Publications

Journal articles

  • [2013] Malhotra D, Diwakar S,Nair B, Srivastava S, BIOQUEST India: A Global Biotechnology Forum for Knowledge-Based Innovation and Sustainable Development, Current Pharmacogenomics and Personalized Medicine (CPPM), 11:8-11, 2013.
  • [2012] Medini C, Nair B, D'Angelo E, Naldi G, Diwakar S, Modeling spike-train processing in the cerebellum granular layer and changes in plasticity reveals single neuron effects in neural ensembles, Computational Intelligence and Neuroscience, vol. 2012, Article ID 359529, 17 pages, 2012. doi:10.1155/2012/359529
  • [2012] Bipin Nair, Remya Krishnan, Nijin Nizar, Rakhi Radhamani, Karthika Rajan, Afila Yoosef, Gopika Sujatha, Vijilamole Radhamony, Krishnashree Achuthan, Shyam Diwakar, Role of ICT-enabled visualization-oriented virtual laboratories in Universities for enhancing biotechnology education – VALUE initiative: Case study and impacts, FormaMente, Vol. VII (2012), n. 1-2, ISSN 1970-7118.
  • [2012] Ray S, Koshy N, Diwakar S, Nair B, Srivastava S. Sakshat Labs: India's Virtual Proteomics Initiative, PLoS Biol 10(7): e1001353. doi:10.1371/journal.pbio.1001353
  • [2011] Raman R, Nedungadi P, Achuthan K, Diwakar S. Integrating Collaboration and Accessibility for Deploying Virtual Labs using VLCAP, International Transaction Journal of Engineering, Management, & Applied Sciences & Technologies. Volume 2 No.5 (Special Issue), Dec 2011, ISSN 2228-9860. eISSN 1906-9642.
  • [2011] Harilal Parasuram, Bipin Nair, Giovanni Naldi, Egidio D’Angelo, Shyam Diwakar, A modeling based study on the origin and nature of evoked post-synaptic local field potentials in granular layer, Journal of Physiology-Paris, Volume 105, Issues 1-3, January-June 2011, Pages 71-82, ISSN 0928-4257, 10.1016/j.jphysparis.2011.07.011
  • [2011] Shyam Diwakar, Paola Lombardo, Sergio Solinas, Giovanni Naldi, Egidio D’Angelo. Local Field Potential Modeling Predicts Dense Activation in Cerebellar Granule Cells Clusters under LTP and LTD Control. PLoS ONE 6(7): e21928. doi:10.1371/journal.pone.0021928.
  • [2011] Shyam Diwakar, Krishnashree Achuthan, Prema Nedungadi and Bipin Nair, “Enhanced Facilitation of Biotechnology Education in Developing Nations via Virtual Labs: Analysis, Implementation and Case-studies ,” International Journal of Computer Theory and Engineering vol. 3, no. 1, pp. 1-8, 2011.
  • [2009] Diwakar S, Magistretti J, Goldfarb M, Naldi G, D’Angelo E. Axonal Na+ channels ensure fast spike activation and back-propagation in cerebellar granule cells. J Neurophysiol. 2009 Feb;101(2):519-32. Epub 2008 Dec 10.
  • [2008] Prestori F, Rossi P, Bearzatto B, Lainé J, Necchi D, Diwakar S, Schiffmann SN, Axelrad H, D’Angelo E. Altered neuron excitability and synaptic plasticity in the cerebellar granular layer of juvenile prion protein knock-out mice with impaired motor control. J Neurosci. 2008 Jul 9;28(28):7091-103. (suppl)
  • [2007] Goldfarb M, Schoorlemmer J, Williams A, Diwakar S, Wang Q, Huang X, Giza J, Tchetchik D, Kelley K, Vega A, Matthews G, Rossi P, Ornitz DM, D’Angelo E. Fibroblast growth factor homologous factors control neuronal excitability through modulation of voltage-gated sodium channels. Neuron. 2007 Aug 2;55(3):449-63. (suppl)


Modeldb

  1. Multi-compartmental Granule neuron ReConv Algorithm to generate evoked LFP in cerebellar granular layer.Reference: Diwakar S, Lombardo P, Solinas S, Naldi G, D’Angelo E (2011) Local Field Potential Modeling Predicts Dense Activation in Cerebellar Granule Cells Clusters under LTP and LTD Control. PLoS ONE 6(7): e21928. doi:10.1371/journal.pone.0021928 [PubMed]
  2. A detailed multicompartmental Multi-compartmental Granule neuron model was used to study neuronal electroresponsiveness of cerebellar granule cells in rats. For details check article.

Reference: Diwakar S, Magistretti J, Goldfarb M, Naldi G, D`Angelo E (2009) Axonal Na+ channels ensure fast spike activation and back-propagation in cerebellar granule cells J Neurophysiol 101(2):519-32 [PubMed]

Books


In book

Invited Chapter – Shyam Diwakar, Krishnashree Achuthan, Prema Nedungadi and Bipin Nair (2012). Biotechnology Virtual Labs: Facilitating Laboratory Access Anytime-Anywhere for Classroom Education, Innovations in Biotechnology, Eddy C. Agbo (Ed.), ISBN: 978-953-51-0096-6, InTech, Available from: http://www.intechopen.com/articles/show/title/biotechnology-virtual-labs-facilitating-laboratory-access-anytime-anywhere-for-classroom-education

Recent Talks

  • Invited talk. Computational Neuroscience of Cerebellar Disorders –Studies of plasticity, timing and dysfunction from a cerebellar granular layer perspective, International Conference on Advances in Molecular Mechanisms of Neurological Disorders, 21-23 February 2013, AIIMS, New Delhi, India.
  • Invited talk. Computations in the cerebellar granular layer microcircuit: Timing, plasticity and extracellular field reconstructions, School of Computer and Systems Sciences and School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi -67, India, Jan 14, 2013
  • Invited talk. Computations in the cerebellar granular layer: Timing, plasticity and extracellular field reconstructions, Moreno Bote Lab, Foundation Sant Joan de Deu, Barcelona, Spain, Nov 6, 2012
  • Invited keynote lecture. “Communication analogies and computing via neuromorphic engineering – a perspective from bio-inspired robotics“, 2012 International Conference on Advances in Computing, Communications and Informatics (ICACCI-2012), Chennai, India, Aug 3-5, 2012.
  • Invited lecture. “Superman’s changing room – Virtualization and virtual labs”, International Conference on technology Enhanced Education, Amritapuri, Kerala, India, Jan 3-5, 2012.
  • “A modeling based study on the origin and nature of evoked post-synaptic local field potentials in granular layer”, Department of Mathematics ‘Federigo Enriques’, University of Milan, Dec 6, 2011.
  • “Virtual Labs: Pervasive education & scenes from an ICT perspective”, Proceedings of the 5TH GUIDE INTERNATIONAL CONFERENCE 2011, “E-learning innovative models for the integration of education, technology and research”, Università degli Studi “Guglielmo Marconi”, Rome, 18 – 19 November 2011.
  • Shyam Diwakar and Bharat Jayaraman, Constrained Objects for Neuronal Modeling and Simulation, International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, Oct 30-Nov 1, 2011.
  • Demo presentation: Virtual labs and computational neuroscience – Education and pedagogies. Bernstein Conference 2011, Bernstein Center Freiburg . Hansastraße 9A . D-79104 Freiburg, October 4-6, 2011.
  • Demo presentation, Virtual Labs – Pervasive education and future scenes from an ICT scenario, International Conference on Advances in Computing and Communications (ACC-2011), Kochi, India, July 22-24, 2011.
  • Invited lecture, Department of Mathematics, University of Milan, Milano, Italy, Dec 9, 2010. Title: Mathematics, virtualization and technical education – An Amrita case study into understanding neuroscience via virtual labs and mathematical models.
  • Neurotalk 2010,Track 2-3: Neuromathematics, Neurophysics, Neuroinformatics and Computation Neurobiology, Singapore EXPO, Singapore, June 25, 2010, Title: Neuronal Models and Exploration of Network Properties: A Case Study into Cerebellar Granular Layer Models and Local Field Potential Modeling.TKK, Helsinki, India and EU, Organized by TKK University, Oct 5, 2009.
  • LFP workshop: Modeling and interpretation of extracellular field potentials, January 15-16, 2009 at Oslo, Norway organized by INCF-Norway.

Recent Peer-reviewed Conferences

  • [Comp Neuro] Parasuram H, Diwakar S. Constraining extracellular matrix by modeling local field potential , INCF workshop - India, Nov. 5-7, 2012.
  • [Comp Neuro] Vijayan A, Diwakar S. Cerebellar neural dynamics with spiking neurons show generalization for inverse kinematics problem, INCF workshop - India, Nov. 5-7, 2012.
  • [Comp Neuro] Medini C, Diwakar S.  Modeling cerebellar granular layer microcircuitry reveals role of single neurons in spatiotemporal encoding, INCF workshop - India, Nov. 5-7, 2012.
  • [Comp Neuro] Nair M, Diwakar S. Quantifying stimulus information in spike trains during plasticity, INCF workshop - India, Nov. 5-7, 2012.
  • [Virtual Lab] Freeman J, Nagarajan A, Parangan M, Kumar D, Diwakar S, Achuthan K, Remote Triggered Photovoltaic Solar Cell Lab: Effective Implementation Strategies for Virtual Labs, Proceedings of ICTEE 2012 IEEE Conference on Technology Enhanced Education, Jan 3-5, 2012.
  • [Virtual Lab] Diwakar S, Achuthan K, Nedungadi P, Nair B. “VirtualLabs: Pervasive education & scenes from an ICT perspective”, Proceedings of the 5TH GUIDE INTERNATIONAL CONFERENCE 2011, “E-learning innovative models for the integration of education, technology and research”, Università degli Studi “Guglielmo Marconi”, Rome, 18 – 19 November 2011.
  • [Comp Neuro] Parasuram H, Nair B, Diwakar S, Using detailed biophysical models to reconstruct cerebellar post-synaptic evoked local field potential reveals single neuron effects in population code, Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, Oct 30-Nov 1, 2011.
  • [Comp Neuro] Melethadathil N, Nair B, Diwakar S, Neuroinformatics database for multi-level physiological mapping based on sematic clustering, Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, Oct 30-Nov 1, 2011.
  • [Comp Neuro] Wayland A, Nair B, Diwakar S, Electroresponsiveness of cerebellar granule neuron and regulation of spatio-temporal processing in the cerebellar granular layer, Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, Oct 30-Nov 1, 2011.
  • [Comp Neuro] Nair M, Nair B, Diwakar S, Information Coding in Single Granule Neuron of the Cerebellum, Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, Oct 30-Nov 1, 2011.
  • [Comp Neuro] Medini C, Nair B, Diwakar S, Modeling cerebellar granular layer microcircuitry reveals role of single neurons in spatio-temporal encoding, Proceedings of the International symposium on `Recent Trends in Neurosciences & XXIX Annual Conference of Indian Academy of Neurosciences, Oct 30-Nov 1, 2011.
  • [Virtual Lab] K. Achuthan, S. Sreelatha, S. Surendran, S. Diwakar, P. Nedungadi, S. Humphreys, S. Sreekala, Z. Pillai, R. Raman, A. Deepthi, R. Gangadharan, S. Appukuttan, J. Ranganatha, S. Sambhudevan, S. Mahesh. “The VALUE @ Amrita Virtual Labs Project: Using Web Technology to Provide Virtual Laboratory Access to Students”, Proceedings of IEEE Global Humanitarian Technology Conference (GHTC), 30 October – 1 November 2011, Seattle, Washington.
  • [Comp Neuro] S. Diwakar, Information processing in the cerebellum granular layer and changes in plasticity revealing single neuron effects in neural ensembles. Front. Comput. Neurosci. Conference Abstract: BC11 : Computational Neuroscience & Neurotechnology Bernstein Conference & Neurex Annual Meeting 2011. doi: 10.3389/conf.fncom.2011.53.00230
  • [Comp Neuro] Diwakar S, Parasuram H, Medini C, Nair M, Melethadathil N, Naldi G, D’Angelo E, Nair B .Modeling evoked local field potentials in the cerebellum granular layer and plasticity changes reveal single neuron effects in neural ensembles . Acta Physiologica, September 2011, Volume 203, Supplement 688.
  • [Virtual Lab] H. Parasuram, B. Nair, K. Achuthan, S. Diwakar. Taking Project Tiger to the Classroom: A Virtual Lab Case Study, A. Abraham et al. (Eds.): ACC 2011, Part II, CCIS 191, pp. 337–348. Springer, Heidelberg (2011).
  • [Virtual Lab] P. Nedungadi, R. Raman, K. Achuthan, S. Diwakar. Collaborative & Accessibility Platform for Distributed Virtual Labs, Proceedings of 2011 IAJC-ASEE International Conference, University of Hartford, NY, USA, April 29-30, 2011.
  • [Comp Neuro] H. Parasuram, N. Abdulmanaph, B. Nair, S. Diwakar. Modeling granular layer local field potential using single neuron and network based approaches to predict LTP/LTD in extracellular recordings. Proceedings of Neurocomp (Lyon, France), 2010, Oct 6-8, 2010.
  • [Comp Neuro] S. Subramaniyam, C. Medini, B. Nair, S. Diwakar. Modeling spatio-temporal processing in cerebellar granular layer and effects of controlled inhibition on plasticity. Proceedings of Neurocomp (Lyon, France), 2010, Oct 6-8, 2010.
  • [Comp Neuro] P. James, N. Abdulmanaph, B. Nair, S. Diwakar. Exploring input-output characteristics of the cerebellar granule neuron: role of synaptic inhibition, spike timing and plasticity. Proceedings of Neurocomp (Lyon, France), 2010, Oct 6-8, 2010.
  • [Virtual Lab] M. Parangan, C. Asok, H. Parasuraman, K. Achuthan, B. Nair, S. Diwakar. Modeling Action Potentials and Bursting Phenomena using Analog Electrical Neurons. Proceedings of ACM A2CWIC (in press), Sept 16-17, 2010.
  • [Comp Neuro] M. Nair, N. Melethdathil, B. Nair, S. Diwakar. Information Processing Via Post-Synaptic EPSP-Spike Complex And Model-based Predictions Of Induced Changes During Plasticity in Cerebellar Granular Neuron. Proceedings of ACM A2CWIC, Sept 16-17, 2010.
  • [Comp Neuro] H. Parasuram, N. Abdulmanaph, B. Nair, S. Diwakar.Reconstructing extracellular local field potential in cerebellar granular layer networks. Proceedings of IEEE BIC-TA (Liverpool, UK), 2010, Sept 8-10, 2010.
  • [Comp Neuro] C. Medini, S. Subramaniyam, B. Nair, S. Diwakar.Modeling cerebellar granular layer excitability and combinatorial computation with spikes. Proceedings of IEEE BIC-TA (Liverpool, UK), 2010, Sept 8-10, 2010.
  • [Comp Neuro] N. Abdulmanaph, P. James, B. Nair, S. Diwakar. Characterizing information transmission in cerebellar granule neuron. Proceedings of IEEE BIC-TA (Liverpool, UK), 2010, Sept 8-10, 2010.
  • [Virtual Lab] S. Diwakar, K. Achuthan, P. Nedungadi. Biotechnology Virtual Labs – Integrating Wet-lab Techniques and Theoretical Learning for Enhanced Learning at Universities. Proceedings of the International Conference on Data Storage and Data Engineering (DSDE 2010), Bangalore, Feb 10, 2010.
  • [Comp Neuro] S. Diwakar, G. Naldi, E. D’Angelo. Computational modeling of LFP and predictions on granular layer plasticity. Front. Neuroinform. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.029.
  • [Comp Neuro] S. Diwakar, G. Naldi, E. D’Angelo. Computational modeling of extracellular local field potentials predicts activation patterns and plasticity in the cerebellar circuit-at the GRC Sensory coding and Natural environment conference at Barga, Italy on July 31-August 2, 2008.
  • [Comp Neuro] S. Diwakar, G. Naldi, E. D’Angelo. Computational modeling predicts activation patterns and plasticity in the cerebellar circuit-at the FENS 2008 meeting at Geneva, Switzerland on July 10-16, 2008.
  • [Comp Neuro] S. Diwakar, G. Naldi, E. D’Angelo. Computational modeling predicts activation patterns and plasticity in the cerebellar circuit-at the SINS 2007 meeting organized by Society of Italian Neuroscience at Verona, Italy on Sept 27-30, 2007.
  • [Comp Neuro] S. Diwakar, G. Naldi, E. D’Angelo. Reconstructing Extracellular field potentials with a multi-compartmental cerebellar granule cell model. at the Node and Network meeting organized by University of Pavia and others commemorating the Golgi Nobel Prize centennial 1906-2006 at Pavia, Italy on Oct 2-4, 2006.
  • [Comp Neuro] S. Diwakar, Does the glomerulus function as a multiclass support vector machine? –Modeling the olfactory system from a machine learning perspective at the joint international conference on Neuroscience organized by IAN SNCI 2004 at Hyderabad, India on May 6-8, 2004.