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: Pankaj Mehta

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: Xue Han

15: Guest speaker: Jay Bohland

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, Jason Ritt

20: The optimality & Flux balance
Readings TBD…

21: Guest speaker: Daniel Segre’

22: Ecosystem Stability-Complexity debate
{Kondoh:2003wc}




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