Bibliography

Additional reading in cellular biophysics, computational neuroscience, and related areas. Publications retain their bibliographic dates. Publisher and library access varies; restricted reading copies are listed with the relevant lectures.

Selected References

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Clark RB, Kondo C, Belke DD, Giles WR. Two-pore domain K⁺ channels regulate membrane potential of isolated human articular chondrocytes. J Physiol. 2011;589 (Pt 21):5071-89 [DOI] Publisher

Corry, Ben. “Understanding ion channel selectivity and gating and their role in cellular signalling.” Molecular Biosystems 2.11 (2006): 527-535 [DOI]

Dolphin AC. A short history of voltage-gated calcium channels. Br J Pharmacol. 2006 Jan;147 Suppl 1(Suppl 1):S56-62. [DOI] PubMed

Ermentrout, G. B., & Terman, D. H. (2010) in Mathematical foundations of neuroscience (Vol. 35). Springer Science & Business Media. Chapter 3 Dynamics [DOI]

Fall, C.P., Marland, E.S., Wagner, J.M. and Tyson, J.J. 2002. Computational cell biology.Amazon [DOI]

Chapter 1 Dynamic Phenomena in Cells.
Chapter 6 Intracellular Communication by John Rinzel.

Finkelstein, Alan, and Alexander Mauro. “Equivalent circuits as related to ionic systems.” Biophysical journal 3.3 (1963): 215-237 [DOI]

Häusser, Michael. “The Hodgkin-Huxley theory of the action potential.” Nature neuroscience 3.11 (2000): 1165-1165. [DOI] Publisher

Heeger, D. The Membrane Equation

Hille, B. Ion Channels of Excitable Membranes

Introduction. Chapter 1
Classical biophysics of the squid giant axon. Chapter 2
Selective Permeability: Independence. Chapter 14

Kiehn O, Eken T. Functional role of plateau potentials in vertebrate motor neurons. Curr Opin Neurobiol. 1998 Dec;8(6):746-52. [DOI] PubMed

Lipscombe D, Helton TD, Xu W. L-type calcium channels: the low down. J Neurophysiol. 2004 Nov;92(5):2633-41. [DOI] PubMed

McCormick 1998 “Membrane properties and neurotransmitter actions” (pp. 37-75 of “The Synaptic Organization of the Brain,” edited by Gordon Shepard). [DOI]

Nelson and Rinzel 2012. “The Hodgkin-Huxley model.” This is Ch 4 of “The Book of GENESIS: Exploring Realistic Neural Models with the GEneral NEural SImulation System” by James M. Bower and David Beeman.

Rinzel, J., & Ermentrout, G. B. (1998). Analysis of neural excitability and oscillations. Methods in neuronal modeling, 2, 251-292. [DOI]

Sigworth FJ. Structural biology: Life’s transistors. Nature. 2003 May 1;423(6935):21-2. [DOI] PubMed

Terman pp. 21-28 “An introduction to dynamical systems and neuronal dynamics.” (Introduction & One Dimensional Equations)

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Pieri M, Caioli S, Canu N, Mercuri NB, Guatteo E, Zona C. Exp Neurol. 2013. Over-expression of N-type calcium channels in cortical neurons from a mouse model of Amyotrophic Lateral Sclerosis. PubMed [DOI]

Estrada,Ernesto 2011. The Structure of Complex Networks: Theory and Application Cover Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 Chapter 12 Chapter 13 Chapter 14 Chapter 15 Chapter 16 Chapter 17 Chapter 18 Chapter 19 Publisher Amazon

Frith, C. and Frith, U., 2005. Theory of mind. Current Biology, 15(17), pp.R644-R645 [DOI] Publisher

Funke, K., Kisvarday, Z.F., Volgushev, M. and Wörgötter, F., 2002. Integrating anatomy and physiology of the primary visual pathway: from lgn to cortex. In Models of Neural Networks IV (pp. 97-182). Springer, New York, NY. [DOI] Publisher

Ganguli, S. and Sompolinsky, H., 2012. Compressed sensing, sparsity, and dimensionality in neuronal information processing and data analysis. Annual review of neuroscience, 35, pp.485-508. [DOI]

Gerstner, W., 2011. Hebbian learning and plasticity. In Arbib, M.A. and Bonaiuto, J.J. eds., 2016. From neuron to cognition via computational neuroscience. pp.0-25. MIT Press. [Amazon] Publisher Amazon

Gerstner, Wulfram. Neuronal Dynamics: From Single Neurons To Networks And Models Of Cognition. Cambridge University Press, 2014. Amazon [DOI]

Gerstner, Wulfram. Spiking Neuron Models: Single Neurons, Populations, Plasticity. Cambridge University Press, 2002. Amazon [DOI]

Gervain, J. and Geffen, M.N., 2018. Efficient Neural Coding in Auditory and Speech Perception. Trends in neurosciences. [DOI] Publisher

Godfrey-Smith, P., 2016. Other minds: The octopus, the sea, and the deep origins of consciousness. Farrar, Straus and Giroux. SWEM Amazon [DOI] Publisher

Green, Joel B. Body, Soul, and Human Life: The Nature of Humanity in the Bible. Baker Academic, 2008. Amazon [DOI] Publisher

Grillner, S., Markram, H., De Schutter, E., Silberberg, G. and LeBeau, F.E., 2005. Microcircuits in action–from CPGs to neocortex. Trends in neurosciences, 28(10), pp.525-533. [DOI] Publisher

Grillner, S., Robertson, B., & Stephenson‐Jones, M. (2013). The evolutionary origin of the vertebrate basal ganglia and its role in action selection. The Journal of physiology, 591(22), 5425-5431. [DOI]

Grillner, S., & Robertson, B. (2016). The basal ganglia over 500 million years. Current Biology, 26(20), R1088-R1100. [DOI] Publisher

Gross, Charles. Gordon Shepherd, Creating Modern Neuroscience: The Revolutionary 1950s. Oxford University Press, 2010. [DOI] Publisher Amazon SWEM

Graupe, D., 2013. Principles of artificial neural networks (Vol. 7). World Scientific. Amazon SWEM [DOI] Publisher

Guo, Y., Liu, Y., Oerlemans, A., Lao, S., Wu, S. and Lew, M.S., 2016. Deep learning for visual understanding: A review. Neurocomputing, 187, pp.27-48. [DOI] Publisher

Gutfreund, Hanoch and Toulouse, Gerard, editors. Biology And Computation: A Physicist’s Choice. World Scientific Publishing Company, 1994. Amazon [DOI]

Hardcastle, K., Ganguli, S. and Giocomo, L.M., 2017. Cell types for our sense of location: where we are and where we are going. Nature neuroscience, 20(11), p.1474. [DOI] PubMed

Hauser, M.D., Chomsky, N. and Fitch, W.T., 2002. The faculty of language: What is it, who has it, and how did it evolve? Science, 298(5598), pp.1569-1579. [DOI] Publisher

Heisenberg, M., 2003. Mushroom body memoir: from maps to models. Nature Reviews Neuroscience, 4(4), p.266. [DOI]

Hendry, S.H. and Calkins, D.J., 1998. Neuronal chemistry and functional organization in the primate visual system. Trends in neurosciences, 21(8), pp.344-349. [DOI] Publisher

Heyes, C. (2012). New thinking: the evolution of human cognition.\ [DOI] Phil. Trans. R. Soc. B 367, 2091-2096. [DOI]

Hochner, B., 2012. An embodied view of octopus neurobiology. Current biology, 22(20), pp.R887-R892. [DOI] Publisher

Isaacson, J.S., 2010. Odor representations in mammalian cortical circuits. Current opinion in neurobiology, 20(3), pp.328-331 [DOI] Publisher

Izhikevich, Eugene M. Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting. MIT Press, 2010. Amazon SWEM ProQuestEBookCentral [DOI] Publisher

Kaminski, 2017. Reading Other Minds. In: Shepherd, S.V. (2017) The Wiley Handbook of Evolutionary Neuroscience. John Wiley & Sons, Ltd. (pp. 514-525; Chapter 19) [DOI] Publisher Amazon SWEM

Kass, J. (2020). Evolutionary Neuroscience. 2nd edition. Publisher

Katz, 2012. Noam Chomsky on Where Artificial Intelligence Went Wrong. The Atlantic. Publisher

Kelley, Edward Kelly and Kelly, Emily Williams. Irreducible Mind: Toward a Psychology for the 21st Century. Rowman & Littlefield Publishers, 2009. [Amazon] SWEM Publisher Amazon

Kline, R.R., 2015. The cybernetics moment: Or why we call our age the information age. JHU Press. [Amazon] [SWEM] Amazon SWEM

Koch, Christof and Idan Segev, eds. Methods in Neuronal Modeling: From Ions to Networks. 2nd edition. MIT Press, 1998. SWEM EBSCO [DOI] Publisher

Koch, Christof. Biophysics of Computation: Information Processing in Single Neurons. Oxford University Press, 2005. Amazon SWEM ProQuestEBookCentral [DOI] Publisher

Krahe, R. and Gabbiani, F., 2004. Burst firing in sensory systems. Nature Reviews Neuroscience, 5(1), p.13. [DOI] Publisher

Laurent, G., 1996. Dynamical representation of odors by oscillating and evolving neural assemblies. Trends in neurosciences, 19(11), pp.489-496. [DOI] Publisher

LeGuin, Ursula. The Author of the Acacia Seeds and Other Extracts from the Journal of the Association of Therolinguistics.

Lettvin, J.Y. and Gesteland, R.C., 1965, January. Speculations on smell. In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 30, pp. 217-225). Cold Spring Harbor Laboratory Press. Publisher

Lettvin, J.Y., 1979. The Gorgon’s Eye. Astronomy of the Ancients, p.133.

Levine, J., 1983. Materialism and qualia: The explanatory gap. Pacific philosophical quarterly, 64(4), pp.354-361. [DOI]

Li, P., Janczewski, W.A., Yackle, K., Kam, K., Pagliardini, S., Krasnow, M.A. and Feldman, J.L., 2016. The peptidergic control circuit for sighing. Nature, 530(7590), p.293. [DOI] Publisher

Lieberman, P. (2009). Human language and our reptilian brain: The subcortical bases of speech, syntax, and thought. Harvard University Press Publisher Amazon

Lieberman, P. (2001). Human language and our reptilian brain–the subcortival bases of speech, syntax, and thought. Perspectives in Biology and Medicine, 44(1), 32-51. [DOI] PubMed

Lieberman, P. (2002). On the nature and evolution of the neural bases of human language. American Journal of Physical Anthropology: The Official Publication of the American Association of Physical Anthropologists, 119(S35), 36-62. [DOI]

Lisman, J., 2015. The challenge of understanding the brain: where we stand in 2015. Neuron, 86(4), pp.864-882. [DOI] Publisher

Lisman, J.E., Fellous, J.M. and Wang, X.J., 1998. A role for NMDA-receptor channels in working memory. Nature neuroscience, 1(4), p.273. [DOI] Publisher

Lytton, W.W., 2007. From computer to brain: foundations of computational neuroscience. Springer Science & Business Media. [Amazon] Publisher Amazon

Machamer, P.K., Grush, R. and McLaughlin, P. eds. Theory and Method in the Neurosciences. University of Pittsburgh Press, 2001. Amazon SWEM

Mainen, Z.F. and Sejnowski, T.J., 1995. Reliability of spike timing in neocortical neurons. Science, 268(5216), pp.1503-1506. [DOI] Publisher

Marinaro, M., Scarpetta, S. and Yamaguchi, Y. Dynamic brain—from neural spikes to behaviors. 12th International Summer School on Neural Networks, Erice, Italy, Revised Lectures (Eds.), 5286. Springer, 2008. AMAZON SWEM [DOI] Publisher

Markram, H., Gerstner, W. and Sjöström, P.J., 2011. A history of spike-timing-dependent plasticity. Frontiers in synaptic neuroscience, 3, p.4. [DOI] Publisher

Marr, David, 2010. Vision: A Computational Investigation into the Human Representation and Processing of Visual Information. MIT Press. General Introduction. Chapter 1 The Philosophy and the Approach. Amazon SWEM Publisher

Masland, R.H. and Martin, P.R., 2007. The unsolved mystery of vision. Current Biology, 17(15), pp.R577-R582. [DOI] Publisher

Masland, R.H., 2001. Neuronal diversity in the retina. Current opinion in neurobiology, 11(4), pp.431-436. [DOI] Publisher

McDonnell, M.D., Ikeda, S. and Manton, J.H., 2011. An introductory review of information theory in the context of computational neuroscience. Biological cybernetics, 105(1), p.55. [DOI] Publisher

Metzinger, Thomas & Windt, Jennifer M. 2015. Open MIND, 2-vol. set Philosophy and the Mind Sciences in the 21st Century. The MIT Press. https://open-mind.net [DOI] Publisher

Miller, P., 2018. An Introductory Course in Computational Neuroscience. MIT Press. Chapter 8 Learning and Synaptic Plasticity [DOI] Amazon

Mnih, V., Kavukcuoglu, K., Silver, D., Rusu, A.A., Veness, J., Bellemare, M.G., Graves, A., Riedmiller, M., Fidjeland, A.K., Ostrovski, G. and Petersen, S., 2015. Human-level control through deep reinforcement learning. Nature, 518(7540), p.529. [DOI] Publisher

Montague, P.R., Hyman, S.E. and Cohen, J.D., 2004. Computational roles for dopamine in behavioural control. Nature, 431(7010), p.760. [DOI] Publisher

Montgomery, S., 2015. The soul of an octopus: A surprising exploration into the wonder of consciousness. Simon and Schuster. SWEM Amazon Publisher

Moser, E.I., Moser, M.B. and McNaughton, B.L., 2017. Spatial representation in the hippocampal formation: a history. Nature Neuroscience, 20(11), p.1448. [DOI] PubMed

Nagel, T., 1974. What is it like to be a bat? The philosophical review, 83(4), pp.435-450. [DOI] JSTOR

Niell, C.M., 2013. Vision: more than expected in the early visual system. Current biology, 23(16), pp.R681-R684. [DOI] Publisher

Newell, A., 1980. Physical symbol systems. Cognitive science, 4(2), pp.135-183. [DOI]

Olshausen, B.A. and Field, D.J., 2004. Sparse coding of sensory inputs. Current opinion in neurobiology, 14(4), pp.481-487. [DOI] Publisher

Palanca-Castan, N. and Köppl, C., 2015. Change in the coding of interaural time difference along the tonotopic axis of the chicken nucleus laminaris. Frontiers in neural circuits, 9, p.43. [DOI] Publisher

Pennartz, Cyriel M.A. The Brain’s Representational Power: On Consciousness and the Integration of Modalities. MIT Press, 2015. Amazon SWEM EBSCO Publisher

Piccinini, G., 2006. Computational explanation in neuroscience. Synthese, 153(3), pp.343-353. [DOI] Publisher

Piccinini, Gualtiero. Physical Computation: A Mechanistic Account. Oxford University Press, 2015. [SWEM] Ch15 Information Processing PDF Publisher SWEM

Piccinini & Shagrir (2014). Foundations of computational neuroscience. Current Opinion in Neurobiology, 25, 25–30. [DOI] Publisher

Poo, C. and Isaacson, J.S., 2009. Odor representations in olfactory cortex: “sparse” coding, global inhibition, and oscillations. Neuron, 62(6), pp.850-861. [DOI] Publisher

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Quanta, Jordana Cepelewicz. Rewards Warp the Brain’s Inner GPS: Cells that control an animal’s spatial awareness can reorient themselves to favor locations that are full of food. April 7, 2019 Publisher

Rieke, Fred and David Warland, Rob de Ruyter van Steveninck, William Bialek. Spikes: Exploring the Neural Code. MIT Press, 1996. Amazon Publisher

Riesenhuber, M. and Poggio, T., 1999. Hierarchical models of object recognition in cortex. Nature neuroscience, 2(11), p.1019. [DOI] Publisher

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Seung, H.S., Lee, D.D., Reis, B.Y. and Tank, D.W., 2000. Stability of the memory of eye position in a recurrent network of conductance-based model neurons. Neuron, 26(1), pp.259-271. [DOI] Publisher

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Shepherd, G. M. (2004). The synaptic organization of the brain. Oxford university press. Publisher Amazon

Shepherd, S.V. (2017) The Wiley Handbook of Evolutionary Neuroscience. John Wiley & Sons, Ltd [DOI] Publisher Amazon SWEM

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Sterling, Peter and Simon Laughlin. Principles of Neural Design. MIT Press, 2017. Amazon SWEM EBSCO Publisher

Stone, James V. Principles of Neural Information Theory: Computational Neuroscience and Metabolic Efficiency. Sebtel Press, 2018. Amazon Publisher

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Trappenberg, Thomas. Fundamentals of Computational Neuroscience. 2nd Edition. Oxford University Press, 2010. Amazon Ch1 Introduction Ch2 Neurons and conductance-based models Ch3 Simplified neuron and population models Ch4 Associators and synaptic plasticity Ch5 Cortical organization and simple networks Ch6 Feed-forward mapping networks Ch7 Cortical feature maps and competitive population coding Ch8 Recurrent associative networks and episodic memory Ch9 Modular networks motor control and reinforcement learning Ch10 The cognitive brain Appendix A Some useful mathematics Appendix B Numerical calculus Appendix C Basic probability theory Appendix D Basic information theory [DOI] Publisher

Wallisch, Pascal and Michael Lusignan, Marc Benayoun, Tanya I. Baker, Adam Seth Dickey, Nicho Hatsopoulos. Matlab for Neuroscientists: An Introduction to Scientific Computing in Matlab. Academic Press, 2008. Amazon SWEM ProQuestEBookCentral SienceDirect [DOI] Publisher

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Bibliography

Selected References

Further Reading