CS379C: Computational Models of the Neocortex

Spring 2013


Invited Talks

  • April 1, Monday: Tom Dean, Google — Administrivia and Introduction to Scalable Neuroscience

  • April 3, Wednesday: Tom Dean, Google — Survey of Alternative Approaches to Scalable Neuroscience [2, 1] (SLIDES) (VIDEO)

  • April 8, Monday: Ed Boyden, MIT — Physical Principles for Interfacing with the Nervous System (SLIDES) (AUDIO)

  • April 10, Wednesday: Ed Boyden, MIT — Architectures and Technologies for Neural System Interfaces (SLIDES) (AUDIO)

  • April 15, Monday: Kevin Briggman, National Institutes of Health — Reverse Engineering Neural Circuits [6, 5] (SLIDES) (AUDIO)

  • April 17, Wednesday: Mike Hawrylycz, Allen Institute — Allen Mouse and Human Brain Atlas Projects [21, 11] (SLIDES) (VIDEO)

  • April 22, Monday: Ed Callaway, Salk Institute — Retrovirus Techniques for Tracing Neural Circuits [17, 7] (VIDEO)

  • April 24, Wednesday: Stephen Smith, Stanford University — Brain Maps to Brain Mechanisms [18, 19] (VIDEO) (AUDIO)

  • April 29, Monday: Adam Marblestone, Harvard — Molecular ticker-tapes and Deep Sequencing [14, 25] (SLIDES) (AUDIO)

  • May 1, Wednesday: Yael Maguire, MIT — Tradeoffs in Designing Hybrid Biomolecular & Silicon Circuits (SLIDES)

  • May 6, Monday: Tony Zador, Cold Spring Harbor Laboratory — Sequencing the Connectome [2, 24] (SLIDES) (AUDIO)

  • May 8, Wednesday: Brian Wandell, Stanford University — Spikes, Synaptic Potentials, Glial Interactions [23, 22] (SLIDES) (AUDIO)

  • May 13, Monday: Work in class on preparing final-project proposals.

  • May 15, Wednesday: Akram Sadek, Caltech — Multiplexing Nanoscale Biosensors with Piezoelectric Resonators [20, 12, 15] (SLIDES) (AUDIO)

  • May 20, Monday: Work in class on jointly-authored technical report.

  • May 22, Wednesday: David Cox, Harvard University — High-resolution 3-D Microelectrode Brain Mapping [8, 9, 10] (VIDEO) (AUDIO)

  • May 27, Monday: Memorial Day — No Class

  • May 29, Wednesday: Work in class on jointly-authored technical report.

  • June 3, Monday: Mark Schnitzer, Stanford University — Massively Parallel Brain Imaging [1, 4, 16] (SLIDES) (AUDIO)

Participants:

Speaker: Ed Boyden, Massachusetts Institute of Technology
Date: April 8 & 10, 2013

Speaker: Kevin Briggman, National Institutes of Health
Date: April 15, 2013

Speaker: David Cox, Roland Institute, Harvard University
Date: May 22, 2013

Speaker: Tom Dean, Google Research
Date: April 1 & 3, 2013

Speaker: Mike Hawrylycz, Allen Institute for Brain Science
Date: April 17, 2013

Speaker: Yael Maguire, Massachusetts Institute of Technology
Date: May 1, 2013

Speaker: Adam Marblestone, Molecular Systems Lab, Harvard University
Date: April 29, 2013

Speaker: Akram Sadek, Nanofabrication Group, California Institute of Technology
Date: May 15, 2013

Speaker: Mark Schnitzer, Stanford University
Date: June 3, 2013

Speaker: Stephen Smith, Stanford University
Date: April 24, 2013

Speaker: Brian Wandell, Stanford University
Date: May 8, 2013

Speaker: Tony Zador, Cold Spring Harbor Laboratory
Date: May 6, 2013

Supplements:

Speaker: Michael Gazzaniga, University of California, Santa Barbara
Title: Gifford Lectures at Edinburgh University in 2009
Video: Available from Edinburgh here or the University’s YouTube channel.

Speaker: Eugene Izhikevich, Brain Corporation — formerly at The Neurosciences Institute, San Diego, CA
Papers: Izhikevich and Edelman [13]
Supplements: Supporting material for the PNAS paper including PDF is available here

Speaker: Eric Kandel, Columbia University
Video: Charlie Rose’s Brain Series (VIDEO)

Speaker: Henry Markram, Brain Mind Institute at EPFL
Title: Simulating the Brain: The Next Decisive Years
Video: Invited talk at the 2011 International Supercomputing Conference (ISC) (VIDEO)

Speaker: Dharmendra S. Modha, IBM, Almaden
Title: Towards Engineering the Mind by Reverse Engineering the Brain
Paper: Ananthanarayanan et al [3] (PDF) Video: Invited talk at the Krasnow Institute’s Decade of the Mind Symposium (VIDEO)

Speaker: Paul Rhodes, Evolved Machines
Title: Synthetic Neural Arrays That Wire Themselves
Video: Nvidia High Performance Computing (VIDEO)

Speaker: Robert Sapolsky, Stanford University
Title: Are Humans Just Another Primate?
Video: Invited lecture at the California Academy of Sciences (VIDEO)

References

[1]   A. Paul Alivisatos, Anne M. Andrews, Edward S. Boyden, Miyoung Chun, George M. Church, Karl Deisseroth, John P. Donoghue, Scott E. Fraser, Jennifer Lippincott-Schwartz, Loren L. Looger, Sotiris Masmanidis, Paul L. McEuen, Arto V. Nurmikko, Hongkun Park, Darcy S. Peterka, Clay Reid, Michael L. Roukes, Axel Scherer, Mark Schnitzer, Terrence J. Sejnowski, Kenneth L. Shepard, Doris Tsao, Gina Turrigiano, Paul S. Weiss, Chris Xu, Rafael Yuste, and Xiaowei Zhuang. Nanotools for neuroscience and brain activity mapping. ACS Nano, 7(3):1850–1866, 2013.

[2]   A. Paul Alivisatos, Miyoung Chun, George M. Church, Ralph J. Greenspan, Michael L. Roukes, , and Rafael Yuste. The brain activity map project and the challenge of functional connectomics. Neuron, 74, 2012.

[3]   Rajagopal Ananthanarayanan, Steven K. Esser, Horst D. Simon, and Dharmendra S. Modha. The cat is out of the bag: cortical simulations with 109 neurons, 1013 synapses. In Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, pages 63:1–63:12, 2009.

[4]   R.P.J. Barretto and M.J. Schnitzer. In vivo optical microendoscopy for imaging cells lying deep within live tissue. Cold Spring Harbor Protocols, 2012(10), 2012.

[5]   K.L. Briggman and D.D. Bock. Current opinion neurobiology. Volume electron microscopy for neuronal circuit reconstruction, 22:154–61, 2012.

[6]   K.L. Briggman, M. Helmstaedter, and W. Denk. Wiring specificity in the direction-selectivity circuit of the retina. Nature, 471:183–188, 2011.

[7]   E.M. Callaway. Transneuronal circuit tracing with neurotropic viruses. Current Opinion Neurobiology, 18(6):617–23, 2008.

[8]   D. D. Cox, A. M. Papanastassiou, D. Oreper, B. B. Andken, and J. J. DiCarlo. High-resolution three-dimensional microelectrode brain mapping using stereo microfocal x-ray imaging. Journal of Neurophysiology, 100(5):2966–2976, 2008.

[9]   James J. DiCarlo and David D. Cox. Untangling invariant object recognition. Trends in Cognitive Sciences, 11(8):333–341, 2007.

[10]   James J DiCarlo, Davide Zoccolan, and Nicole C Rust. How does the brain solve visual object recognition? Neuron, 73:415–34, 2012.

[11]   Michael Hawrylycz, Richard A. Baldock, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann E. Martone, Lydia Ng, Christopher Lau, Stephen D. Larson, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky, and Jyl Boline. Digital atlasing and standardization in the mouse brain. PLoS Computational Biology, 7, 2011.

[12]   Heng Huang, Savas Delikanli, Hao Zeng, Denise M. Ferkey, and Arnd Pralle. Remote control of ion channels and neurons through magnetic-field heating of nanoparticles. Nature Nanonotechnology, 5:602–606, 2010.

[13]   Eugene M. Izhikevich and Gerald M. Edelman. Large-scale model of mammalian thalamo-cortical systems. Proceedings of the National Academy of Science, 105(9):3593–3598, 2008.

[14]   Konrad Kording. Of toasters and molecular ticker tapes. PLoS Computational Biology, 7(12):e1002291, 2011.

[15]   Mo Li, W. H. P. Pernice, C. Xiong, T. Baehr-Jones, M. Hochberg, and H. X. Tang. Harnessing optical forces in integrated photonic circuits. Nature, 456:480–484, 2008.

[16]   Jesse D. Marshall and Mark J. Schnitzer. Optical strategies for sensing neuronal voltage using quantum dots and other semiconductor nanocrystals. ACS Nano, 7:4601–4609, 2013.

[17]   J.H. Marshel, T. Mori, K.J. Nielsen, and E.M. Callaway. Targeting single neuronal networks for gene expression and cell labeling in vivo. Neuron, 67(4):562–574, 2010.

[18]   Kristina D. Micheva and Stephen J. Smith. Array tomography: A new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron, 55(1):25–36, 2007.

[19]   Nancy A. O’Rourke, Nicholas C. Weiler, Kristina D. Micheva, and Stephen J. Smith. Deep molecular diversity of mammalian synapses: Why it matters and how to measure it. Nature Review Neuroscience, 10:365–379, 2012.

[20]   A.S. Sadek, R.B. Karabalin, J. Du, M.L. Roukes, C. Koch, and S.C. Masmanidis. Wiring nanoscale biosensors with piezoelectric nanomechanical resonators. Nano Letters, 10:1769–1773, 2010.

[21]   Susan Sunkin, Lydia Ng, Christopher Lau, Tim Dolbeare, Terri L. Gilbert, Carol L. Thompson, Michael Hawrylycz, and Chinh Dang. Allen brain atlas: an integrated spatio-temporal portal for exploring the central nervous system. Nucleic Acids Research, 41:996–1008, 2013.

[22]   B.A. Wandell and J.D. Yeatman. Biological development of reading circuits. Current Opinion Neurobiology, 23:261–268, 2013.

[23]   Brian A. Wandell, Serge O. Dumoulin, and Alyssa A. Brewer. Visual field maps in human cortex. Neuron, 56(2):366–383, 2007.

[24]   Anthony M. Zador, Joshua Dubnau, Hassana K. Oyibo, Huiqing Zhan, Gang Cao, and Ian D. Peikon. Sequencing the connectome. PLoS Biology, 10(10):e1001411, 2012.

[25]   Bradley Michael Zamft, Adam H. Marblestone, Konrad Kording, Daniel Schmidt, Daniel Martin-Alarcon, Keith Tyo, Edward S. Boyden, and George Church. Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing. PLoS ONE, 7(8):e43876, 2012.