Tutorial) - http://www.cnsorg.org/cns-2018-tutorials#T2
  13. Dura-Bernal, S. Development of large scale data-driven network models in NetPyNE, a high-level interface to NEURON. Computation Neuroscience (CNS 2018) Workshop on "Developing, standardizing and sharing large scale cortical network models" (Workshop talk)
  14. VII Latin American School on Computational Neuroscience (LASCON) (2018) Institute of Mathematics and Statistics, University of Sao Paulo, Brazil (Course)
  15. NSG was used during the Human Brain Project School on the Brain Simulation Platform, Palermo 17-21 Sep. 2018. https://www.humanbrainproject.eu/en/follow-hbp/events/the-brain-simulation-platform-hbp-school/
  16. NSG was used by the students attending the Computational Neuroscience Training at the University of Missouri, June, 2018.
  17. NSG was used as a part of a EU HBP workshop titled, "Neuroscience for ICT: Applications to Computation and Robotics", in KALKSCHEUNE BERLIN, GERMANY, July 4-6, 2018. https://education.humanbrainproject.eu/web/2nd-hbp-curriculum-workshop-series/ict-workshop
  18. NSG was used by the students of the course " Neuroscience Simulation" taught by EPFL researchers, May, 2018
  19. Neuroscience Information Framework (NIF) organized webinar on the Neuroscience Gateway Project, Subhashini Sivagnanam, September 29, 2017.
  20. A. Majumdar, S. Sivagnanam (all SDSC), T. Carnevale, Yale U., The Neuroscience Gateway and Large Scale Neural Systems Simulations and Tools, CNS 2018 Workshop, 17 July, 2018, Seattle, WA
  21. NSG was used at the NEURON Workshop at the Janelia Research Campus, September, 2017.
  22. Masters Thesis: Effects of Abstraction and Assumptions on Modeling Motoneuron Pool Output, Allen, John Michael, Write State University, 2017
  23. A. Majumdar, S. Sivagnanam (all SDSC), T. Carnevale, Yale U., Alex Peyser, Jülich Supercomputing Center, High Performance Computing Resources for Parallel Simulations and Data Analysis: NSG and HPAC, Society for Neuroscience Annual Conference Workshop, 11 November 2017, Washington D.C.
  24. A. Majumdar, S. Sivagnanam (all SDSC), T. Carnevale, Yale U., Enabling Developers and Users to Utilize Open High Performance Computing Resources for Large Scale Simulatioons, 20 July, 2017, CNS 2017, Antwerp, Belgium
  25. NSG webinar tutorial was given for the NIH BRAIN Initiative Summer Course on Models and Neurobiology. at University of Missouri, Columbia, MO, June 13, 2016. 24 pre- and post-docs and faculties attended this workshop which was funded by NIH R25 Research and Training grant http://engineering.missouri.edu/neuro/outreach/nih-neuroscience-course/
  26. Dervinis, Martynas 2016. Pathophysiological mechanisms of absence epilepsy: a computational modelling study. PhD Thesis, Cardiff University
  27. The Hir, N. (2016). Digital models of the optical stimulation of neurons assisted by plasmonic nanoparticles (Masters thesis, École Polytechnique de Montréal). https://publications.polymtl.ca/2351/
  28. NSG was used at a tutorial at the New Mexico State University, March 2015.
  29. S. Sahand, .Science Gateways for biomedical big data analysis,. Ph. D Thesis, 2015, University of Amsterdam, http://hdl.handle.net/11245/1.490613
  30. Alexandre Guet McCreight, .Predicting Cell-Type Specific Active Properties by Developing Multi-Compartment Models Using Databases and Electrophysiological Feature Constraints: Application to Interneuron Specific 3 (IS3) Cells in the Hippocampus., Master.s Thesis, University of Toronto, August, 2015.
  31. Kait Folweiler, .Computational Model of the Dentate Gyrus,. Ph.D qualifying research, 2015, University of Pennsylvania.
  32. Bill Lytton, Michael Hines, NEURON and the Neuroscience Gateway Portal, CNS2015, July 23, 2015, Prague
  33. Another research project, titled, .Dendritic Excitation Dependence on Synaptic Democracy in CA1 Pyramidal Neurons,. Chung, P, George, V, and Hermiz, J used the NSG for their research. Ref. http://www.isn.ucsd.edu/courses/bggn260/2013/reports/Chung_George_Hermiz.pdf (2014)
  34. NSG was used in a class project by graduate student Nikki Pelot, Biomedical Engineering, Duke University, 2014.
  35. A. Majumdar, S. Sivagnanam, K. Yoshimoto (all SDSC), T. Carnevale, Yale U., Running Parallel Simulations on HPC Resources , July 30, 2014, CNS 2014, Quebec City, Canada
  36. The NSG was used by attendees of the Open Source Brain Hackathon in London in November, 2013 (http://www.opensourcebrain.org/projects/osb/wiki/Hackathon2013), where users tested large scale models of cortical networks on the NSG provided resources during the meeting. This was reported by Padraig Gleeson who ran the workshop and is from the Department of Neuroscience, Physiology and Pharmacology, University College of London.
  37. A. Majumdar, S. Sivagnanam (all SDSC), T. Carnevale, Yale U., Using the Neuroscience Gateway Protal for Parllele Simulation, Society for Neuroscience Annual Conference Workshop, November 9, 2013, San Diego, CA