BI502 - Topics in the theory of Biological Networks
This course examines mathematical principles underlying the activity of various biological networks.
The subject matter ranges from abstract boolean networks to bacterial chemotaxis, systems neuroscience, and ecosystems.
We examine how interesting dynamical properties arise from simple rules and the geometry of network connections.
We focus particularly on the properties of adaptive networks networks whose geometry changes as a result of the activity of the network.
The final projects in this course are computer programs written in matlab, with an accompanying presentation.
1: Boolean networks
{Kauffman:1969up}{Bornholdt:2005vr}{Ptashne:1997wd}
Review paper
{Goldenfeld:1999wv}
2: Yeast Transcription network
{Fangting:2004tp}{Guelzim:2002tb}
Review paper – epistasis and missing heritability
{Maher:2008ux}
3: Topological evolution of dynamical networks: Global Dynamics from Local Plasticity
{Bornholdt:2000vf}
Review: Evolving a conscious machine
{Taubes:1998vc}
4: Biological Graphs
{Barabasi:1999uu}{Watts:1998tv}{Eguiluz:2005um}
5: Self Organized Criticality
{Bak:1988vb}{Malamud:1998wi}{Bak:1989vq}
6: Emergent complex neural dynamics
{Haldeman:2005tf}{Beggs:2003uv}
7: Neuronal Avalanches 2
{Shew:2009vr}{Petermann:2009tn}{Plenz:2007up}
Optional
{Chialvo:2006vz}{Kinouchi:2006wt}
8: Local learning rules: cellular adaptation synaptic scaling
{Turrigiano:1998tb}{Stellwagen:2006vb}
8b: Dynamic stabilization of excitation and inhibition through nonlinear feedback inhibition
{Diesmann:1999in}{Hao:2009jg}{Spruston:2008ft}
9: Robust networks for dynamic fixed points
{Alon:1999vf}{Barkai:1997vj}
reviews
{Lauffenburger:2000vn}{Baker:2007tu}
background
{Berg:1977uj}{Purcell:1977tk}
10: Guest speaker:
11: Associative neural networks, energy landscapes, and stem cells
{Hopfield:1982vm}{Enver:2009ts}{Huang:2005vx}
review
{Vogels:2005ta}
12: Role of sleep in the erasure of spurious memories
{Crick:1983wa}{Hopfield:1983ty}{Rudoy:2009ta}
13: Dynamics of Sleep
{Vyazovskiy:2011wu}{Krueger:2008vg}
14: Guest speaker:
15: Guest speaker:
16: Antihebbian plasticity and sparse memories
{Magnasco:2009wz}{Rochefort:2009tt}{Stopfer:2003vf}
18: Case study – dynamics of vocal imitation in songbirds
{Gardner:2005uv}{Hahnloser:2002ux}{Long:2010to}{Olveczky:2005vz}{Andalman:2009vy}
19: Guest speaker
20: Optimality & Flux balance
21: Guest speaker:
22: Ecosystem Stability-Complexity debate
{Kondoh:2003wc}
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Hao, Jiang, Xu-dong Wang, Yang Dan, Mu-ming Poo, and Xiao-hui Zhang. “An arithmetic rule for spatial summation of excitatory and inhibitory inputs in pyramidal neurons..” Proceedings of the National Academy of Sciences 106, no. 51 (December 22, 2009): 21906–21911.
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Lauffenburger, D.A “Cell signaling pathways as control modules: Complexity for simplicity?.” Proceedings of the National Academy of Sciences 97, no. 10 (2000): 5031.
Long, M.A., D.Z. Jin, and M.S. Fee. “Support for a synaptic chain model of neuronal sequence generation.” Nature 468, no. 7322 (2010): 394–399.
Magnasco, M.O., O. Piro, and G.A. Cecchi. “Self-Tuned Critical Anti-Hebbian Networks.” Physical Review Letters 102, no. 25 (2009): 258102.
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Olveczky, BP, A.S. Andalman, and M.S. Fee. “Vocal experimentation in the juvenile songbird requires a basal ganglia circuit.” PLoS Biol 3, no. 5 (2005): e153.
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Plenz, D., and T.C. Thiagarajan. “The organizing principles of neuronal avalanches: cell assemblies in the cortex?.” TRENDS in Neurosciences 30, no. 3 (2007): 101–110.
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