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Published Papers

 

  1. Cataldo E, Brunelli M, Av-Ron E, Cai Y, Baxter DA. Geometry, activity-dependent mechanisms, membrane kinetics and channel density distribution interplay in single neuron plasticity.  A computational study. In: Proceedings of BIOMAT 2007 - International Symposium on Mathematical and Computational Biology - World Scientific Co. Pte. Ltd, in press, 2008.

  2. Av-Ron, E., Byrne, M.J., Byrne, J.H., and Baxter, D.A. SNNAP: A tool for teaching neuroscience. Brains, Minds and Media, 3: in press, 2008.
     
  3. Hurwitz, I., Ophir, A., Dorngreen, A., Koester, J., and Susswein, A.J. Currents contributing to decision-making in neurons B31/32 of Aplysia. J. Neurophysiol.[Epub ahead of print] 2007.
     
  4. Bortz, B., Cushing, D., and Watrous, J. Pacemaker neurons and their role in simple neural networks. Proc. Natl. Conf. Undergrad. Res., 21: 905-907, 2007.
     
  5. Scuri, R., Lombardo, P., Cataldo, E., Ristori, C.and Brunelli, M. The inhibition of the Na+/K+ ATPase potentiates synaptic transmission in T sensory neurons of the leech. Eur. J. Neurosci., 25: 159-167, 2007.
     
  6. Watrous, J.J. Group learning neural network education using SNNAP. FASEB Journal, 20: A13, 2006.
     
  7. Oliver, M. and Watrous, J. The role of conductances in long-term potentiation of a five cell neuronal network. Proc. Natl. Conf. Undergrad. Res., 21: 894-900-907, 2006.
     
  8. Cataldo, E., Byrne, J.H. and Baxter, D.A. Computational model of a central pattern generator. Lec. Notes Bioinform., 4210: 242-256, 2006.
     
  9. Av-Ron, E., Byrne, J.H. and Baxter, D.A.  Teaching basic principles of neuroscience with computer simulations.  J. Undergrad. Neurosci. Edu., 4: A40-A52, 2006.

  10. Cai, Y., Flynn, M., Baxter, D.A. and Crow, T.  Role of A-type K+ channels in spike broadening observed in soma and axon of Hermissenda type-B photo receptors: A simulation study.  J. Comput. Neurosci., 21: 89-99, 2006.

  11. Baxter, D.A. and Byrne, J.H. Simulator for neural networks and action potentials (SNNAP): Description and application.  In: Crasto, C. (Ed.) Methods in Molecular Biology: Neuroinformatics, Totowa, N.J. : Humana Press, in press, 2007.

  12. Bharatam, P.V. et al.,  Pharmacoinformatics – Expanding horizons.  PHARMABIZ.COM, January 10, 2006, 08:00 IST. http://www.pharmabiz.com/article/detnews.asp?articleid=31336&sectionid=46.
     
  13. Potamias, G.  (ed.)  State of the Art on Systems for Data Analysis, Information Retrieval and Decision Support.  http://www.infobiomed.org, 2006. 
     
  14. Fierro, M. and Watrous J.  Using SNNAP (Simulator for Neural Networks and Action Potentials) to model the behavior of networked Moris-Lecar cells.  20th National Conference on Undergraduate Research,  http://www.ncur20.ws/, 2006.
     
  15. Glassman, E.L.  A wavelet-like filter based on neuron action potentials for analysis of human scalp electroencephalographs.  IEEE Trans Biomed Eng, 52: 1851-1862, 2005.
     
  16. Wooley, J.C. and Lin, H.S. (eds.)  Catalyzing Inquiry at the Interface of Computing and Biology, 2005 Report of the National Research Council of the National Academies.  http://genomicsgtl.energy.gov/pubs/NRCComputingandBiology/, 2005.
     
  17. Vehovszky, A., Szabo, H., and Elliott, C.M.  Octopamine increases the excitability of neurons in the snail feeding system by modulation of inward sodium current but not outward potassium currents.  BMC Neurosci., 6:70, 2005. http://www.biomedcentral.com/1471-2202/6/70.
     
  18. Moss BL, Fuller AD, Sahley CL, Burrell BD  (2005)  Serotonin modulates axo-axonal coupling between neurons critical for learning in the leech.  J Neurophysiol, 94: 2575-2589.
     
  19. Wustenberg, D.G.,  Byrne, J.H. and Baxter, D.A. (2005) Roles of excitatory interneuron PL-17 and homosynaptic plasticity in information processing by the tail-withdrawal circuit in Aplysia.  22nd Annual Houston Conference on Biomedical Engineering Research.
     
  20. Av-Ron, E., Cai, Y., Byrne, J.H. and Baxter, D.A. (2005)  Parallel SNNAP: from object oriented design to multithreading.  22nd Annual Houston Conference on Biomedical Engineering Research .
     
  21. Cataldo, E. (2005) Non-synaptic mechanisms of short-term plasticity: a computational analysis.  University of Pisa Ph.D. thesis: 6739.
     
  22. Cataldo, E., Brunelli, M., Byrne, J.H., Av-Ron, E., Cai, Y. and Baxter, D.A. Computational model of touch mechanoafferent (T cell) of the leech: role of afterhyperpolarization (AHP) in activity-dependent conduction failure. J. Comput. Neurosci., 18: 5-24, 2005.
     
  23. Calabrese RL, Hill AV, van Hooser SD,  Realistic modeling of small neuronal circuits.  In: De Schutter E (Ed.)  Computational Neuroscience: Realistic Modeling for Experimentalists, (pp259-287), New York , CRC Press, 2001.
     
  24. Lorenz S, Horstmann W, Oesker M, Gorezytza H, Dieckmann A, Egelhaaf M.  The monist project: A system for learning and teaching with educational simulations.  In: Cantoni L, McLoughlin C (Eds.),  Proceedings of ED-MEDIA 2004, World Conference on Education Media, Hypermedia & Telecommunications, AACE 2004.
     
  25. Hayes, R.D., Byrne, J.H., Cox, S.J. and Baxter D.A. Estimation of single-neuron model parameters from spike train data. Neurocomputing, in press, 2004.
     
  26. Xiao, J., Cai, Y., Yen, J. Steffen, M., Baxter, D.A., Feigenspan, A. and Marshak, D.  Voltage clamp analysis and computational model of dopaminergic neurons from mouse retina.  Vis. Neurosci., 21: 835-849, 2004.
     
  27. Lombardo, P., Scuri, R., Cataldo, E., Calvani, M., Nicolai, R., Mosconi, L., Brunelli, M. Acetyl-L-carnitine induces a sustained potentiation of the afterhyperpolarization. Neurosci., 128: 293-303, 2004.
     
  28. Wustenberg, D.G., Boytcheva, M., Grunewald, B., Byrne, J.H., Menzel, R. and Baxter, D.A. Current- and voltage-clamp recordings and computer simulations of Kenyon cells in the honeybee. J. Neurophysiol., 92: 2589-2603, 2004.
     
  29. Hines ML, Morse T, Migliore M, Carnevale NT and Shepherd GM.  ModelDB: a database to support computational neuroscience. J. Comput. Neurosci. 17: 7-11, 2004.
     
  30. Kroupina, O. and Rojas, R. A survey of compartmental modelling packages. Free University of Berlin, Institute of Computer Science, Technical Report B-04-08, 2004. http://www.inf.fu-berlin.de/inst/ag-ki/ger/b-04-08.pdf.
     
  31. Murray E, Watrous JJ, Simulating the behavior of a net-worked R15 neuron using SNNAP , FASEB JOURNAL 18 (4): A343-A343 Suppl. S MAR 23 2004.
     
  32. Jukes, N. and Chiuia, M.  From Guinea Pig to Computer Mouse, Second Edition. InterNICHE, Leicester, England, 2003.
     
  33. Pekala, A.D. and Watrous, J.J. (2003) Using SNNAP to develop a model of the Morris-Lecar equations for barnacle muscle.  In: The 14th Annual Saint Joseph’s University Sigma Xi Student Research Symposium, pg. 55.
     
  34. Cai, Y, Baxter, D.A. and Crow, T. Computational study of enhanced excitability in Hermissenda: Membrane conductances modulated by 5-HT. J. Comput. Neurosci., 15: 105-121, 2003.
     
  35. Flynn, M., Cai, Y., Baxter, D.A. and Crow, T. A computational study of the role of spike broadening in synaptic facilitation of Hermissenda. J. Comput. Neurosci., 15: 29-41, 2003.
     
  36. Phares, G.A., Antzoulatos, E.G., Baxter, D.A. and Byrne, J.H. Burst-induced synaptic depression and its modulation contribute to information transfer at Aplysia sensorimotor synapses: empirical and computational analyses. J. Neurosci., 23: 8392-8401, 2003.
     
  37. Tutorial abreviado para SNNAP (Simulator of Neural Networks and Action Potentials), Universidad de Buenos Aires, 2003.
     
  38. Raicheigauz, I. and Odinaev, K. Simulation of biological realistic neural networks. Israel Institute of Technology, Department of of Electrical Engineering, The Vision and Image Sciences Laboratory (2003). http://visl.technion.ac.il/projects/2003s30/2003s30report.pdf.
     
  39. Steffen, M., Seay, C., Amini, B., Cai, Y., Feigenspan, A., Baxter, D.A. and Marshak, D.W. Spontaneous activity of dopaminergic neurons in the retina: a computer model. Biophy. J., 85(4):2158-69, 2003.
     
  40. Watrous JJ, Hayes RD, Baxter DA, Using SNNAP7.1 (Simulator for Neural Networks and Action Potentials) in an undergraduate neurobiology course. FASEB JOURNAL 17 (4): A391-A391 Part 1 Suppl. S, MAR 14 2003.
     
  41. Baxter, D.A., Canavier, C.C. and Byrne, J.H. Dynamical properties of excitable membranes. In: Byrne, J.H. and Roberts, J. (Eds.), From Molecules to Networks: An Introduction to Cellular and Molecular Neuroscience (pp. 161-196). New York, Academic Press, 2003.
     
  42. Hayes, R.D., Byrne, J.H., and Baxter, D.A. Neurosimulation: Tools and resources. In: Arbib, M.A. (Ed.), The Handbook of Brain Theory and Neural Networks, Second Edition (pp. 776-780). Cambridge, MIT Press, 2003.
     
  43. Abraham J. Susswein, Itay Hurwitz, Richard Thorne, John H. Byrne, and Douglas A. Baxter Mechanisms Underlying Fictive Feeding in Aplysia: Coupling Between a Large Neuron With Plateau Potentials and a Spiking Neuron. J Neurophysiol 87: 2307-2323, 2002.
     
  44. Chen, H., Yaun, B., Baxter, D.A. and Byrne, J.H. Parallel computational in computer simulation for neural networks. Proc. IEEE TENCOM ’02, 1: 641-644, 2002.
     
  45. Chen, H., Yaun, B., Baxter, D.A. and Byrne, J.H. Research and implementation of computer simulation system for neural networks. ICSP’02 Proc., 2: 1834-1837, 2002.
     
  46. Chen, H., Yaun, B., Baxter, D.A. and Byrne, J.H. Signal processing and computational model for neural networks. ICSP ’02 Proc., 2: 1532-1535, 2002.
     
  47. Ekins S, Boulanger B, Swaan PW, et al.Towards a new age of virtual ADME/TOX and multidimensional drug discovery J COMPUT AID MOL DES 16 (5-6): 381-401 MAY-JUN 2002.
     
  48. Northrop, R.B. Introduction to dynamic modeling of neurosensory systems. CRC Press, New York, 2000.
     
  49. Baxter, D.A., Canavier, C.C., Lechner, H., Butera, R.J., DeFranceschi, A.A., Clark, J.W. and Byrne, J.H. Coexisting stable oscillatory states in single cell and multicellular neuronal oscillators. In: Levine, D., Brown, V. and Shirey, T. (Eds.), Oscillations in Neural Systems (pp. 51-77). Hillsdale: Lawrence Erlbaum and Associates, 2000.
     
  50. Ekins S, Boulanger B, Swaan PW, et al.Towards a new age of virtual ADME/TOX and multidimensional drug discovery MOL DIVERS 5 (4): 255-275 2000.
     
  51. Huang, W. (2000) A Java implementation of a Simulator of Neural Networks and Action Potentials. Masters Thesis 515 2000.H82, Department of Computer Science, University of Houston.
     
  52. Komendantov, A.O. and Kononenki, N.I. (2000) Caffeine-induced oscillations of the membrane potential in Aplysia neurons. Neurophyiol. 32:77-84. The results of a simulation are illustrated in L7_01_smu.gif.
     
  53. Baxter, D.A., Canavier, C.C., Clark, J.W. and Byrne, J.H. (1999) Computational model of the serotonergic modulation of sensory neurons in Aplysia. J. Neurophysiol. 82: 2914-2935. The results from one simulation (excite.smu) are illustrated in Baxter_excite.gif.
     
  54. Dunn, S.J. (1999) Modelling the neural network underlying feeding behavior in the snail Lymnaea stagnalis. Sussex Ph.D. theses: S4781, The University of Sussex.
     
  55. Pelz, C., Jander, J., Rosenboom, H., Hammer, M. and Menzel, R. (1999) IA in Kenyon cells of the mushroom body of honeybees resembles shaker currents: kinetics, modulation by K+, and simulation. J. Neurophysiol. 81: 1749-1759.
     
  56. David, K.  Analgoikai Elemi Teridobeli CNN Algorithmusik: Archetekcio es Elemi Retinaeffektusok.  http://lab.analogic.sztaki.hu/~balya/publications/PhD/balya_diploma.pdf, 1999.
     
  57. Rolls, E.T. and Treves, A.  Neural Networks and Brain Function.  Oxford University Press, New York, 1998.
     
  58. Wyler K, Stainhauser D, Best RE, Boddeke HWGM. From neuron to network: Measurement, analysis and modeling .5. Models and simulation tools of biological neurons and networks. TECHNISCHES MESSEN 64 (3): 121-130 MAR 1997.
     
  59. Stainhauser, D. Evaluation von simulatoren fur biologische neuronale netze. Diploma thesis, Instititut fur Informatik und angewandte Mathematik, Universitat Bern, 1995.
     
  60. D. Stainhauser, K. Wyler, L. Muller, W. Senn, J. Kleinle, M. Larkum, H.-R. Luscher, J. Streit, K. Vogt, and T. Wannier. An Evaluation Aid for Neuronal Modeling Software. Technical Report IAM-95-013, Institut fur Informatik und angewandte Mathematik, Universitat Bern, 1995.
    http://citeseer.nj.nec.com/stainhauser95evaluation.html
     
  61. Wenyao, J. (1995) User interface design in Simulator for Neural Networks and Action Potentials. Masters Thesis 515 1995.J52, Department of Computer Science, University of Houston.
     
  62. Kabotyanski, E.A., Ziv, I., Baxter, D.A. and Byrne, J.H. Experimental and computational analyses of a central pattern generator underlying aspects of feeding behavior in Aplysia. Netherlands J. Zool., 44: 357-373, 1994.
     
  63. White, J.A., Baxter, D.A. and Byrne, J.H. (1994) Analysis of the modulation by serotonin of the voltage-dependent potassium current in sensory neurons of Aplysia. Biophy J, 66: 710-718.
     
  64. Ziv, I, Baxter, D.A. and Byrne, J.H. Simulator for neural networks and action potentials: description and application. J. Neurophysiol. 71: 294-308, 1994.
     
  65. DeSchutter, E., Uhley, J.D. and Bower, J.M..  Neural simulation software demonstration: 23rd meeting Society for Neuroscience, Washington D.C., 1993.
    Available online at: http://www.bbf.uia.ac.be/publications/pub014/TNB_pub14.shtml.
     
  66. White, J.A., Ziv, I., Baxter, Cleary, L.J., Baxter, D.A. and Byrne, J.H. (1993) The role of interneurons in controlling the tail-withdrawal reflex in Aplysia: A network model. J. Neurophysiol. 70 1777-1786.
    The results of a simulation are illustrated in White_control.gif.
     
  67. Wiggins, Vince L., Larry T. Looper, and Sheree K. Engquist. Neural Networks, A Primer. AL-TP-1991-0011, Brooks AFB, Tex.: Armstrong Laboratory, 1991.
     
  68. Byrne, J.H., Cleary, L.J. and Baxter, D.A. Aspects of the neural and molecular mechanisms of short-term sensitization in Aplysia: modulatory effects of serotonin and cAMP on duration of action potentials, excitability and membrane currents in tail sensory neurons. In: L. Squire and E. Lindenlaub (Eds.), The Biology of Memory (pp. 7-28). New York, F. K. Schattauer Verlag, 1990. 
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