Chen Z, Headley DB, Gomez-Alatorre LF, Kanta V, Ho KC, Pare D, Nair SS (2023) Approaches to characterizing oscillatory burst detection algorithms for electrophysiological recordings, Journal of Neuroscience Methods, https://doi.org/10.1016/j.jneumeth.2023.109865 PDF
Latimer B, Dopp D, Perumal M, Sah P, Nair SS (2023) A novel biophysical model for the generation of sharp wave ripples in CA1 hippocampus, IEEE Transactions on Circuits and Systems II: Express Briefs 10.1109/TCSII.2023.3262207
Banks TJ, Scherrer JF, Tung TN, Uhlmann JK, Nair SS (2023) Predicting opioid abuse and dependence before and after the opioid prescribing peak in the United States: a machine learning tool using electronic healthcare records, Health Informatics Journal, Open access online version PDF
(i) Chen Z, Carroll M, Nair SS, Identification of pyramidal neurons using EAP data 10.1109/ner52421.2023.10123903 PMC10259830 Link; (ii) Glickert G, Latimer B, Sah P, Nair SS, Reverse engineering information processing in lateral amygdala during auditory tones doi:10.1109/ner52421.2023.10123856 PMC10292606 Link; (iii) Fague D, Rautenfeld J, Nair SS, Reduced order realistic neuron models for network simulations (poster + 1-page paper), Proc. 11th International IEEE/EMBS Conference on Neural Engineering (2023), April 25-27, Baltimore, MD
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 International IEEE/EMBS Conference on Neural Engineering (NER), Italy, 2021, pp. 91-94, doi: 10.1109/NER49283.2021.9441199. Link
Chen Z, Dopp D, Headley DB, Nair SS (2021) Inferring morphology of a neocortical neuron from in vivo LFP data, Proc. 10th International IEEE/EMBS Conference on Neural Engineering (NER), Italy, 2021, pp. 774-777, doi: 10.1109/NER49283.2021.9441161. Link
Opsal N, Canfield P, Banks T, Nair SS (2021) An efficient pipeline for biophysical modeling of neurons, Proc. 10th International IEEE/EMBS Conference on Neural Engineering (NER), Italy, 2021, pp. 99-102, doi: 10.1109/NER49283.2021.9441222. Link
Donley D, Chen Z, Bergin D, Schulz DJ, Nair SS (2021) Multi-platform simulations facilitate interdisciplinary neuroscience in the undergraduate classroom, Proc. 10th International IEEE/EMBS Conference on Neural Engineering (NER), Italy, 2021, pp. 738-741, doi: 10.1109/NER49283.2021.9441407. 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 International IEEE/EMBS Conference on Neural Engineering (NER), Italy, 2021.
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 International IEEE/EMBS Conference on Neural Engineering (NER), Italy, 2021.
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 LINK.
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 Audio-Summary
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