Readings

Notes:
- Readings indicated as 'FYI' are optional.
- Student summaries are posted 'as is'. They are expected to be about 15 slides long (~20mins). Please make a genuine effort to be original and creative. Simply 'regurgitating' slides from the previous lecture would defeat the purpose of this exercise, which is to allow you to present a different perspective on the material.

Week1 (8/26)
An introduction to the basic terminology of 'computations' in neural networks. Neural modeling examples, simple neurons, simple networks, simple computations (pattern completion, pattern separation, denoising, reinforcement learning).

• Brain Facts (from the Society for Neuroscience)
• Some neuroscience resources (links to tutorials, atlases...). From Psyc 302.
• 1st class...no specific readings.
• Student summaries: Ryan

Week2 (9/2)
Channels and excitability (neuronal computation) : Review of fundamental neural signaling mechanisms; membranes, channels, ionic equilibria, action potential and neuronal excitation.
- Suggested Readings:

• Squire et al., Fundamental Neuroscience 2 nd Ed. (Chapter 3 & 6) - OR
• Delcomyn, Foundations of Neurobiology (Chapters 2, 4, 5) - OR
• Purves et. al. Neuroscience 2nd edition (Chapters 2,3,4)
• FYI only: Tough read (need some background), but quite possibly the best 'modeling'/'computation' paper ever written: The original Hodgkin-Huxley 1952 paper.
• FYI only: The landmark Neher and Sakmann 1976 paper introducing the patch-clamp technique.
• Student perspective: JeanMarie

Week3 (9/9)
Synaptic transmission (synaptic computations: Part I) : Basic synaptic physiology. Transmitter release, excitation/inhibition in postsynaptic cell. Role of Calcium. Short-term plasticity.
- Suggested Readings:

• Kandel et. al, Principles of Neuroscience: Chapt 10 & 12 - OR
• Squire et al. Fundamental Neuroscience 2 nd Ed.: Chapt 8 - OR
• Purves et. al. Neuroscience 2nd edition: Chapt 5, Chapt 7 (Chapt 8)
• FYI: Jessell and Kandel 1993 : A nice review of synaptic transmission.
• FYI: Bennett 2000 : A nice review of electrical synapses.
• Student perspective: Lauritz

Week4 (9/16)
Dendrites and Axons (dendritic computations): morphology, physiology and integrative properties. Rall's theory, structure-function examples, impedance mismatch, electrotonus.
- Suggested Readings:

• Fundamental Neuroscience (Squire et al., Chapters 5 & 12)
• FYI: Additional (very comprehensive) readings: ‘Dendrites' (Stuart, Spruston, Hauser), Oxford University Press 1999.
• FYI: Additional (historical, theoretical) reading: Selected papers from W. Rall: 'The theoretical foundation of dendritic function', MIT press, 1993.
• FYI: Spruston 2008 : A nice review on dendritic integration in pyramidal cells. Neuronal arithmetic (Silver 2010): Review of synaptic, dendritic phenomena underlying sungle neuron 'arithmetic'
• FYI: Goldgerg abd Yuste 2005 : About calcium distribution and dendrites
• FYI: London and Hausser 2005: Dendritic computations. Review of sensory or behavioral functions that rely on dendritic morphology.
• FYI: Better understanding the details of the eletrotonic distance and neuromorphic transform: (Shepperd et al, 1990) and (Carnavale et al 1997).
• Student perspective: Jose

Week5 (9/23)
Synaptic plasticity (synaptic computations: part II) : Modification of synaptic communication through experience; short and long-term changes; associative vs. non-associative synaptic plasticity, LTP,LTD, pre and postsynaptic mechanisms.
- Suggested Readings:

• Kandel et al., (Eds) Principles of Neural Science, Chapt 63 - OR
• Purves et al, Chapt 25 - OR
• Squire et al, Fundamental Neuroscience, Chapt 49.
• FYI: Lomo: discovery of long term potentiation 2003 (historical review of LTP). Original 1982 paper describing the BCM rule.
• FYI: Feldman 2009: A more modern overview of synaptic plasticity mechanisms in cortex.
• FYI: Malenka and Nicoll 1999: LTP, a decade of progress (review of LTP up to 1998).
• FYI: Collingridge et al 2010 :Review of LTD.
• FYI: Kotaleski and Blackwell, 2010: Modeling the molecular mechanisms of plasticity.
• Student summaries: Andrew

Week6 (9/30) CLASS POSTPONED to 10/14. Do this homework instead.
Neural Circuits (network computations): Some typical and some atypical synaptic networks in the brain. Spinal cord and Pain, Auditory processing, Cerebellum, (Interneurons and electrical synapses).
- Suggested Readings:

• Kandel et al. (Eds) Principles of Neural Science, Chapt 42 - OR
• Squire et al, Fundamental Neuroscience, Chapt 32, 26
• Ramnani 2006: Cerebellar circuit
• Fettiplace et al, 2006 : Auditory hair cells
• Sherman 2004: Triadic synapses in the thalamus
• FYI: Baliki et al, 2009 : Pain perception
• Student perspective: Micah

Week7 (10/7)
Computing with noise: Neurophysiology of Sleep, Reactivation, Reliability and Precision.
- Suggested Readings:

• Squire et al, Fundamental Neuroscience, Chapt 42
• FYI: Discovering Spike patterns (Fellous 2004)
• FYI: J Siegel. Sleep viewed as a state of adaptive inactivity . Nature Reviews Neuroscience, 2009.
• FYI: Hobson, REM sleep and dreaming: towards a theory of protoconsciousness . Nature Reviews Neuroscience, 2009.
• FYI: Hobson and Pace-Schott.: The cognitive neuroscience of sleep: neuronal systems, consciousness and learning , Nature Reviews Neuroscience, 2002.
• Students perspective: Natalie

Midterm (10/14) . We will do the Neural Circuit lecture here, after a short in-class portion of the midterm. The takehome portion can be found here.

Week8 (10/21)
Computing in the context of memory: Associative memory- Basic principles of associative memory; pattern completion; constraints on storage capacity; sequence storage and retrieval.
- Suggested Readings:

• McNaughton and Morris 1987 : Hippocampal synaptic enhancement and information storage within a distributed memory system. Trends in Neurosciences, 1987.
• FYI: Marr 1970: A theory for cerebral neocortex.
• FYI: Marr 1971: Simple Memory: A Theory for Archicortex .
• FYI: Compte (2006) . Computational and in vitro studies of persistent activity: Edging towards cellular and synaptic mechanisms of working memory.
• FYI: Vaina, L. M., editor (1990). From the retina to the neocortex: selected papers of David Marr. Birkhauser, Boston, MA.
• Students perspective: Adam

Week9 (10/28)
Memory Consolidation and reconsolidation: Hippocampus and cortex. (L. Nadel)
- Suggested Readings:

• FYI: Multiple Trace Theory of Human Memory:Computational, Neuroimaging,and Neuropsychological Results . L. Nadel, A. Samsonovich, L. Ryan, and M. Moscovitch, 2000
• FYI: Functional neuroanatomy of remote episodic, semantic and spatial memory: a unified account based on multiple trace theory . Moscovitch et al. 2005.
• FYI: Recent critical reviews of memory consolidation: (Sutherland and Lehmann 2011), (Sutherland,Sparks,Lehman 2010)
• Students perspective: Molly

Week10 (11/4)
Computing in the context of spatial navigation: Spatial Representation in the Hippocampus (L. Schimanski)
- Suggested Readings:

• A manifold of spatial maps in the brain. Derdikman and Moser, 2010.
• FYI: Place Cells, Grid Cells, and the Brain's Spatial Representation System. Edvard I. Moser, Emilio Kropff, and May-Britt Moser. 2008
• FYI: Path integration and the neural basis of the ‘cognitive map' . Bruce L. McNaughton, Francesco P. Battaglia, Ole Jensen, Edvard I. Moser and May-Britt Moser.2006
• FYI: Dominance of the Proximal Coordinate Frame in Determining the Locations of Hippocampal Place Cell Activity During Navigation Jennifer J. Siegel, Joshua P. Neunuebel, and James J. Knierim, 2007.
• Students perspective: Goffredina

No Class (11/11) - Veteran's day.

Week11 (11/18)
Computing at the systems level. Higher brain functions. Introduction to the fMRI technique (G. Alexander)
- No Suggested Readings.

• Students perspective: Vanessa

No Class (11/25) - Thanksgiving

Week12 (12/2)
Representation in the brain (L. Nadel)
- Suggested Readings:

• FYI: The hippocampus as a spatial map. Preliminary evidence from unit activity in the freely-moving rat . O'Keefe and Dostrovsky, 1971.
• FYI: Latency and Selectivity of Single Neurons Indicate Hierarchical Processing in the Human Medial Temporal Lobe . Mormann et. al. 2008.
• FYI: What the frog's eye tells the frog's brain . Letvin et. al. 1968.
• FYI: Receptive fields and functional architecture of monkey striate cortex . Hubel and Wiesel 1968.
• Students perspective: Rafael

Final: Thursday Dec 15th - 9am