Publications

Ongoing Research

  • Chen, Z, Headley DB, Gomez-Alatorre LF, Kanta V, Ho KC, Pare D, Nair SS (2022) A principled approach to the characterization and detection of oscillatory bursts in the local field potential (in review)

  • IEEE International Conference on Neural Engineering (IEEE-NER 2023), April 25-28, Baltimore, MD (in review) - (i) Chen Z, Carroll M, Nair SS, Identification of pyramidal neurons using EAP data, (ii) Glickert G, Latimer B, Sah P, Nair SS, Reverse engineering information processing in lateral amygdala during auditory tones, (iii) Fague D, Rautenfeld J, Nair SS, Reduced order realistic neuron models for network simulations

  • Banks TJ, Scherrer JF, Tung TN, Uhlmann JK, Nair SS (2022) Predicting opioid abuse and dependence before and after the opioid prescribing peak in the United States: a machine learning tool using electronic healthcare records (in review)

  • S Nair, G Glickert, M Wacker, SS Nair (2022) Neuroscience modules for mental health training (in review)

  • Nine posters at the Neuroscience 2022, Annual Meeting of the Society for Neuroscience, Nov 12-16, 2022, San Diego: (i) Z Chen, SS Nair: Inference of neuron morphology and orientation from LFP data; (ii) Z Chen, D Fague, SS Nair: Intrinsic oscillatory dynamics in a neocortical circuit; (iii) D Dopp, G Glickert, B Latimer, M Perumal, P Sah, SS Nair: Modeling sharp waves in the hippocampal slice; (iv) G Glickert, B Latimer, P Sah, SS Nair: Role of NMDA receptors in signal transmission in a model lateral amygdala; (v) D Fague, J Von Rautenfeld, S Johnson, J Velasquez, W Tanner, SS Nair: Reduced order realistic neuron models for network simulations; (vi) T. Tuna, T Banks, C Cevinc, SS Nair, G Unal: Anatomical and computational investigation of ventral pallidal modulation of the basolateral amygdala; (vii) S Nair, G Glickert, M Wacker, SS Nair: Self-Learning Neurophysiology Tutorials in the Medical Curriculum; (viii) G Glickert, S Nair, S Johnson, J Velasquez, I Banks, SS Nair: Computational tutorials to illustrate fear learning in the amygdala; (ix) D Donley, Z Chen, G Glickert, D Bergin, SS Nair: Reducing barriers-to-entry for computational neuroscience using web-based tools in the classroom

  • Ten posters at the Neuroscience 2021, Annual Meeting of the Society for Neuroscience, Nov 8-13, 2021, Chicago, IL (virtual): (i) Z Chen, D Dopp, DB Headley, SS Nair: Cell assemblies and population vector in neocortical circuits; (ii) M Carroll, Z Chen, D Headley, SS Nair: Deep architectures for predicting LFP; (iii) G Glickert, B Latimer, P Sah, SS Nair: NMDA receptors in signal transmission: a computational perspective; (iv) G Glickert, B Latimer, M Perumal, P Sah, SS Nair: Generation of sharp wave ripples in the CA1 Hippocampus: a role for chandelier interneurons; (v) T. Tuna, T Banks, M Stroud, SS Nair, G Unal: Localization and contribution of basal forebrain GABAergic input to the basolateral amygdala; (vi) P Canfield, T Banks, SS Nair: Automated tool for development of biophysical single neuron model; (vii) M Stroud, Z Chen, Feng F, SS Nair: Generation of oscillatory bursts in different model brain regions; (viii) D Dopp, M Stroud, F Feng, Z Chen, SS Nair: Effects of variations in network features on characteristics of oscillatory bursts; (ix) P Canfield, M Stroud, V Guntu, A Hummos, SS Nair: Parsing mechanisms that support theta rhythm in a hippocampal CA3 model; (x) E Shappell, D Dopp, J Rautenfeld, L Deal, K Thomas, R Rao, Z Zhao, SS Nair: Neural engineering in K-12.

  • Dopp D, Samarth P, Wang J, Kick D, Schulz DJ, Nair SS (2021) Crustacean cardiac ganglion model reveals constraints on morphology and conductances, BioRxiv 464612, doi: https://doi.org/10.1101/2021.10.21.464612

  • Dopp D, Bergin D, Nair SS (2021) Robotics-based engineering approaches in the G4-12 curriculum, Proc. of the ASEE Annual Conference, July 26-29 2021, 11 pages, https://peer.asee.org/37690. Link.

  • Headley DB, Pinelopi K, Feng F, Nair SS, Pare D (2021) Gamma oscillations in the basolateral amygdala: localization, microcircuitry, and behavioral correlates, Journal of Neuroscience 41(28) 6087-6101. PDF Link

  • Perumal MB, Latimer B, Xu L, Stratton P, Nair SS, Sah P (2021) Microcircuit mechanisms for the generation of sharp wave ripples in the basolateral amygdala: a role for chandelier interneurons, Cell Reports 35 109106, https://doi.org/10.1016/j.celrep.2021.109106. PDF

  • Zhang Y, Calyam P, Joshi T, Nair SS, Xu D (2021) Domain-specific topic model for knowledge discovery in computational and data-intensive scientific communities, IEEE Transactions on Knowledge and Data Engineering doi: 10.1109/TKDE.2021.3093350. Link

  • Feng F, Headley DB, Nair SS (2021) Model neocortical microcircuit supports beta and gamma rhythms, Proc. 10th IEEE EMBS International Conference on Neural Engineering (NER’21), 91-94, 4-6 May 2021, San Diego CA. Link

  • Chen Z, Dopp D, Headley DB, Nair SS (2021) Inferring morphology of a neocortical neuron from in vivo LFP data, Proc. 10th IEEE EMBS International Conference on Neural Engineering (NER’21), 774-777, 4-6 May 2021, San Diego CA. Link

  • Opsal N, Canfield P, Banks T, Nair SS (2021) An efficient pipeline for biophysical modeling of neurons, Proc. 10th IEEE EMBS International Conference on Neural Engineering (NER’21), 99-102, 4-6 May 2021, San Diego CA. Link

  • Donley D, Chen Z, Bergin D, Schulz DJ, Nair SS (2021) Multi-platform simulations facilitate interdisciplinary neuroscience in the undergraduate classroom, Proc. 10th IEEE EMBS International Conference on Neural Engineering (NER’21), 738-741, 4-6 May 2021, San Diego CA. Link

  • Banks T, Tuna T, Canfield P, Unal G, Nair SS (2021) Computational model of the generation of the amygdala theta rhythm, Poster at the 10th IEEE EMBS International Conference on Neural Engineering (NER’21), 4-6 May 2021, San Diego CA.

  • Shappell E, Dopp D, Opsal N, Bergin D, Nair SS (2021) Integrating engineering and science standards into the K-12 curriculum, Poster at the 10th IEEE EMBS International Conference on Neural Engineering (NER’21), 4-6 May 2021, San Diego CA.

  • Three interactive talks at Neuromatch.io, Online conference: (i) A Aberbach, B Latimer, DB Headley, SS Nair (2020) Optimizing detailed L5 pyramidal cell model in the rodent motor cortex to predict in vivo characteristics (Adin is a high school student mentored by Latimer); N Opsal, P Canfield, T Banks, SS Nair (2020) Segregation of current modules for efficient and accurate single neuron models; D Dopp, Z Chen, D Headley, SS Nair (2020) Automated estimation of morphology of a neocortical neuron using in vivo LFP records.

  • Vekaria K, Calyam P, Sivarathri SS, Wang S, Zhang Y, Pandey A, Chen C, Xu D, Joshi T, Nair SS (2020) Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway, Concurrency and Computation: Practice and Experience, Wiley Press. PDF

  • Feng F, Li Y, Latimer B, Zhang C, Nair SS, Hu Z (2020) Prediction of maximum algal productivity in membrane bioreactors with a light-dependent growth model, Science of the Total Environment 753:141922 doi: 10.1016/j.scitotenv.2020.141922. Link

  • Guntu V, Latimer B, Shappell E, Schulz DJ, Nair SS (in press) Challenges in modeling the neural control of LUT, Chapter in Bladder Physiology – Computational Insights, Manchanda and Appukuttan (Editors), Narosa, New Delhi. PDF

  • Joshi SR, Headley DB, Ho, KC, Pare D, Nair SS (2019) Classification of brainwaves using convolutional neural network, Proc. 27th European Signal Processing Conf (EUSPICO), A Coruña, Spain. pp. 1-5.

  • Sivarathri S, Calyam P, Zhang Y, Pandey A, Chen C, Xu D, Joshi T, Nair SS (2019) Chatbot Guided Domain-science Knowledge Discovery in a Science Gateway Application, 14th Gateway Computing Environments Conference (Gateways). PDF

  • Eight posters at the Neuroscience 2019, Annual Meeting of the Society for Neuroscience, Oct 19-23, 2019, Chicago, IL: (i) F Feng, D Headley, V Kanta, D Pare, SS Nair: Closed-loop control of gamma oscillations in BLA – a computational perspective; (ii) Z Chen, F Feng, D Headley, KC Ho, D Pare, SS Nair: Detection and characterization of gamma bursts in LFP signals; (iii) V Guntu, T Banks, A Hummos, SS Nair: Characterizing resonant and synchronizing mechanisms in a hippocampal theta model; (iv) D Dopp, J Wang, P Samarth, D Kick, D Schulz, SS Nair: Structure of large cells in crab cardiac ganglion – a computational study; (v) E Shappel, B Latimer, T Banks, V Guntu, D Schulz, SS Nair: Computational modeling of the neural circuit of a rodent lower urinary tract; (vi) Q Wei, Z Chen, T Banks, B Latimer, Z Chen, SS Nair: Automating development of biophysical single cell and network models; (vii) T Banks, B Latimer, Z Chen, Z Lyu, Z Chen, D Dopp, A Fotoohighiam, P Calyam, T Joshi, D Xu, SS Nair: Software Automation for research and training in neural engineering; (viii) E Shappell, B Latimer, SS Nair: Neural engineering lesson plans for grades 5-12.

  • Feng F, Headley DB, Amir A, Kanta V, Chen Z, Pare D, Nair SS (2019) Gamma oscillations in the basolateral amygdala: biophysical mechanisms and computational consequences, eNeuro 6(1) e0388-18.2018 1–25 PDF Source Code at Model DB – http://modeldb.yale.edu/247968

  • Latimer B, Bergin DB, Guntu V, Schulz DJ, Nair SS (2019), Integrating model-based approaches into a neuroscience curriculum – An interdisciplinary neuroscience course in engineering, IEEE Transactions on Education 62(1) 48-56 PDF

  • Lane BJ, Kick DR, Wilson DK, Nair SS, Schulz DJ (2018) Dopamine maintains network synchrony via direct modulation of gap junctions in the crustacean cardiac ganglion, eLife 10.7554/eLife.39368.001 PDF

  • Latimer B, Bergin DB, Guntu V, Schulz DJ, Nair SS (2018), Open source software tools for teaching neuroscience, Journal of Undergraduate Neuroscience Education 16(3):A197-A202. PDF

  • Calyam P, Nair SS (2018) Science gateway development to aid cyber and software automation for neuroscience researchers and educators, 13th Gateway Computing Environments Conference (Gateways), Austin, TX (Sept 25-27, 2018) PDF

  • Zhang Y, Calyam P, Joshi T, Nair SS, Xu D (2018) Domain-specific topic model for knowledge discovery through conversational agents in data intensive scientific communities, IEEE International Workshop on Conversational Agents and Chatbots with Machine Learning (ChatbotML), in conjunction with IEEE Big Data, Seattle, WA (Dec 10-13, 2018). PDF

  • Six posters at Neuroscience 2018, Annual Meeting of the Society for Neuroscience, Nov 3-7, 2018, San Diego CA: Closed loop control of gamma oscillations in BLA – a computational perspective; Artificial neural networks for prediction of the local field potential; Alteration of IL-BLA connectivity by stimulation – a computational perspective; Interplay of resonant and synchronizing generators in a hippocampal theta model; A new model for large cells of the crab cardiac ganglion; Network model of the dynamics of the neural circuitry controlling micturition.

  • Latimer B, Banks T, Feng F, Ankathatti A, Calyam P and Nair S , Sept. 6-7, 2018: Software automation for biologically realistic neuro big data simulations. Poster In: Big Data Neuroscience Workshop organized by the Advanced Computational Neuroscience Network (ACNN), Case Western Reserve University, Cleveland, OH.

  • Hummos A, Nair SS (2017) An integrative model of the intrinsic hippocampal theta rhythm, PLoS ONE 12(8): e0182648 PDF Source Code at Model DB – http://modeldb.yale.edu/168314

  • Guntu V, Feng F, Alturki A, Nair A, Samarth PS, Nair SS (2017) Amygdala Models, Chapter in Computational Models of Brain and Behavior, John Wiley and Sons (in press)

  • Five posters at the Annual Meeting of the Society for Neuroscience, Nov 11-15, 2017, Washington DC: Gamma oscillations in BLA – a computational perspective; Formation of tone responsive cells in a central amygdala model during fear conditioning; Characterizing conductance variations in model crab cardiac ganglion large cells; Variation across network output, excitatory post synaptic potentials, ionic conductances, and ion channel and receptor mRNAs within motor neurons of the crustacean cardiac ganglion; Modeling the dynamics of the neural circuitry controlling micturition. PDF

  • Nair SS, Pare D, Vicentic A (2016) Biologically-based neural circuit modeling for the study of fear learning and extinction, npj Science of Learning 1:16015 PDF

  • Lane BJ, Samarth PS, Ransdell JL, Nair SS, Schulz DJ (2016) Synergistic plasticity of intrinsic conductance and electrical coupling restores synchrony in an intact motor network, eLife 5:e16879 PDF

  • Alturki A, Feng F, Nair A, Guntu V, Nair SS (2016) Distinct current modules shape cellular dynamics in model neurons, Neuroscience 334: 309-331. PDF Source Code at Model DB – http://modeldb.yale.edu/223649

  • Samarth PS, Ball JM, Unal G, Pare D, Nair SS (2016) Mechanisms of memory storage in a model perirhinal network, Brain Structure & Function, DOI 10.1007/s00429-016-1210-4. PDF

  • Feng F, Samarth PS, Pare D, Nair SS (2016) Mechanisms underlying the formation of the amygdala fear memory trace: a computational perspective, Neuroscience 322:370-376. PDF

  • Kim D, Samarth PS, Feng F, Pare D, Nair SS (2016) Synaptic competition in the lateral amygdala and the stimulus specificity of conditioned fear: A biophysical modeling study, Brain Structure & Function, 221:2163–2182.

  • Hummos A, Nair SS (2015) Multiple mechanisms of theta rhythm generation in a model of the hippocampus, BMC Neuroscience 16(Suppl 1):O17 doi:10.1186/1471-2202-16-S1-O17. PDF

  • Two posters at the Annual Meeting of the Society for Neuroscience, Oct 17-21, 2015, Chicago, IL: Distinct current modules shape cellular dynamics in model neurons; Biophysical model of perirhinal cortex reveals memory storage mechanism.

  • Hummos A, Franklin CC, Nair SS (2014) Intrinsic mechanisms stabilize encoding and retrieval circuits differentially in a hippocampal network model, Hippocampus 24(12):1430-48. PDF Source Code at Model DB – http://modeldb.yale.edu/168314

  • Six posters at the Annual Meeting of the Society for Neuroscience, Nov 14-19, 2014, Washington DC.

  • Pendyam S, Bravo-Rivera C, Burgos-Robles A, Sotres-Bayon F, Quirk GJ, Nair SS (2013) Fear signaling in the prelimbic-amygdala circuit: A computational modeling and recording study, Journal of Neurophysiology 110: 844 – 861.

  • Kim D, Pare D, Nair SS (2013) Assignment of model amygdala neurons to the fear memory trace depends on competitive synaptic interactions, Journal of Neuroscience 33(36):14354 –14358. PDF

  • Kim D, Pare D, Nair SS (2013) Mechanisms contributing to the induction and storage of Pavlovian fear memories in the lateral amygdala, Learning & Memory 20: 421-430. PDF Source Code at Model DB – http://modeldb.yale.edu/150288

  • Ransdell J, Nair SS, Schulz DJ (2013) Neurons within the same network independently achieve conserved output by differentially balancing variable conductance magnitudes, Journal of Neuroscience 33(24):9950 –9956. PDF

  • Six posters at the Annual Meeting of the Society for Neuroscience, Nov 9-13, 2013, San Diego.

  • Ball JM, Hummos A, Nair SS (2012) Role of sensory input distribution and intrinsic connectivity in lateral amygdala during auditory fear conditioning, Neuroscience 224:249–267. PDF

  • Nair SS (2012) Auditory fear circuits in the amygdala – Insights from computational models, chapter 6 in The Amygdala – A Discrete Multi-Tasking Manager, pg. 141-170, InTech Publishing, Barbara Ferry, Editor. doi:10.5772/47814. PDF

  • Ransdell J, Nair SS, Schulz DJ (2012) Rapid homeostatic plasticity of intrinsic excitability in a central pattern generator network stabilizes functional neural network output, Journal of Neuroscience 32(28):9649-58. PDF

  • Pendyam S, Mohan A, Kalivas PW, Nair SS (2012) Role of perisynaptic parameters in neurotransmitter homeostasis – computational study of a general synapse, Synapse 66(7):608–621. PDF

  • Six posters at the Annual Meeting of the Society for Neuroscience, Oct 13-16, 2012, New Orleans.

  • Moussawi K, Riegel A, Nair S and Kalivas PW (2011) Extracellular glutamate: functional compartments operate in different concentration ranges, Frontiers in Systems Neuroscience 5:94. doi: 10.3389/fnsys.2011.00094 PDF

  • Li G, Amano T, Pare D, Nair SS (2011) Impact of infralimbic inputs on intercalated amygdala neurons: a biophysical modeling study, Learning & Memory 18:226-240 PDF

  • Mohan A, Pendyam S, Kalivas PW, Nair SS (2011) Molecular diffusion model of neurotransmitter homeostasis around synapses supporting gradients, Neural Computation 23:984:1014 PDF

  • Franklin CC, Ball JM, Schulz DJ, Nair SS (2010) Generation and preservation of the slow underlying membrane potential oscillation in model bursting neurons, Journal of Neurophysiology 104: 1589-16410.

  • Ball JM, Franklin CC, Tobin AE, Schulz DJ, Nair SS (2010) Coregulation of ion channel conductances preserves output in a computational model of a crustacean cardiac motor neuron, Journal of Neuroscience 30: 8637-8649. PDF

  • Li G, Nair SS, Quirk GJ (2009) A biologically realistic network model of acquisition and extinction of conditioned fear associations in lateral amygdala neurons, Journal of Neurophysiology 101: 1629-1646. PDF

  • Pendyam S, Mohan A, Kalivas PW, Nair SS (2009) Computational model of extracellular glutamate in the nucleus accumbens incorporates neuroadaptations by chronic cocaine, Neuroscience 158(4):1266-76. PDF

  • Mohan A, Pendyam S, Li G, Kalivas P, Nair SS (2008) Computational models of neuronal networks – Modeling plasticity in Glu transmission due to cocaine, chapter in New Research on Neuronal Networks, Yoshida and Sato (Eds.), Nova Science Publishers, New York, 65-107.

  • Li G, Nair J, Quirk GJ, Nair SS (2008) Computational modeling – a tool for new psychiatric medication development, Psychiatric Annals, 28(4):296-304. PDF

Selected Other Publications

– Systems & Control, Machine Learning, Uncertainty Modeling/System Identification, ….

  • Iyoho A, Jang TS, Gall A, Nair SS (2007) Predicting individual differences in human thermal strain using computational models, ASHRAE Transactions 113(1):586-597.

  • Burd RS, Jang T, Nair SS (2007) Evaluation of the relationship between mechanism of injury and outcome in pediatric trauma, Journal of Trauma and Acute Care Surgery 62(4):1004-14.

  • Burd RS, Jang T, Nair SS (2006) Predicting mortality among injured children using a national trauma database, Journal of Trauma and Acute Care Surgery 60:792-801.

  • Zhang X, Xu W, Nair SS, Chellaboina V (2005) PDE modeling and control of a flexible two-link manipulator, IEEE Transactions on Control Systems Technology 13(2):301-312.

  • Zhang X, Xu W, Nair SS (2004) Comparison of some modeling and control issues for a flexible two-link manipulator. ISA Transactions 43(4): 509-525.

  • Du H, Nair SS (2002) Robust adaptive compensation for a class of nonlinear systems. ASME Journal of Dynamic Systems, Measurement, and Control 124: 231-234.

  • Thornton SB, Nair SS (2000) Parametric studies of human thermal mechanisms and measurements, IEEE Transactions on Biomedical Engineering 47(4):444-451.

  • Du H, Nair SS (1999) Modeling and compensation of low velocity friction with bounds. IEEE Transactions on Control Systems Technology 7(1): 110-121.

  • Swamidass P, Mistry SI, Nair SS (1999) The use of a neural factory to investigate the effect of product line width on manufacturing performance. Management Science 45(11):1524-1538.

  • Nair J, Nair SS, Kashani JH, Reid JC, Mistry SI, Vargas VG (1999) Analysis of the symptoms of depression: A neural network approach, Psychiatry Research, 87:193-201.

  • Vargas V, Du H, Nair SS, Reid JC (1999) Sensitivity analysis for modeling and decision making using neural networks, Intl. Journal of Knowledge-Based Intelligent Engineering Systems vol. 3 (3).

  • Kashani JH, Nair SS, Rao V, Nair J, Reid JC (1996) Relationship of personality, environmental and DICA variables to adolescent hopelessness: A neural network sensitivity approach, Journal of the American Academy of Adolescent and Child Psychiatry 35(5):640-645.

  • Reid JC, Nair SS, Mistry SI, Beitman BD (1996) Effectiveness of stages of change and adinazolam SR in panic disorder: A neural network analysis, Journal of Anxiety Disorders 10(5):331-345.

Peer Reviewed Publications Related to Teaching and K-12

Focus – Professional skills, and Concepts from Cognitive Neuroscience for Grad students; and Neuro-Robotics for K-12

Teaching

  • Franklin CC, Mohan A, Merle D, Lannin J and Nair SS (2012) Perceptions of professional skills by graduate students— A comparative study between Engineering, Education and Biology, International Journal of Engineering Education 28(3):588-598. PDF

  • Mohan A, Merle D, Jackson C, Lannin J and Nair SS (2010) Professional skills in the engineering curriculum, IEEE Transactions on Education 53(4): 562-571. PDF

  • Bergin D, Khanna SK, Lynch J, and Nair SS (2007) Infusing design into the G6-9 curriculum – Two example cases, International Journal of Engineering Education 23(1):43-49. PDF

K-12

Note: Per information from TEACHEngineering.org, the neuro-LEGO lessons and activities cited below had a total of 107,765 page views in 2015 (91,336 for the lessons and 16,429 for the activities). During 2015, six of our lessons were among their “top 10” for page views, from over 1400+ lessons and activities hosted at the site.